3,619 Matching Annotations
  1. Last 7 days
    1. 5

      Case5: Female, 10m, Chinese, part of Family 1

      HPOsFreeText: (at 20 days) 1.38 C4 umol/L, 0.19 C4/C2, 1.79 C4/C3, 2.58 (mmol/mol creatinine) urine isobutyrylglycine

      Case5 (Level 2):


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_014384.2:c.286G>A (p.Gly96Ser)

      ClinVar: n/a

      CAID: CA6372895

      gnomAD: 0.001453 (East Asian)

      Variant2: NM_014384.2:c.1092+1G>A

      ClinVar: n/a

      CAID: CA6373205

      gnomAD: 0.00005790 (Latino)


      CaseAddInfo: younger sister of patient 6, trans heterozygous, inherited one allele from each parent

    1. 22

      Case22: 28 mo (at biopsy), Korean

      Case 22 (Level 2)


      CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 0.8 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      Variant2: NM_000255.3:c.1481T>A (p.Leu494Ter)

      ClinVar: 551275

      CAID: CA3846864

      gnomAD: 0.0001088 (East Asian)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans

    2. 21

      Case21: 2 mo (at biopsy), White

      Case 21 (Level 2)


      CasePreviousTesting: same as group. found 0.6 nmol/mg protein/18 h propionate incorporation, 0.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      Variant2: NM_000255.3:c.1287C>G (p.Tyr429Ter)

      ClinVar: 554278

      CAID: CA364398724

      gnomAD: 0.00006483 (European non-Finnish)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

    3. 20

      Case20: 5 days (at biopsy), White

      Case 20 (Level 2)


      CasePreviousTesting: same as group. found 2.1 nmol/mg protein/18 h propionate incorporation, 1.9 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      Variant2: NM_000255.3:c.1106G>A (p.Arg369His)

      ClinVar: 203846

      CAID: CA312764

      gnomAD: 0.0001504 (East Asian)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

    1. 18

      Case18 Female, 9.9yo report, Ethnicity: Austrian

      CasePresentingHPOs HP:0003571, HP:0008872, HP:0001531, HP:0001254, HP:0002789, HP:0002045

      (propionicacidemia, feeding difficulties in infancy, failure to thrive in infancy, lethargy, tachypnea, hypothermia)

      HPOsFreeText feeding difficulties, failure to thrive, lethargy, tachypnea, hypothermia, exanthema (5do). Scored 55 on Snijders-Omen Test for IQ

      CaseNotHPOs n/a

      CasePreviousTesting Diagnosed by selective metabolic screening. PCC activity in patient lymphoblasts was 0.4% of control.

      Variant NM_000532.4:c.1199-2A>G (Gly400fs), homozygous

      ClinVar n/a

      CAID CA354648962

      gnomAD not in gnomAD

      CaseAddInfo parents not consanguineous

      CasePMIDs n/a

    1. Case 4

      Case# Case 4, F, Chinese, 5day onset

      CasePresentingHPOs HP:0008344, HP:0011968, HP:0001954, HP:0002373

      CasePreviousTesting Tested blood aa levels with liquid chromatography-mass spectrum spectrometry, several branched chain amino acids were overly abundant. Whole exome targeted capture sequencing was applied for the mutation screening of the suspicious patients. A total of 712 genes associated with inherited metabolic diseases were selected and their coding regions were captured.

      CaseMethod1 Whole Exome

      CaseMethod2 Sanger

      CaseGenotypingMethod validated whole exome findings with sanger and qPCR.

      Variant NM_000056.4(BCKDHB):c.93_103dupGGCGCGGGGCT (p.Phe35Trpfs), NM_000056.3:c.550del

      ClinVar 189101 (dup)

      CAID CA658820648 (del)

      gnomAD low quality site (dup)

    1. Patient 11

      Case11: Male, 3 wk at initiation of follow up, African American ancestry

      HPOsFreeText: NBS C4-acylcarnitine 1.4 umol/L, lasma C4 acylcarnitine 1.87 umol/L, in vitro probe isoC4-acylcarnitine 0.053 umol/ g protein

      NotHPOsFreeText: normal in vitro probe C4-aclycarnitine, normal urine isobutyrylglycine, normal urine C4-acylcarnitine, normal urine C4/C3 ratio

      CaseAddInfo: mild biochemical phenotype observed. Suggested to be at minimum a carrier of IBD deficiency- however presence of promoter mutation, large deletion, or splice-site alteration undetectable by direct gene sequencing cannot be ruled out.

      Case11 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant2: NM_014384.2(ACAD8):c.1129G>A (p.Gly377Ser)

      ClinVar: 5356

      CAID: CA117435

      gnomAD: 0.0001551 (European non-Finnish)


      CaseAddInfo: heterozygous for mutation

    1. 5-2

      Patient5-2 Female, 1yo, sibling to patient 5-1

      CasePresentingHPOs:

      HPOsFreeText: Blood C5-carnitine (μM) = 13.47, under a protein restricted diet with carnitine and glycine supplementation, normal development

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: 2mo and asymptomatic at diagnosis

      CasePMIDs:

      CasePreviousTesting: Blood amino acids and acylcarnitine analyzed with ESI-MS/MS, urine organic acid analysis with GC/MS

      GroupMethod1: PCR (primers in table 2)

      GroupMethod2: Direct sequencing

      CaseGenotypingMethod: genomic DNA extracted from peripheral blood leukocytes, IVD exons amplified via PCR, then products were purified and underwent direct sequencing for variant analysis

      Variant1: NM_002225.4:c.347C>T (p.Ser89Phe) listed in paper as (p.Ser87Phe)

      CAID: CA391716394, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391716394

      gnomAD: n/a

      Variant2: NM_002225.4(IVD):c.1199A>G (p.Tyr400Cys) listed in paper as (p.Tyr371Cys)

      ClinVar: 371390, https://www.ncbi.nlm.nih.gov/clinvar/variation/371390/

      gnomAD: n/a

    1. P43

      Case43: Male, Chinese, 2.3y (end of study)

      HPOsFreeText: 2y onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case43 (Level 2)


      CasePreviousTesting: NBS

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.2107G>A (p.Gly703Arg)

      ClinVar: n/a

      CAID: CA364394252

      gnomAD: 0.00006152 (African)


      CaseAddInfo: one variant, not homozygous.

    2. P42

      Case42: Female, Chinese, 2.3y (end of study)

      HPOsFreeText: 10 mo onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case42 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.2080C>T (p.Arg694Trp)

      ClinVar: 218996

      CAID: CA347907

      gnomAD: 0.00006534 (South Asian)


      Variant2: NM_000255.3:c.2179C>T (p.Arg727Ter)

      ClinVar: 218998

      CAID: CA347913

      gnomAD: 0.0001504 (East Asian)


      CaseAddInfo: heterozygous mutations in trans.

    3. P41

      Case41: Male, Chinese, 10.3y (end of study)

      HPOsFreeText: 8.8y onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case41 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1790T>G (p.Ille597Arg)

      ClinVar: 551764

      CAID: CA364395663

      gnomAD: n/a


      Variant2: NM_000255.3:c.2106delA (p.VAl704Ter)

      ClinVar: 555523

      CAID: CA658821513

      gnomAD: n/a


      CaseAddInfo: both variants novel. heterozygous mutations in trans.

    1. Patients 2–4

      Family2to4: Maltese

      FamilyPresentingHPOs: N/A

      HPOsFreeText: N/A

      FamilyNotHPOs: HP:0001270, HP:0007018, HP:0001252, HP:0000750, HP:0000252 (Motor delay, Attention deficit hyperactivity disorder, Muscular hypotonia, Delayed speech and language development, Microcephaly)

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: Whole exome sequencing was performed as a trio with both parents. Identified DHTKD1 mutations were evaluated for possible effects and filtered for frequencies and predicted pathogenicity. No other candidate genes were found during the WES analysis for either patient sequenced. Sanger sequencing confirmed the proband's siblings are homozygous for the variant and that each parent is a carrier.

      FamilyPreviousTesting: Amino acid and organic acid testing showed elevated urinary 2-aminoadipic, 2-ketoadipic, and glutaric acids in the proband as well as in two elder brothers, ages 5 and 7.

      FamilyAddInfo: Parents are consanguineous, All three affected siblings are clinically normal

      Variant: NM_018706.6:c.915G>C (p.Gln305His)

      CAID: CA5407680 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA5407680

      gnomAD: Other 0.0001630, https://gnomad.broadinstitute.org/variant/10-12131182-G-C

      Affected: 3

      Unaffected: 2

      AddSegregationInfo: Candidate gene sequencing

    1. Biallelic

      Case#: Patient 2, male, 5 years (report), Turkish

      CaseHPOs: HP:0003235, HP:0002240 (hypermethioninemia, hepatomegaly)

      CaseHPOsFreeText: Identified by newborn screening.

      CaseNotHPOsFreeText: No signs of hepatic failure, no clinical symptoms.

      CasePreviousTesting: On day of life 3, elevated methionine concentration in blood of 390 µmol/L (normal 20–40). Total homocysteine in plasma was 59 µmol/L (normal 5–15). At later age (not specified), plasma methionine ranged from 1000 to 2070 µmol/L, while total homocysteine in plasma ranged from 30 to 55 µmol/L.

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: All 9 exons and intron-exon junctions of MAT1A were amplified by PCR from genomic DNA. This was followed by SSCP analysis and sequence analysis of PCR products with abnormal mobility.

      Variant: c.125T>C (p.Leu42Pro) (homozygous)

      ClinVar: N/A

      CAID: CA377363776

      gnomAD: The highest population minor allele frequency in gnomAD is 0.000008791 (European non-Finnish); no homozygotes in any population.

      VariantEvidence: When expressed in E. Coli, the variant resulted in reduction of methionine adenosyltransferase (MAT) and tripolyphosphatase (PPPase) activities to ~10 and ~20% of wild type respectively (Fernandez-Irigoyn et al, 2010, PMID 20675163; Fig 2).

      Points: 0.5

    1. Lo

      Case# Lo, M, 10mo diagnosis---originally 1985

      CasePresentingHPOs HP:0011968, HP:0001531, HP:0000737, HP:0007281, HP:0002013, HP:0001259, HP:0005979, HP:0001943

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod

      Variant NM_000709.3:c.1265A>G(p.Lys422Arg), NM_000709.3:c.137dup(p.Ser47IlefsTer4)

      CAID CA406015486(miss), CA658820686(dup)

      VariantEvidence 3978850: in patient fibroblasts-rate of decarboxylation of alpha-ketoacids: alpha ketoisovalerate[0<0.31], Pyruvate[0.40>.34], alpha-ketoglutarate[0.14>0.10] (Table 1), BCKDH activity[0.0003<0.107] (Table 2), E1 subunit activity[0.6<5.9] (Table 3)--[ProbandvsNormal]

      CaseAddInfo 3978850( a positive dinitrophenylhydrazine test and elevated urinary a-ketoisocaproate, a-methyl-P-OH-valerate and a-OH-isoval- erate,

      CasePMIDs 3978850, 2914958

    1. Patient1

      Case1: female, 2.3y (initial referral), Italian, Family 1

      CasePresentingHPOs: HP:0001508, (failure to thrive)

      HPOsFreeText: birthweight 3060 g, SGOT 11 mo 150 U/L, SGPT 11 mo 160 U/L, 1.8y elevated plasma lactic acid 2.9 mmol/L. 3.9 y alkaline phosphatase 928 U/L, 4.7 y serum tricglycerides 184 mg/dl, fasting plasma methionine 644 umol/L. increased urinary methionine excretion 40 umol/mmol. increased lactic acid excretiom 107 umol/mmol. mild centrilobular fibrosis in liver. some eosinophils present in liver.

      CaseNotHPOs: HP:0001404, HP:0001397, HP:0012465, HP:0001396, (hepatocellular necrosis, hepatic steatosis, elevated hepatic iron concentration, cholestasis)

      NotHPOsFreeText: hepatic dysfunction. normal tHcy.

      CaseAddInfo: proband, second child, low methionine diet (300 mg/day) at 2.4 y decreased plasma methionine to normal.

      Case (Level 2)


      Variant1: NM_018960.5(GNMT):c.149T>C (p.Leu50Pro)

      ClinVar: 4169

      CAID: CA248600

      gnomAD: 0.0002319 (East Asian)


      Variant2: NM_018960.5(GNMT):c.529C>A (p.His177Asn)

      ClinVar: 4170

      CAID: CA248601

      gnomAD: 0.0006993 (European non-Finnish)


      CaseAddInfo: compound heterozygote, Leu50Pro maternal mutation, His177Asn paternal mutation. The amino acid shifts are one # different than those predicted in the paper (Leu49Pro and His176Asn).

    1. d

      CaseST-11: Male, 1 day onset, Turkey

      CasePresentingHPOs: HP:0001319, HP:0000316, HP:0008070, HP:0001410, HP:0001987, HP:0004322, HP:0004482 (Neonatal hypotonia, Hypertelorism, Sparse hair, Liver dysfunction, Hyperammonemia, Short stature, Relative macrocephaly)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Family is consanguineous, Proband is homozygous for this variant

      CasePreviousTesting: See Group

      CaseGenotypingMethod: See Group

      Variant: NM_001123.3:c.905T>C (p.Phe302Ser)

      CAID: CA377399030, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA377399030

      gnomAD: Not in gnomAD

    1. SERPING1P1003Ac.120_121delAGp.Gly41Argfs*16Increased exon 3 skipping (band B) → p.Asp18Glyfs*26 (NMD?), decreased down IRDecreased expression of full-length mutant allele compared to wt allele

      Patient: P100

      Variant: c.120_121delAG p.Gly41Argfs*16

      CAID: CA2580612030

      Functional effect: Decreased expression of full-length mutant allele compared to wt allele. Observed in blood.

    1. GII-3

      Case: Family G Proband GII-3, male, 13yo at report

      CasePresentingHPOs: HP:0000953, HP:0000998, HP:0030053, HP:0000054, HP:0002240, HP:0001642, HP:0000365, HP:0001822, HP:0100490, HP:0002619

      CasePresentingHPOsFreeText: subcutaneous masses in genital area, dilated lateral scleral vasculature

      CaseNOTHPOs: HP:0034373, HP:0007380, HP:0001256, HP:0000520

      CaseNOTHPOSFreeText:

      CasePreviousTesting: Direct sequencing of AIFM2, ADAMTS14, EIF4EBP2, C10ORF54, PPA1, H2AFY2, LRRC20, NODAL, PRF1, TYSND1, SAR1A, PSAP, NPFFR1, and C10ORF27

      CaseGenotypingMethod: Microarray, homozygosity mapping, haplotype analysis, direct sequencing of exons of SLC29A3, restriction digestion

      Variant: G437R homozygous

      ClinVarID: or CAID: 565/CA114352

      gnomAD: The missense variant G437R is present in gnomAD v4.0.0 with a MAF=0.00006666 (4/60002 alleles) in the Admixed American population and 0 homozygotes.

      AddCaseInfo: Female cousin, GII-10, is also affected but lacks the classical cutaneous findings

      PreviouslyPublished: n/a

      VariantEvidence: Functional characterization of G437R in Xenopus oocytes showed that transport activity was approximately half of WT SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated accelerated turnover of the G437R mutant compared to WT, suggesting decreased stability (Kang et al. 2010; PMID: 20595384)

    2. Figure 2Haplotype Analysis Performed in Six Families with H SyndromeAffected individuals are marked by gray symbols. The disease-associated haplotypes in the linked interval on chromosome 10q21.3–q22.1 are shown by vertical bars (red and green) in families A–F. Alleles excluded by recombination events are marked in pink. The physical locations of the polymorphic microsatellites are given near the haplotype for individual AI-2.

      Case: Family A Proband AII-8, male, Arabic, Israeli, 13yo at report

      CasePresentingHPOs: HP:0000953, HP:0000998, HP:0000054, HP:0001433, HP:0011025, HP:0000365, HP:0000520, HP:0012385, HP:0001684, HP:0000823, HP:0030053, HP:0100324, HP:0100727

      CasePresentingHPOsFreeText: Scrotal masses, Dilated scleral vessels

      CaseNOTHPOs: HP:0008064, HP:0002619, HP:0007380

      CaseNOTHPOSFreeText:

      CasePreviousTesting: direct sequencing of AIFM2, ADAMTS14, EIF4EBP2, C10ORF54, PPA1, H2AFY2, LRRC20, NODAL, PRF1, TYSND1, SAR1A, PSAP, NPFFR1, and C10ORF27

      CaseGenotypingMethod: microarray, haplotype analysis, direct sequencing of exons of SLC29A3, restriction digestion

      Variant: G427S; G437R

      ClinVarID: or CAID: 563/CA114349; 565/CA114352

      gnomAD: The missense variant G427S is present in gnomAD v4.0.0 with a MAF=0.00005339 (4/74926 alleles) in the African/African American population and 0 homozygotes. The missense variant G437R is present in gnomAD v4.0.0 with a MAF=0.00006666 (4/60002 alleles) in the Admixed American population and 0 homozygotes.

      AddCaseInfo: consanguineous parents; mother was het for G427S, but father's genotype was not provided

      PreviouslyPublished: PMID: 18410979

      VariantEvidence: Functional studies in Xenopus oocytes demonstrated that G427S results in a total loss of transport activity (Kang et al. 2010; PMID: 20595384).

      Kang et al. (2010) performed functional characterization of the G437R mutation in Xenopus oocytes and observed transport activity that was approximately half that of wildtype SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated accelerated turnover of the G437R mutant compared to wildtype, suggesting decreased stability.

    3. JII-1

      Case: Family J Proband JII-1, male, 12yo at report

      CasePresentingHPOs: HP:0000953, HP:0030053, HP:0000998, HP:0000054, HP:0002240, HP:0031664, HP:0000365, HP:0012385, HP:0034373, HP:0001084, HP:0000771

      CasePresentingHPOsFreeText: subcutaneous masses in genital area, dilated lateral scleral vasculature

      CaseNOTHPOs: HP:0001822, HP:0000520, HP:0002619, HP:0007380, HP:0001256

      CaseNOTHPOSFreeText:

      CasePreviousTesting: Direct sequencing of AIFM2, ADAMTS14, EIF4EBP2, C10ORF54, PPA1, H2AFY2, LRRC20, NODAL, PRF1, TYSND1, SAR1A, PSAP, NPFFR1, and C10ORF27

      CaseGenotypingMethod: Microarray, homozygosity mapping, haplotype analysis, direct sequencing of exons of SLC29A3

      Variant: c.1045delC homozygous

      ClinVarID: or CAID: 566/CA351488

      gnomAD: The frameshift variant p.Leu349fs, located in exon 6/6, is present in gnomAD v4.0.0 with a MAF=0.000001799 (2/1112010 alleles) in the European Non-Finnish population and 0 homozygotes.

      AddCaseInfo: Consanguineous, unaffected parents. 6 unaffected siblings

      PreviouslyPublished: n/a

      VariantEvidence: Kang et al. (2010; PMID: 20595384) performed functional characterization of the 1045delC mutation in Xenopus oocytes and observed near-total loss of transport activity compared to wildtype SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated mistrafficking of the mutant protein to the endoplasmic reticulum or Gogli apparatus

    4. HII-2

      Case: Family H Proband HII-2, female, 50yo at report

      CasePresentingHPOs: HP:0000823, HP:0002240, HP:0001822, HP:0034373, HP:0100490, HP:0002619, HP:0000520, HP:0001838, HP:0007380, HP:0001084, HP:0001871, HP:0004322, HP:0000135, HP:0000141, HP:0012410, HP:0011974

      CasePresentingHPOsFreeText: stasis ulcers

      CaseNOTHPOs: HP:0000953, HP:0000998, HP:0030053, HP:0001256

      CaseNOTHPOSFreeText: dilated lateral scleral vasculature

      CasePreviousTesting: Direct sequencing of AIFM2, ADAMTS14, EIF4EBP2, C10ORF54, PPA1, H2AFY2, LRRC20, NODAL, PRF1, TYSND1, SAR1A, PSAP, NPFFR1, and C10ORF27

      CaseGenotypingMethod: Microarray, homozygosity mapping, haplotype analysis, direct sequencing of exons of SLC29A3, restriction digestion

      Variant: G437R homozygous

      ClinVarID: or CAID: 565/CA114352

      gnomAD: The missense variant G437R is present in gnomAD v4.0.0 with a MAF=0.00006666 (4/60002 alleles) in the Admixed American population and 0 homozygotes.

      AddCaseInfo: Consanguineous parents, not genotyped. 3 unaffected, not genotyped siblings

      PreviouslyPublished: n/a

      VariantEvidence: Functional characterization of G437R in Xenopus oocytes showed that transport activity was approximately half of WT SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated accelerated turnover of the G437R mutant compared to WT, suggesting decreased stability (Kang et al. 2010; PMID: 20595384)

    1. 13

      Case: Individual 13, male, AOR= 8 years 4 months

      CasePresentingHPOs: HP:0000252, HP:0000750, HP:0001263, HP:0001290, HP:0000527, HP:0006332, HP:0001212, HP:0004279, HP:0000202, HP:0010289, HP:0000540

      CasePresentingHPOText: Began walking 18 Noted as limited vocabulary and saccadic speech. Noted to have short fingers.

      CaseNOTHPOs: HP:0001250, HP:0002376, HP:0002360, HP:0000708, HP:0000924, HP:0002719

      CaseNOTtextHPO: no ID per the WISC-V. CT scan normal

      CasePreviousTesting: Karyotyping, Fragile X Syndrome (FMR1), and Array-CGH (Agilent 180K) were all normal

      CaseGenotypingMethod: Trio WES (exome capture Agilent CRE and HiSeq 4000).

      Variant: hg19:chr2: g.4804618 6_4804619 0del, c.1825_1829del, p.(Glu609) OR* NM_001190274.1:c.1825_1829del

      CA ID: CA658820930

      de novo

      gnomAD: n/a

      AddCaseInfo:

      VariantEvidence: The Gln609Ter mutation occurs in exon 15 which encodes the second CASH domain. The nonsense mutation most likely disrupts the second and third CASH domains and the zinc-finger ubiquitin binding region. No functional assays or variant evidence was provided, so I have downgraded the score.

    2. 15

      Case: Individual 15, male, AOR= 11 years 5 months

      CasePresentingHPOs: HP:0002167, HP:0002342, HP:0001250, HP:0002376, HP:0002360, HP:0000717, HP:0007018, HP:0000718, HP:0000735, HP:0002553, HP:0000154, HP:0000289, HP:0000179, HP:0000293, HP:0009909, HP:0004209, HP:0000403, HP:0009921, HP:0002020

      CasePresentingHPOText: Began walking at 14 months old. Noted as having limited vocabulary, short sentences and single words. Noted as having one single seizure at 5 years old. Developmental regression noted at 1 year old. Has food seeking behavior.

      CaseNOTHPOs: HP:0000202, HP:0000924,

      CaseNOTtextHPO:

      CasePreviousTesting: ArrayCGH, Prader will and Anglican syndrome methylation studies, and RAI1 analysis (by DHPLC) were all normal

      CaseGenotypingMethod: Trio-WES performed through the DDD consortium, 2017 PMID:PMID: 28135719.

      Variant: hg19:chr2: g.4804051 5_4804052 2dup, c.2084- 6_2085dup, p.(Gly697) OR* NM_001190274.1:c.2084-6_2085dup

      CA ID: CA658765223

      de novo

      gnomAD: n/a

      AddCaseInfo:

      VariantEvidence: The c.2084−6_2085dup id suggested to lead to a stop codon at Gly697, which is located in exon 18. Exon 18 is upstream of the third CASH domain, which regulates substrate recognition. No functional assays or variant evidence was provided, so I have downgraded the score.

    3. 3

      Case: Individual 3, male, 7.5 yo

      CasePresentingHPOs: HP:0000750, HP:0001263, HP:0001290, HP:0002360, HP:0007018, HP:0000736, HP:0004673, HP:0000735, HP:0000629, HP:0000316, HP:0004209, HP:0001212, HP:0001382,

      CasePResentingHPOText: Subject began walking at 18 months. Testing for autism gave the following results: WPPSI-III-NL: TIQ 98, VIQ 106, PIQ 96.

      CaseNOTHPOs: HP:0001250, HP:0002376, HP:0000202, HP:0000504,

      CasePreviousTesting: Metabolic screening, SNP-array, and Fragile X (FMR1) testing were normal

      CaseGenotypingMethod: Trio-WES. Individual is noted as being mosaic (60%) for the FBXO11 mutation. Testing also identified a VUS in TP73 (NM_0054 27.3):chr1: g.3644250 G>A, c.901G>A; p.(Asp301Asn). Not noted as de novo, so assume inherited and parents were not noted as having behavioral abnormalities or intellectual disability.

      Variant: hg19:chr2: g.4806611 8=/T>C, c.467=/A> G p.(Gln156Arg) or NM_001190274.1:c.467A>G

      CA ID: CA346813225

      de novo Trio-WES performed so maternity and paternity could be investigated with this method.

      gnomAD: n/a

      AddCaseInfo:

      VariantEvidence: Individual is noted as being mosaic (60%) for the FBXO11 mutation. Gln156 is located just N-terminal to the F-box region of FBXO11, and is conserved across species. Pathogenicity algorithms showing varying predictions, from tolerated to damaging, thus indicating a VUS. No functional assays were performed to indicate the impact of the Q156R mutation on FBXO11 function.

    1. F2:II.2

      Case# F2:II.2, F, 5mo onset, Turkey

      CasePresentingHPOs HP:0001263, HP:0006846, HP:0003201, HP:0011675, HP:0002925, HP:0100543, HP:0001250, HP:0002061, HP:0012444, HP:0001943, HP:0002151, HP:0002919, HP:0045045, HP:0040145, HP:0001270, HP:0001259, HP:0003236, HP:0000648

      HPOcont: Global developmental delay, Acute encephalopathy, Rhabdomyolysis, Arrhythmia, Elevated TSH, Cognitive impairment, Seizures, Lower limb spasticity, Brain atrophy, Hypoglycemia, Elevated lactate, Ketonuria, Elevated acylcarnitine, Dicarboxylic acidemia, Motor delay, Coma, Elevated CK, Optic atrophy

      HPOFreeText: "starting from the age of five months, psychomotor development appeared delayed. At the age of one year, spasticity predominantly involving the legs was noted. Nevertheless, the child was relatively active and was able to sit and crawl. However, after an episode of infection, she lost already acquired skills. Laboratory investigations during this episode showed transiently elevated CK activity (up to 2,970 U/l; NR < 269 U/l). At the age of 15 months, the girl suffered from a febrile upper airway infection during which she suddenly became comatose."

      CasePreviousTesting "Sequence analysis of the mitochondrial DNA and CPT2 did not show clinically relevant variants. Laboratory investigations revealed hypoglycemia (31 mg/dl; NR >50 mg/dl) and severe lactic acidosis (lactate up to 16.6 mmol/L; NR < 2.1 mmol/L). Biochemical analysis of fresh muscle tissue showed moderately reduced ATP production rate and a mildly reduced activity of mitochondrial complex I. Brain MRI demonstrated mild global brain atrophy without focal abnormalities. Eye examination showed bilateral optic atrophy. Acylcarnitine profiling showed normal free carnitine concentrations in dried blood while C14:1 acylcarnitine was mildly elevated (0.31 μmol/L; NR 0-0.25 μmol/L). Analysis of organic acids in urine revealed increased concentrations of dicarboxylic acids and ketone bodies as well as massive excretion of lactate." Then at 12 years, elevated TSH concentration (7.17 μIU/ml; NR 0.28-4.31 μIU/ml).

      CaseMethod1 WES

      CaseMethod2 Sanger

      CaseGenotypingMethod WES, confirmed with Sanger in patient and parents

      Variant NM_001283106.2(TANGO2):c.418C>T (p.Arg140Ter)

      ClinVar 224774

      CAID CA358667

      gnomAD 1.501e-05(European (Non-Finnish)), 8.254e-06(Total)

      VariantEvidence (Figure 3) In assessment of Palmitate-Dependent Mitochondrial Respiration, oxygen consumpition rates were decreased in patient fibroblasts by ~20% compared to control.

      CaseAddInfo "measurement of pyruvate-dependent oxygen consumption rates in fibroblast cell lines from individuals F1:II.2 and F2:II.2 was unremarkable." consanguineous parents, healthy older sibling

      CasePMIDs n/a

    2. F1:II.2

      Case# F1:II.2, F, 2yo onset, European

      CasePresentingHPOs HP:0001263, HP:0006846, HP:0003201, HP:0011675, HP:0002925, HP:0001250, HP:0012444, HP:0001943, HP:0002151, HP:0045045, HP:0040145, HP:0001259, HP:0002133, HP:0002913, HP:0003128, HP:0002061, HP:0001664, HP:0008936, HP:0001344, HP:0000252, HP:0003236, HP:0001946, HP:0100543

      HPOcont: Global developmental delay, Acute encephalopathy, Rhabdomyolysis, Arrhythmia, Elevated TSH, Seizures, Brain atrophy, Hypoglycemia, Elevated lactate, Elevated acylcarnitine, Dicarboxylic acidemia, Coma, Status epilepticus, Myoglobinuria, Lactic acidosis, Lower limb spasticity, Torsade de pointes, Trunk hypotonia, Absent Speech, Microcephaly, Elevated CK, Ketosis, Cognitive Impariment

      HPOFreeText: "At the age of 2 7/12 years, she suffered from an infection and suddenly became comatose with status epilepticus. Her renal function was transiently impaired due to massive rhabdomyolysis with myoglobinuria. The girl’s condition subsequently improved but she was unable to sit due to truncal hypotonia. She developed progressive spasticity in the legs, and communicated only non-verbally. Two months later a second episode occurred, which was again triggered by an infection and presented with similar clinical and laboratory findings. A third metabolic decompensation with lactic acidosis, hypoglycemia and rhabdomyolysis occurred six weeks later. This time, additional cardiac involvement with long QT syndrome and torsade de pointes tachyarrhythmia required intensive care treatment and implantation of a cardioverter-defibrillator (ICD) device. Seizures occurred which were responsive to antiepileptic medication. The girl remained with severely impaired psychomotor capabilities, marked truncal muscular hypotonia, moderate spasticity in the lower limbs, dystonic movements in the upper limbs, absent speech, and impaired social interaction. Secondary microcephaly became evident (head circumference < P3)."

      CasePreviousTesting "marked hypoglycemia (18 mg/dl; normal range (NR) > 50 mg/dl). Initial laboratory testing documented massively elevated plasma creatine kinase (CK) activity (maximum 300,000 U/l, NR < 227 U/l) as well as elevated plasma lactate concentrations up to 3.8 mmol/l (NR < 1.6 mmol/l). Urine organic acid analyses during crises showed a massive excretion of ketone bodies (around 2,000 mmol/mol creatinine), lactate (2,000 mmol/mol creatinine; NR < 285 mmol/mol creatinine), and dicarboxylic acids (values given in mmol/mol creatine: adipic (1,513; NR < 34), glutaric (24; NR = not detectable), sebacic (712; NR < 1.4), suberic (494; NR < 10), decenedioic (581; NR = not detectable), and of note malonic (145; NR = not detectable) acid). Acylcarnitine profiling in dried blot spots collected during the crisis showed free carnitine concentrations within normal ranges while several acylcarnitines were elevated 2-5-fold above the respective normal range (i.e. C5DC, C6DC, C10:1, C12, C12:1, C14:1, C14:2). In addition, an elevated TSH concentration (16.6 mU/l; NR 0.5-4.5 mU/l) was detected and treatment with L-thyroxine was initiated. Targeted sequencing of CPT2, ETFA, ETFB, ETFDH, and GCDH did not reveal clinically relevant variants."

      CaseMethod1 WES

      CaseMethod2 Sanger

      CaseGenotypingMethod WES, confirmed with Sanger in patient and parents

      Variant (1) NM_001283106.2(TANGO2):c.4delT (p.Cys2Alafs) (2) NM_152906.5:c.(56+1_57-1)(*1?)del

      ClinVar (1) 224773

      CAID (1) CA358861

      gnomAD n/a

      CaseAddInfo "measurement of pyruvate-dependent oxygen consumption rates in fibroblast cell lines from individuals F1:II.2 and F2:II.2 was unremarkable." Healthy twin brother.

      CasePMIDs n/a

    1. Pt15

      CasePt15 Male, 2mo report, Italian

      CasePresentingHPOs HP:0002789, HP:0001950, HP:0001987, HP:0003572, HP:0003217 (Tachpnea, Respiratory alkalosis, Hyperammonemia, Low plasma citrulline, High plasma glutamine)

      HPOsFreeText Tachypnoeic, respiratory alkalosis(36h), coma(48h), hyperammonemia, low citrulline, elevated glutamine

      CaseNotHPOs n/a

      CasePreviousTesting Metabolic testing plasma citrulline(6[normal 16-40μmol/l]), glutamine(1824[normal 530–913μmol/l]) and ammonia(1300[normal< 75 μg/dl])

      CaseMethod1 PCR

      CaseMethod2 n/a

      CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

      Variant 1. NM_001875.4:c.1145C>T (p.Pro382Leu), 2. NM_001875.4:c.2891G>A (p.Gly964Asp) compound heterozygous

      ClinVar n/a

      CAID 1. CA2086267, CA64723299

      gnomAD 1. 0.00007189(European (Non-Finnish)), 0.00003664(Total), 2. n/a

      VariantEvidence n/a

      CaseAddInfo n/a

      CasePMIDs 21120950

    2. Pt12

      CasePt12 Female, 2do death, Italian

      CasePresentingHPOs HP:0001290, HP:0002098, HP:0001987, HP:0003572, HP:0003217 (Hypotonia, Respiratory distress, Hyperammonemia, Low plasma citrulline, High plasma glutamine

      HPOsFreeText Hypotonia and respiratory stress at birth, hyperammonemia, low citrulline, elevated glutamine

      CaseNotHPOs n/a

      CasePreviousTesting Metabolic testing plasma citrulline(0[normal 16-40μmol/l]), glutamine(2300[normal 530–913μmol/l]) and ammonia(1831[normal< 75 μg/dl])

      CaseMethod1 PCR

      CaseMethod2 n/a

      CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

      Variant NM_001875.4:c.1981G>C (p.Gly661Arg) homozygous

      ClinVar n/a

      CAID CA350438282

      gnomAD n/a

      VariantEvidence n/a

      CaseAddInfo n/a

      CasePMIDs n/a

    3. Pt11

      CasePt11 male, 3yo report, Italian

      CasePresentingHPOs HP:0001987 (Hyperammonemia)

      HPOsFreeText severe hyperammonemia at 48h of life

      CaseNotHPOs n/a

      CasePreviousTesting Metabolic testing plasma citrulline(<2[normal 16-40μmol/l]), glutamine(1600[normal 530–913μmol/l]) and ammonia(3400[normal< 75 μg/dl])

      CaseMethod1 PCR

      CaseMethod2 n/a

      CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

      Variant 1. NM_001875.4:c.2440C>T (p.Arg814Trp), 2. NM_001875.4:c.3953T>A (p.Leu1318Ter) compound heterozygous

      ClinVar n/a

      CAID 1. CA2086638, 2. CA350439297

      gnomAD n/a

      VariantEvidence n/a

      CaseAddInfo n/a

      CasePMIDs 21120950

    4. Pt 9

      CasePt9 male, 5do death, Italian

      CasePresentingHPOs HP:0001987 (Hyperammonemia)

      HPOsFreeText Hyperammonemia

      CaseNotHPOs n/a

      CasePreviousTesting Metabolic testing: ammonia(2750[normal< 75 μg/dl])

      CaseMethod1 PCR

      CaseMethod2 n/a

      CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

      Variant 1. NM_001875.4:c.2429A>G (p.Gln810Arg), 2. NM_001875.4:c.3953T>A (p.Leu1318Ter) compound heterozygous

      ClinVar n/a

      CAID 1. CA350440293, 2. CA350439297

      gnomAD n/a

      VariantEvidence n/a

      CaseAddInfo n/a

      CasePMIDs 12955727

    5. Pt5

      CasePt5 male, 15mo death, Italian

      CasePresentingHPOs HP:0001987, HP:0001254, HP:0001252, HP:0003572, HP:0003217 (Hyperammonemia, Lethargy, Hypotonia, Low plasma citrulline, High plasma glutamine)

      HPOsFreeText neonatal severe hyperammonemia, mildly hypotonic, lethargy, low plasma citrulline, elevated glutamine

      CaseNotHPOs n/a

      CasePreviousTesting Metabolic testing plasma citrulline(6[normal 16-40μmol/l]), glutamine(1500[normal 530–913μmol/l]) and ammonia(1214[normal< 75 μg/dl])

      CaseMethod1 PCR

      CaseMethod2 n/a

      CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

      Variant 1. NM_001875.4:c.1440_1441del (p.Thr481CysfsTer?), 2. NM_001122634.3:c.3004C>T (p.Arg1002Trp) compound heterozygous

      ClinVar n/a

      CAID 1. CA2086366, 2. CA64748170

      gnomAD 1. 0.00001802(European (Non-Finnish), 0.000008153(Total), 2. n/a

      VariantEvidence n/a

      CaseAddInfo Older brother who died with post-mortem suspicion of CPSD or NAGS deficiency.

      CasePMIDs 21120950

    6. Pt7

      Family#PresentingHPOs HP:0001987 (Hyperammonemia)

      HPOFreeText: Severe hyperammonemia

      FamilyNotHPOs n/a

      CountryOrigin n/a

      Ethnicity Italian

      Race n/a

      Family#PreviousTesting Elevated plasma ammonia in both siblings (3454 in Pt7 and 1858 in Pt8[normal<75 μg/dl]).

      Family#Method1 PCR

      Family#Method2 n/a

      Family#GenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

      Affected 2

      Unaffected n/a

      Segregations n/a

      PublishedLOD n/a

      eLOD n/a

      AddSegregationInfo n/a

      ProbandLabel Pt7, Female, 5mo death

      CasePresentingHPOs HP:0002283, HP:0100806, HP:0003572, HP:0003217 (Diffuse brain atrophy, Sepsis, Low plasma citrulline, High plasma glutamine)

      CaseHPOsFreeText Severe hyperammonemia(2do), Severe diffuse brain atrophy on MRI(1mo), sepsis(5mo)

      CasePreviousTesting Low plasma citruline(0[normal 16-40μmol/l]) and elevated glutamine(2488[normal 530–913 μmol/l])

      Variant 1. NM_001875.4:c.1263+5G>C, 2. NM_001875.4:c.2429A>G (p.Gln810Arg)

      ClinVar n/a

      CAID 1. To register, 2. CA350440293

      gnomAD n/a

      VariantEvidence c.1263+5G>C causes a splice defect (Table 2)

      FamilyAddInfo Brother, Pt8, died with similar clinical features and was diagnosed with CPS1D post-mortem.

      FamilyPMIDs 12955727, 12655559

    7. Pt1

      CasePt1 female, 3yo diagnosis, Italian

      CasePresentingHPOs HP:0001508, HP:0002014, HP:0000505, HP:0002167, HP:0002013, HP:0001252, HP:0002321, HP:0001987, HP:0003217, HP:0002910, HP:0012747, HP:0100543, HP:0001256 (Failure to thrive, Diarrhea, Visual impairment, Speech impairment, Vomiting, Hypotonia, Vertigo, Hyperammonemia, Hyperglutaminemia, Elevated transaminases, Abnormal brain MRI signal intensity, Cognitive impairment, Mild ID)

      HPOsFreeText normal psychomotor dev, failure to thrive and diarrhea(first years), visual/speech impairment, vomiting, hypotonia, vertigo(referred at 3y,2mo), , hyperammonemia, high glutamine, elevated transaminases, normal orotic levels, hyperintense signal in cortical-subcortical frontal region on brain MRI, cognitive impairment:IQ 53(3yo) mild ID(21yo)

      CaseNotHPOs n/a

      CasePreviousTesting Metabolic testing plasma citrulline(17.3[normal 16-40μmol/l]), glutamine(1244[normal 530–913μmol/l]) and ammonia(300[normal< 75 μg/dl]), elevated transaminases 350 UI/L, normal orotic levels, CPS1 residual enzyme activity "low" in liver biopsy.

      CaseMethod1 PCR

      CaseMethod2 n/a

      CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

      Variant 1. NM_001875.4(CPS1):c.3047A>G (p.Asn1016Ser), 2. NM_001875.4:c.3500C>G (p.Thr1167Arg) compound het

      ClinVar 1. 551211

      CAID 2. CA350437190

      gnomAD 1. 0.00006534(African), 0.000008123(Total) 2. n/a

      VariantEvidence enzyme assay showing low CPS1 activity mentioned

      CaseAddInfo n/a

      CasePMIDs 21120950

    1. {"type":"entrez-nucleotide","attrs":{"text":"NM_017890.4","term_id":"384551660","term_text":"NM_017890.4"}}NM_017890.4:c.6879delT

      Case# RQMR10_V-2

      Demographics: Female, 20 yrs at report,

      CasePresentingHPOs HP:0000729, HP:0001763, HP:0001761, HP:0001956, HP:0000577

      CaseNotHPOs

      CasePreviousTesting

      CaseMethod1

      CaseMethod2

      CaseGenotypingMethod

      Variant NM_017890.4:c.6879delT(p.Phe2293Leufs*24)

      ClinVar

      CAID CA4824093

      gnomAD 0.00003250 (South Asian)

      VariantEvidence The proband is homozygous for the variant. This variant introduces a frameshift, resulting in premature protein truncation. The variant was found to cosegregate with disease in the family and was not found in 293 healthy ethnicity-matched controls. It is reported in a heterozygous state at a frequency of 0.00003250 in South Asians in gnomAD.

      CaseAddInfo

      CasePMIDs

    2. c.6879 T

      Case#: ATM02_V-3

      Demographics: Male, 18 yrs at report

      CasePresentingHPOs: HP:0000752, HP:0001581

      CaseNotHPOs:

      CasePreviousTesting:

      CaseMethod1:

      CaseMethod2:

      CaseGenotypingMethod:

      Variant: NM_017890.4:c.6879delT

      ClinVar:

      CAID: CA4824093

      gnomAD:

      VariantEvidence: This variant has been reported in two apparently unrelated families of common ethnicity, and therefore likely founder mutation. Hence, the score is reduced from default.

      CaseAddInfo:

      CasePMIDs:

    1. Nb 60 M – c.768C>G p.S256R + + + + Spasticity c.854A>G p.Q285R Ob 64 F – c.768C>G p.S256R + + + + Spasticity c.854A>G p.Q285R

      The individuals mentioned are from a previous publication (PMID: 20157015) which has already been included in the VCI. But may add cell line data demonstrating mitochondrial dysfunction and increasing PP4 to moderate.

    1. HA91MalayIntron22-c.6429+2T>A-NovelModerate+2 Donor splice site

      Case#: Zahari_HA91

      Demographics: Malay

      CasePresentingHPOs: HP:0003125 Moderate hemophilia FVIII:C:1-5%

      CaseNotHPOs:

      CasePreviousTesting: No

      CaseMethod1: PCR

      CaseMethod2: Sanger

      CaseGenotypingMethod: F8 coding regions (26 exons) including the intron/exon boundaries and the promoter regions were amplified using 26 sets of primers and subsequently sequenced.

      Variant: NM_000132.3:c.6429+2T>A

      ClinVar:

      CAID: CA414899265

      gnomAD: Not found

      VariantEvidence: The splice donor site variant occurs in the intron 22. However, the proband did not carry the intron 22 inversion. The variant is scored default points.

      CaseAddInfo:

      CasePMIDs:

    1. 14 CC, CFF, DM, HM, JC, SS Hurler–Scheie No 10 years Male [c.158 + 5delinsAA] + [c.895G>T] [c.158 + 5delinsAA] + [p.Glu299*] [Intron 1] + [7] Known 0.26(R*) Yes, father-carrier for c.158 + 5delGCinsAA; mother-carrier for E299* No

      another individual with this variant, but PM3 has already been met and this variant is path without this additional case

    1. III:2

      Case#: Family 1-III:2

      CaseHPOs: HP:0003563, HP:0001397 (decreased LDL cholesterol, hepatic steatosis)

      CaseNotHPOs: HP:0002910, HP:0000819 (elevated liver enzymes, diabetes)

      CasePreviousTesting: TC 104 mg/dl, LDL-C 7 mg/dl, HDL-C 91 mg/dl, TG 31 mg/dl (see additional values in Table 1). Normal ranges- total cholesterol (TC) 92-234 mg/dl, LDL-cholesterol (LDL-C) 136-174 mg/dl, HDL-cholesterol (HDL-C) 60-95 mg/dl), triglyceride (TG) 35-132 mg/dl.

      Variant: NM_000384.2:c.2533C>T (p.Gln845Ter), heterozygous

      ClinVar: N/A

      CAID: CA346011071

      gnomAD: 0.000008796 (European non-Finnish)

    2. I:1

      Case#: Family IV-I:1, male, 84 year old man

      CaseHPOs: HP:0003563, HP:0001397 (decreased LDL cholesterol, liver steatosis)

      CaseNotHPOs: HP:0000819 (Diabetes)

      CasePreviousTesting: TC 106 mg/dl, LDL-C 33 mg/dl, HDL-C 60 mg/dl, TG 60 mg/dl (see additional values in Table 1). Normal ranges- total cholesterol (TC) 92-234 mg/dl, LDL-cholesterol (LDL-C) 136-174 mg/dl, HDL-cholesterol (HDL-C) 60-95 mg/dl), triglyceride (TG) 35-132 mg/dl.

      CaseGenotypingMethod: Next generation sequencing panel for high-throughput sequencing of the coding regions of genes previously linked to FHBL (APOB, PCSK9, ANGPTL3) and ABL (MTTP, SAR1B). Sanger sequencing was performed for validation and co-segregation analysis among family members.

      Variant: NM_000384.2:c.11153C>G (p.Ser3718Ter), heterozygous

      CAID: CA345983128

      gnomAD: Absent

      Variant evidence: APOB- p.Ser3718* mutations lead to the formation of expected truncated ApoB forms (ApoB-81) of 418 kDa (Fig. 1C, right panel) that can be secreted by the liver and lipidated.

    3. III:1

      Case#: Family 1-III:1, male, 17 years, son of Family 1-III:2

      CaseHPOs: HP:0003563 (decreased LDL cholesterol)

      CaseNotHPOs: HP:0000819 (Diabetes mellitus)

      CasePreviousTesting: TC 98 mg/dl, LDL-C 14 mg/dl, HDL-C 79 mg/dl, TG 2 mg/dl (see additional values in Table 1). Normal ranges- total cholesterol (TC) 92-234 mg/dl, LDL-cholesterol (LDL-C) 136-174 mg/dl, HDL-cholesterol (HDL-C) 60-95 mg/dl), triglyceride (TG) 35-132 mg/dl.

      Variant: NM_000384.2:c.2533C>T (p.Gln845Ter), heterozygous

      ClinVar: N/A

      CAID: CA346011071

      gnomAD: 0.000008796 (European non-Finnish)

    4. Family IV

      Family#: Family IV

      PresentingHPOs: HP:0003563 (decreased LDL cholesterol)

      PresentingHPOsFreeText: FHBL diagnosis was based on low levels of fasting calculated plasma LDL-C < 50 mg/dL without lipid lowering therapy. Affected relatives were diagnosed by LDL-C < 80 mg/dL and/or ApoB <50 mg/dL.

      FamilyMethod1: Next generation sequencing

      FamilyGenotypingMethod: Next generation sequencing panel for high-throughput sequencing of the coding regions of genes previously linked to FHBL (APOB, PCSK9, ANGPTL3) and ABL (MTTP, SAR1B). Sanger sequencing was performed for validation and co-segregation analysis among family members.

      ProbandLabel: Family IV-I:1

      Variant: NM_000384.2:c.11153C>G (p.Ser3718Ter)

      CAID: CA345983128

      gnomAD: Absent

    5. II:2

      Case#: Family 1- II:2, female, 49 years

      CaseHPOs: HP:0003563 (decreased LDL cholesterol)

      CaseNotHPOs: HP:0001397, HP:0000819 (liver steatosis, diabetes)

      CasePreviousTesting: TC 143 mg/dl, LDL-C 20 mg/dl, HDL-C 120 mg/dl, TG 18 mg/dl (see additional values in Table 1). ApoB100 <10 mg/dl (normal range 49-88) (Supplemental data) Normal ranges- total cholesterol (TC) 92-234 mg/dl, LDL-cholesterol (LDL-C) 136-174 mg/dl, HDL-cholesterol (HDL-C) 60-95 mg/dl), triglyceride (TG) 35-132 mg/dl.

      Variant: NM_000384.2:c.2533C>T (p.Gln845Ter), heterozygous

      ClinVar: N/A

      CAID: CA346011071

      gnomAD: 0.000008796 (European non-Finnish)

    1. Subject 5

      Case# Subject 5, F, 7yo onset, Hispanic

      CasePresentingHPOs HP:0001270, HP:0000750, HP:0005184, HP:0001250, HP:0008942, HP:0003236, HP:0001664, HP:0004756, HP:0011675, HP:0001943, HP:0002151, HP:0003201, HP:0001249, HP:0002913, HP:0003324, HP:0001695, HP:0006956

      HPOcont: Motor Delay, Speech Delay, Prolonged QTc interval, Seizures, Elevated CPK, Torsade de pointes, Ventricular tachycardia, Arrhythmia, Hypoglycemia, Elevated Lactate, Acute rhabdomyolysis, Intellectual Disability, Myoglobinuria, Generalized Muscle Weakness, Cardiac Arrest, Enlarged lateral ventricles

      HPOFreeText: speech and motor delay, prolonged QTc interval, seizures, prior to her acute presentation. (7 years) acute rhabdomyolysis, high CPK and myoglobinuria. (13 years) muscle weakness, cardiac arrest, torsade de pointes from prolonged QTc interval, ventricular tachycardia with recurrent pulseless arrest and arrhythmia, able to ambulate.

      CaseNotHPOs n/a

      CasePreviousTesting highest CPK (60,000 U/L), 953 U/L for AST, 540 U/L for ALT, and CPK-MB of 291 U/L.

      CaseMethod1 WES

      CaseMethod2 Sanger

      CaseGenotypingMethod WES and cSNP results confirmed with Sanger

      Variant (1) NM_152906.6:c.460G>A (p.Gly154Arg)

      ClinVar (1) 208823

      CAID (1) CA358646

      gnomAD (1) 0.001549(Other), 0.0001208(Overall)

      VariantEvidence (Figure 3) using "EBV-transformed B-lymphoblastoid cell lines (BLCLs) from another individual, subject 4 with homozygous c.460G>A (p.Gly154Arg) mutation, and evaluated the Golgi by intracellular staining with WGA, as well as cis Golgi marker, anti-GM130 antibody." WGA stain resolved lower area of golgi bodies in p.Gly154Arg cells than WT. Measured immunoglobulin heavy chain binding protein levels in WT and and patient fibroblasts, BiP levels in patient cells lower than WT after ER induced stress by Brefeldin A.

      CaseAddInfo nonconsanguineous, parents confirmed heterozygotes

      CasePMIDs n/a

    1. A 37-year-old woman

      Case# Fam1Pat1, F, 21yo onset, Turkish

      CasePresentingHPOs HP:0002061, HP:0002066, HP:0002070, HP:0001260, HP:0001310, HP:0000563, HP:0006986,

      CasePreviousTesting Neurologic examination revealed dysarthria, spasticity in lower >> upper extremities, mild weakness in proximal leg muscles, Achilles tendon contracture, mild dysmetria, dysdiadochokinesia, and a spastic-ataxic gait. Cranial MRI and nerve conduction studies were unremarkable.

      CaseMethod1 Whole Exome

      Variant NM_001198868.1:c.994G>A

      CAID CA381247865

      gnomAD 0.00005842(East Asian), 0.000008204(Overall)

      VariantEvidence none

    1. The index patient in this family is a 13-year-old female

      Case# ObeidIndex, F, 13yo report, Palestinian-Emirati

      CasePresentingHPOs HP:0006829, HP:0010864, HP:0001263, HP:0000252, HP:0001344, HP:0001250, HP:0002650, HP:0000574, HP:0000414, HP:0000179, HP:0000307, HP:0000218, HP:0040079, HP:0030787, HP:0002136, HP:0001344

      HPOcont: Severe muscular hypotonia, Severe intellectual disability, Global developmental delay, Microcephaly, Absent speech, Seizures, Scoliosis, Thick eyebrow, Bulbous nose, Thick lower lip vermilion, Pointed chin, High palate, Irregular dentition, Cerumen abnormality, Broad-based gait, Absent speech

      Free Text: "birth weight of 2.6 Kg (< 10th centile), head circumference of 33 cm (< 3rd centile). At the age of 8 months, her developmental delay was noticed as she was unable to sit unsupported. Formally evaluated at one year of age, at which point EEG was suggestive of symptomatic localization-related epilepsy. EEG revealed ill-defined low spikes over the left temporooccipital area, suggesting symptomatic partial epilepsy. At age 11 developed subtle facial dysmorphic features, including bushy eyebrows, bulbous nose, anteverted nostrils, thick lower lip, pointed chin, high arched palate, irregular teeth, and waxy ears. As an eleven years and three months old girl, she is able to sit independently, without support. However, she has difficulty in standing from squat position. She can ambulate independently with a wide based gait with hands on flexion position, but is not able to run, jump, or pedal tricycle. She can climb stairs, but with support. She demonstrated a pincer grasp. She can do purposeful movements; as in the ability to reach, hold and transfer objects, and she can bring food to mouth. She can also dress herself with help, but does not zip or button. She does not have any meaningful speech, but babbles socially."

      CaseNotHPOs HP:0002540, HP:0002019, HP:0011968, HP:0002014

      NotHPOcont: Inability to walk, Constipation, Feeding difficulties, Diarrhea

      CasePreviousTesting Brain MRI, thyroid function tests, metabolic screening, and eye examination were normal; as were the following genetic investigations: chromosomal microarray, karyotyping, FISH for 15q11–13 deletion, subtelomeric FISH, methylation analysis for Angelmann, and molecular analysis for UBE3A gene. "A 186 such variants were looked at individually in order to uncover any connections with the patient’s phenotype in the context of various modes of inheritance in the analyzed trio. For example, heterozygous mutations in NDRG4, RELN, TYRP1, REEP6, FABP2 and others were found and given low priority when looked at in the light of the patient’s phenotype. None of the other variants from that list appeared to have enough functional links to the patient’s condition to merit discussing it along with the UNC80 variant."

      CaseMethod1 WES

      CaseMethod2 Sanger

      CaseGenotypingMethod WES results confirmed with Sanger sequencing in trio

      Variant NM_032504.1:c.8525G>A (p.Arg2842Gln)

      CAID CA350413877

      gnomAD 0.00006667(European (Non-Finnish), 0.00003230(Overall)

      CaseAddInfo parental consanguinity, confirmed in trans

    1. the effect of the mutations was a small decrease (5%) in the maximum sliding speed in the presence of saturating calcium (Table)

      ExperimentName: Karibe 2001 In vitro motility

      NonPatientCell: mechanical actin-myosin functional assay

      GeneFunction: GO:0030049 (muscle filament sliding)

      GeneAlteration: PCR-based mutagenesis of Ala to Ser was used at nucleotide position 340 (GenBank M19713) to produce cDNA encoding the V95A variant. This coding sequence was inserted into the pET3d expression vector and the wild-type or mutant tropomoysin protein was expressed in DE3 cells before being purified to homogeneity for use in the in vitro assays.

      FunctionalEvidence: Mutant tropomyosin-containing actin-troponin-tropomyosin filaments combined with rhodamine-phalloidin had slightly decreased (5%) sliding speed on a heavy meromyosin-coated surface compared to wild-type tropomyosin-containing filaments under saturating calcium conditions (Table 1).

      FAVariants: NM_001018005.2(TPM1):c.284T>C (p.Val95Ala), CA017934

    1. Blood samples were collected from 28 MPSI H patients treated and followed up at the Royal Manchester Children’s Hospital over a 4-year period. The samples were collected with informed consent and under permission REC 08H101063 of the hospital’s ethical commission. The patients’ blood samples were processed within 6 h and the serum was separated and stored at −80°C. One group of patients was followed longitudinally and comprised patients who received ERT prior to HSCT (n=8). The second was a cross-sectional group of patients (n=20) studied at least 1 year after HSCT. One patient (patient 5) rejected the donor cells following HSCT and had autologous cells returned to restore hematologic function. This patient subsequently received a second allogeneic HSCT which was successful. Longitudinal data for this patient during both transplants are included in the results. The demographics, enzyme levels, details of HSCT, immune reconstitution, and immunosuppression for all patients in the longitudinal series are presented in Table 1. The transplant details and information on immunosuppression for all patients in the cross-sectional series are shown in Table 2.

      This seems like it could be the same proband as from the Kuwait family in PMID:22718273 since both were said to be cases at Royal Manchester Hospital

    1. The results indicated that large structural changes had occurred in the core region in the severe MPS I group and small ones on the molecular surface in the attenuated MPS I group.

      Article is a PDF, so annotating here. This paper created structural models to predict the phenotype. This variant is predicted to cause a severe phenotype, but this model is not used for PS3 or any other codes.

    1. Proband VII:7.—The index patient presented at theage of 3 years with rubbery swellings in her eyelids.These were excised and histological analysis of these

      Case: Family 1 Moynihan Proband, male, Pakistani

      CasePresentingHPOs: HP:0000407, HP:0004322, HP:0000135, HP:0100540, HP:0012385, HP:0002716, HP:0034920, HP:0034677, HP:0034391, HP:0030075, HP:0002862

      CasePresentingHPOsFreeText: Eyelid swellings due to histiocytic deposits, diverse cytoplasmic inclusions in phagocytes and reticulum cells of bone marrow, Lymph node and eyelid show reactive features with small reactive lymphoid follicles and histiocytes within dilated sinuses resembling RDD. invasive ductal carcinoma grade 3 ER negative breast aged 43 years and carcinoma bladder (grade 3 papillary TCC) age 46 years

      CaseNOTHPOs:

      CaseNOTHPOSFreeText:

      CasePreviousTesting: direct sequencing of PRF1 and UNC5B

      CaseGenotypingMethod: autozygosity mapping, genotyping (genome-wide linkage scan was performed using Affymetrix 250k SNP arrays), direct sequencing, PCR

      Variant: c.300+1G>A homozygous

      ClinVarID: or CAID: 130339/CA155238

      gnomAD: This splice site variant in intron 2 is present in gnomAD v4.0.0 at a MAF=0.0002197 (20/91048 alleles) in the South Asian population with 0 homozygotes.

      AddCaseInfo: brother is affected as well

      PreviouslyPublished: PMID: 9545394

      VariantEvidence: n/a

    1. From supplemental tables S2 and S3 (authors used hg19 alignment).

      MONDO: MONDO:0005145 for SALS

      Case#1: Smith 2014 SALS, G43V, M, 52 y.o. onset, Italy

      CasePresentingHPOs: HP:0002145, HP:0007354

      CaseHPOFreeText: spinal-onset ALS with upper and lower motor neuron signs

      CasePreviousTesting: Only the FALS cases were pre-screened for other mutations

      CaseMethod1: This case identified through case-control study

      CaseGenotypingMethod: Exome sequencing, confirmed with Sanger sequencing.

      Variant: NM_006000.3(TUBA4A):c.128G>T p.Gly43Val

      CAID: CA2122536

      gnomAD: 2-220116828-C-A, Total overall AF (non-neuro) = 0.00002402; TUBA4A_p.G43V_gnomAD

      CaseAddInfo: This is the sole SALS case in this report of TUBA4A variants, while the others are FALS. This is also the only N-terminal variant, while the rest are C-terminal variants with more supporting functional evidence. This variant found in 1/13023 control samples.

    1. Mapping and identification of the Jeff mutation

      ExperimentName: Jeff mouse has FBXO11 Q491L mutation

      NonHumanModel: mouse (mus musculus)

      GeneAlteration: ENU (ethylnitrosourea) was used to induce random mutatgeneiss in the mouse (PMID: 10932191). Animals were screened based on the development of otitis media. Sequencing of the mouse genome FBXO11 gene, c. 1472A>T (. Q491L) that is located after the First CASH domain. The Gln at amino acid position 491 is conserved across several species.

      HumanPhenotype: HP:0000175

      ModelEvidence: HP:0000175

      ModelPhenotype: The Jeff/ FBXO11 Q491L mice heterozygotes were originally shown to have increased susceptibility to developing otitis media (ear infections) (PMID: 10932191). Homozygote Jeff mouse mutants were shown to demonstrate perinatal lethality (death just after birth). this premature death was suspected to be due to respiratory problems as air was found in the stomach. Furthermore, the mice were shown to have eye abnormalities (upper eyelid open at birth) and cleft palate (hard or soft) and facial clefting (Fig. 2B). Of note, only the homozygotes Jeff mice showed the cleft palate, heterozygote Jeff mice were shown to have normal palates at 5, 13, 28, 56, and 120 days old.

      ModelVariant: NM_001190274.1:c.1724A>T (p. Gln575Leu) consistent with ENST00000402508.5:c.1472A>T(p.Gln491Leu)

      CA ID: CA346764369

    1. Pedigree of family 1

      Family#PresentingHPOs HP:0002721, HP:0001905

      FamilyNotHPOs HP:0002721, HP:0002141, HP:0002863

      CountryOrigin Sweden

      Family#PreviousTesting Absolute lymphocyte counts and assays of cytotoxic lymphocyte phenotype and function

      Family#Method1 WES

      Family#Method2 Sanger

      Family#GenotypingMethod WES then variant confirmed with Sanger in I-3, III-1, III-2, II-4, and I-4

      Affected 7

      Unaffected 3

      Segregations 5

      eLOD 1.5

      ProbandLabel F1:III-1, M, 4yo diagnosis

      CasePresentingHPOs HP:0002503, HP:0000639, HP:0002317, HP:0008969, HP:0007340 (in addition to family not presenting)

      HPO Free Text: congenital cytomegalovirus infection, trilineage cytopenia and MDS −7 diagnosis at the age of 4 years. Concurrent cellular immunodeficiency with decreased peripheral blood B and NK cell numbers and borderline monocyte numbers. Immunoglobulin (Ig) levels were also low (IgG, 3.36 g/L; IgA, 0.37 g/L; IgM, 0.49 g/L). MDS with −7 and −22 at 4 y of age; severely hypoplastic bone marrow diagnosed as pediatric refractory cytopenia. Hb[102-139(0/9) vs 117-153], MCV[89-95(6/6) vs 75-87], Platelets[87-128(8/9) vs 125-140], WBC[2.4-4.5(9/9) vs 5-15]

      Variant NM_152703.4(SAMD9L):c.698C>A (p.Thr233Asn)

      CAID CA4343828

      VariantEvidence (Figure 5) 293FT cells transfected with p.Arg986Cys showed more limited cell proliferation than WT SAMD9L

      FamilyAddInfo Aunt(II-1)/Mother(II-2) have NM_152703.3:c.689A>C(p.Asn230Thr), CA368201553 in cis with index's variant and have milder symptoms. Another aunt(II-4) has a NM_152703.3:c.2957G>T(p.Arg986Leu) and NM_152703.3:c.1204_1208del(p.Leu402ArgfsTer8) with cytopenias.

      FamilyPMIDs 28852709

    1. Case#: Cluruk_1993_IN-16, male, 13 y.o., Indian ancestry reported (Mandla and Jabalpur districts of Madhya Pradesh)

      CasePresentingHPOs: decreased RBCs (3.34), decreased Hb (9.2), elevated HbS (68.2), elevated HbF (21.9), MCH 27.5%, HB A2 4.5%, HB A 5.4%

      CaseHPOFreeText: S - B+ - thal (aax/aax) x = variant

      CaseNotHPOs:

      CaseNotHPOFreeText:

      CasePreviousTesting:

      CaseMethod1: Sanger

      CaseMethod2: hybridization probing

      CaseGenotypingMethod: Sanger + probing

      Variant: NM_000558.5(HBA1):c.96-1G>A

      ClinVarID: 801169

      CAID: CA7770244

      gnomAD: allele frequency of 0.0009851 (21/21318 alleles) in the South Asian population (PopMax 0.0006591)

      VariantEvidence: Also seen in compound het with 4 patients with a4.2 deletion and 7 patients with 3.7 deletion in this paper. Heterozygotes (aa/aax) had similar levels of Hb S

      CaseAddInfo:

      CasePMIDs:

    1. results showed VPSl3B gene mutation: c.5086 C > T, inherited from his father; c.6940 + 1 G > T, inherited from his mother, both were heterozygous mutations

      Case#: Yang_Proband 1

      Demographics: 2 yr old Male at diagnosis, Chinese

      CasePresentingHPOs: HP:0001263, HP:0100840, HP:0000750, HP:0001290, HP:0001347, HP:0002205, HP:0001875

      Height: 76 cm, Weight: 11 Kg, OFC: 43 cm, mild oblique palpebral fissure, low tendon hyperreflexia, intermittent neutropenia

      CaseNotHPOs:

      CasePreviousTesting: None

      CaseMethod1: NGS

      CaseMethod2: Sanger sequencing

      CaseGenotypingMethod: Single-read sequencing of whole genome of patient and his parents, subsequently validated by Sanger sequencing

      Variant1: NM_017890.4:c.5086C>T

      ClinVar1: 56803

      gnomAD: 0.00005805 (East Asian)

      Variant2: NM_017890.4:c.6940+1G>T

      CAID2: CA183029776

      gnomAD: 0.00005821 (East Asian)

      VariantEvidence: The individual is a compound heterozygote with the variant, c.5086C>T, inherited from the father and the variant, c.6940+1G>T, inherited from the mother. Both variants are found at a frequency of 0.000058 in East Asians in gnomAD. The c.5086C>T change is a nonsense mutation resulting in premature termination of protein product, while the c.6940+1G>T is a splice donor alteration. The proband is scored default points.

      CaseAddInfo:

      CasePMIDs:

    1. Patient 1 is a 13-year-old male, originating from a non-consanguineous Spanish family ( Fig. 1 D ). He first presented at the age of 4-year-old with an enlarging cutaneous mass over his left thigh with sclerodermoid induration and slight hyperpigmentation and hypertrichosis. Over the years the cutaneous changes gradually spread to involve the left shin, left lower abdomen and right thigh ( Fig. 1 A). Progressive bilateral sensorineural hearing loss presented when the patient was eight. At age 10 he developed diffuse alopecia of the scalp and halo nevi on the trunk. Additional significant findings on physical examination included gynecomastia ( Fig. 1 A), splenomegaly, scrotal masses, varicose veins and fixed flexion contractures of the proximal interphalangeal joint of his left fifth finger ( Fig. 1 A). Several weeks of prednisone treatment induced partial improvement of the thickened and indurated thigh masses and abdominal plaques.

      Case: Mohlo-Pessach Patient 1, male, 13yo at report, 4yo at onset, Spanish

      CasePresentingHPOs: HP:0000953, HP:0000998, HP:0000407, HP:0001596, HP:0003764, HP:0000771, HP:0001744, HP:0002619, HP:0100490, HP:0001935, HP:0003565, HP:0011227, HP:0002716, HP:0100727

      CasePresentingHPOsFreeText: Enlarging cutaneous mass over the left thigh with sclerodermoid induration. Hyperpigmentation onset at 4yo; located on thighs, left shin, and left lower abdomen. Alopecia of the scalp. Halo nevi on the trunk. Scrotal masses. Fixed flexion contractures of the proximal interphalangeal joint of his left fifth finger. Skin biopsy included dermal infiltrate consisting of lymphocytes, plasma cells and CD68+ histiocytes, and dermal and subcutaneous fibrosis

      CaseNOTHPOs:

      CaseNOTHPOSFreeText:

      CasePreviousTesting:

      CaseGenotypingMethod: SLC29A3 exons and splice junctions were PCR-amplified using intronic primers. PCR products were purified and sequenced on ABI 3700 capillary sequencer.

      Variant: c.1087C>T (p.Arg363Trp) homozygous

      ClinVarID: or CAID: CA129561

      gnomAD: This missense variant, Arg363Trp, is present in gnomAD v4.0.0 with a MAF=0.0001734 (1/5768 alleles) in the Middle Eastern population and 0 homozygotes.

      AddCaseInfo: non-consanguineous family

      PreviouslyPublished: n/a

      VariantEvidence: n/a

    2. Patient 2 is a 20-year-old male, originating from a consanguineous Arab family ( Fig. 1 D). He presented with hearing loss since age 4 and cutaneous induration and hyperpigmentation of the thighs which first appeared when he was 8-year-old and gradually extended to the genitals, back and lower limbs with overlying hypertrichosis. On physical examination, short stature (128 cm) and dysmorphic facies with downslanting palpebral fissures, short nose, anteverted nares and retrognathism were seen. Additional findings included arcus senilis, scrotal masses, hepatosplenomegaly and fixed flexion contractures of the proximal interphalangeal joints of the right fourth and fifth fingers and the left fifth finger.

      Case: Mohlo-Pessach Patient 2, male, 20yo at report, Arab

      CasePresentingHPOs: HP:0000365, HP:0000953, HP:0000998, HP:0004322, HP:0001999, HP:0000494, HP:0003196, HP:0000463, HP:0001084, HP:0001433, HP:0100490, HP:0001935, HP:0003565, HP:0011227, HP:0002716, HP:0100727

      CasePresentingHPOsFreeText: Cutaneous induration and hyperpigmentation of the thighs appeared at 8yo, spread to genitals, back, and lower limbs. Retrognathism. Scrotal masses. Fixed flexion contractures of the proximal interphalangeal joints of the right fourth and fifth fingers and the left fifth finger. Skin biopsy included dermal infiltrate consisting of lymphocytes, plasma cells and CD68+ histiocytes, and dermal and subcutaneous fibrosis.

      CaseNOTHPOs:

      CaseNOTHPOSFreeText:

      CasePreviousTesting:

      CaseGenotypingMethod: SLC29A3 exons and splice junctions were PCR-amplified using intronic primers. PCR products were purified and sequenced on ABI 3700 capillary sequencer.

      Variant: c.1088G>A (p.Arg363Gln)

      ClinVarID: or CAID: CA129562

      gnomAD: This missense variant, Arg363Gln, is present in gnomAD v4.0.0 with a MAF=0.0002666 (16/60010 alleles) in the Admixed American population and 0 homozygotes.

      AddCaseInfo: consanguineous parents

      PreviouslyPublished: n/a

      VariantEvidence: n/a

    1. plified from DNA derived from affected individuals offamily MI. In addition to the guanine residue at nucleotideposition

      Case#: Family MI, Northern European

      CasePresentingHPOs: HP:0001639

      CaseHPOFreeText:

      CaseNotHPOs:

      CaseNotHPOFreeText:

      CasePreviousTesting:

      CaseMethod1:

      CaseMethod2:

      CaseGenotypingMethod: PCR amplification followed by Cycle Sequencing

      Variant: The nucleotide variant positions here refer to those described in the initial cloning of the gene in 1988 (PMID: 3336363), but nucleotide G579A here aligns to NM_001018005.2(TPM1):c.523G>A (p.Asp175Asn).

      ClinVar: 12456

      CAID: CA018106

      gnomAD: Grpmax FAF = 7.900e-7, SNV: 15-63060899-G-A, gnomADv4_D175N

      VariantEvidence:

      CaseAddInfo:

      CasePMIDs: PMID:8327508

    1. V

      Case#: Family V, Patient 9, female, 1yo at diagnosis, 5yo at death, Tunisia (Mahdia), black

      DiseaseAssertion: MPS1, Hurler

      FamilyInfo: Parental consanguinity (first cousins). Age of parents at proband's birth: 50 years (M) 62 years (F). 6 unaffected siblings

      CasePresentingHPOs: HP:0010864, HP:0004322, HP:0001537, HP:0000692, HP:0006482, HP:0030812, HP:0001999, HP:0007957, HP:0000943

      CaseHPOFreeText: Height=102cm (-3DS). Weight=18kg (-1 DS). IDUA activity in leukocytes=0,020 μKat/kg (Normal values 1.7-3.5 μKat/kg of protein).

      CaseNotHPOs:

      CaseNotHPOFreeText:

      CasePreviousTesting: n/a

      GenotypingMethod: Direct sequencing of PCR products from each of 14 exons and flanking intron-exon junctions

      PreviouslyPublished: n/a

      Variant: p.R628X homozygous. Proband also had the following polymorphisms: A8A, A20A, H33Q, R105Q, A314A, N181N, T410T, V554I, IVS6+21c>a, IVS7+79c>t, IVS7-45g>c, IVS9+36t>c, IVS10+140c>a, IVS11+33c>t, IVS12+13c>t, IVS12-31c>g

      ClinVar: 550421

      CAID: CA2802462

      gnomAD: The highest population minor allele frequency in gnomAD v4.1.0. is 0.00005038 (2/39700 alleles) in the East Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting).

      SupplementalData: n/a

    1. Molecular screening of 980 cases of suspected hereditary optic neuropathy with a report on 77 novel OPA1 mutations

      PMID:

      Gene: OPA1

      Disease: hereditary optic neuropathy

      980 patients in this study with suspected hereditary optic neuropathies were evaluated by searching for the ten primary LHON-causing mtDNA mutations and examining the entire coding sequences of the OPA1 and OPA3 genes. 295 had variants in OPA1; however the exact count for this variant was not provided and neither was any additional phenotypic information.

    1. Patient`s sister was a 41-year-old woman (Patient 2) with a long history of speech impairment that started during adolescence and was not associated to any other neurological symptoms. Physical examination revealed normal muscle strength, without muscle atrophy or fasciculations. Deep tendon reflexes were normal and there were no signs of sensory or cerebellar disfunction. Speech was also described as spastic and dystonic leading to stuttering.

      Case: Alonso-Perez_Patient 2, Female, 41yo, Spanish

      DiseaseAssertion: Sandhoff Disease

      CasePresentingHPOs: HP:0000007, HP:0001260

      CaseHPOFreeText:

      CaseNOTHPOs: HP:0002380, HP:0001324, HP:0003202

      CaseNOTHPOFreeText: No signs of cerebellar or sensory dysfunction, deep tendon reflexes were normal

      CasePreviousTesting: Nerve conduction studies and EMG were performed with normal results. Serum CK levels were tested and found to be elevated with the rest of the biochemical analysis normal. MRI was normal with no involvement of the brain. Serum β-hexosaminidase-enzyme activity assay showed low levels.

      GenotypingMethod: Sanger sequencing of SMN1, DYNC1H1 and BICD2 genes showed no pathogenic variants. WES revealed HEXB mutations.

      PreviouslyPublished: n/a

      SupplementalData: n/a

      Variant: NM_000521.4, c.171delG (p.Trp57Cysfs7)

      CAID: CA3305751

      gnomAD: MAF: unavailable in gnomAD, gnomAD variant ID: 5-73981254-TG-T

      VariantEvidence: This variant is known to be pathogenic and was previously published only in infantile cases of SD, PMID: 22789865. Total hexosaminidase activity in fibroblasts from the patients with this variant in that paper range from 2.3-9.5% of the normal control levels.

      MultipleGeneVariants AR, allele on second allele

      Variant: c.1510C>T (p.Pro504Ser)

      CAID: CA116493

      gnomAD: MAF: 0.0002259, Latino/admixed American, gnomad variant ID: 5-74016469-C-T

      VariantEvidence: This variant is known to be pathogenic and was previously published in adult cases of SD, PMID: 9694901. This study concluded the effect of the mutation on ganglioside hydrolysis, combined with its effect on intracellular transport, produces chronic Sandhoff disease.

    1. 10-year-old male

      Case# Postma 3:1, male, 10yo, white

      CasePresentingHPOs HP:0004758, HP:0000980, HP:0005184, HP:0000961, HP:0002789

      CasePreviousTesting no

      CaseMethod1 PCR

      CaseGenotypingMethod amplified/screen of CASQ2, SCN5A, HRC, PLN, RYR2, KCNQ1, KCNH2, and KCNK1 genes

      Variant NM_001232.3:c.532+1G>A

      CAID CA341763774 link

      VariantEvidence not in this article

    1. AU-135F++++++c.1635C>Gp.S545RDynamin

      Case#: Family AU-1, 35yo, female, Austrian

      DiseaseAssertion: DOA+

      FamilyInfo: positive family history, 2 relatives in table 1

      CasePresentingHPOs: HP:0000648, HP:0000365, HP:0001251, HP:0000590, HP:0001138

      CaseHPOFreeText:

      CaseNotHPOs: HP:0003198

      CaseNotHPOFreeText:

      PreviouslyPublished: n/a

      GenotypingMethod: The entire OPA1-coding region and flanking exon–intron boundaries were amplified by the polymerase chain reaction (PCR) and sequenced with BigDye terminator cycle chemistries on an appropriate genetic analyser. All genetic variants were confirmed by reverse sequencing

      Variant: c.1635C>G (p.S545R) aka c.1800C>G (p.S600R)

      ClinVar: 30461

      CAID: CA10575554

      SupplementalData:

    1. Table 2.

      Case#: He_12

      CasePresentingHPOs: skeletal deformities: HP:0000924, HP:0012069, reduced GALNS activity in leukocytes (0.8 pmol/g protein/17hr)

      CaseGenotypingMethod: Sanger of GALNS exons

      Variant: p.R386C & p.W403_T404delinsCS

      ClinVar: 700 & 1048331

      CAID: CA221040 & CA916079760

      gnomAD: 16-88891261-G-A & n/a

      Case#: He_21

      CasePresentingHPOs: HP:0000924, HP:0012069, GALNS activity in leukocytes 0 pmol/g protein/17hr

      CaseGenotypingMethod: Sanger of PCR amplified GALNS exons 1-14

      Variant: p.W520X & p.G290R

      ClinVar: 1048427 & 93171

      CAID: CA397076034 & CA221049

      gnomAD: n/a & 16-88880857-C-T

    1. family

      Family#: Family M

      PresentingHPOs: HP:0003563 (decreased LDL cholesterol concentration)

      PresentingHPOsFreeText: <5th percentile for LDL cholesterol

      CountryOrigin: United States

      Ethnicity: Caucasian

      Race:

      Family#PreviousTesting: No other genetic testing performed.

      Family#Method1: PCR

      Family#Method2: Sanger sequencing

      Family#GenotypingMethod: PCR amplification of the entire APOB coding region, exon/intron junctions, 5' upstream, 5' and 3' untranslated regions, followed by cloning and sequencing in proband. Slot blot analysis of genomic DNA from family members.

      AddSegregationInfo: Father (43 yo) and two sibs of the proband are heterozygous for an APOB variant and have <5th percentile LDL-cholesterol (47 mg/dl, 29 md/dl, and 16 mg/dl respectively)) based on https://www.ncbi.nlm.nih.gov/books/NBK351/ (Table 31.9); LDL-cholesterol level was no available for the mother but she is heterozygous for an APOB variant; two affected sibs have 0 LDL-cholesterol and are compound heterozygous.

      ProbandLabel: CM (II:3)

      Variant: Compound heterozygous: Variant 1: NM_000384.2:c.537+1G>T (paternal) Variant 2: NM_000384.2:c.1315C>T (p.Arg439Ter) (maternal)

      ClinVar: N/A

      CAID: Variant 1: CA345962364 ; Variant 2: CA052017

      gnomAD: Variant 1: Not in gnomAD; Variant 2: 0.00002640 (Euro non-Finnish)

      FamilyAddInfo: Inheritance pattern is consistent with semi-dominant, in that father and both heterozygous sibs have low levels of LDL-cholesterol (levels not available for mother), which rules out abetalipoproteinemia (in which heterozygotes have normal LDL-cholesterol levels).

    1. Case 7

      Case#: 7, female, 2 y 5 m (current), Chinese

      CasePresentingHPOs: HP: 0008344, HP: 0012751, HP: 0012696 (elevated A keto acids in urine, abnormal signals in cerbral ganglia, abnormal thalamic MRI signal intensity)

      HPOsFreeText: leucin: 621.72 uM, valine: 594.15 uM, isoleucine: 225.21 uM, Alloisoleucine: 76.62 uM

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: detected by newborn screening, unsure cis or trans

      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group

      Variant: NM_183050.3:c.482T>G (p.Val161Gly), NM_183050.3:c.508C>T (p.Arg170Cys)

      ClinVar: not found, 96590

      CAID: CA364657700, CA224301

      gnomAD: not found, 0.00001759 (European, non-Finnish)

    1. II-3 Daughter

      CaseII-3: Female, 2 years, Turkey

      CasePresentingHPOs: HP:0004912, HP:0004322, HP:0002970 (Hypophosphatemic rickets, Short stature, Genu varum)

      HPOsFreeText: -2.09 standard deviation score

      CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)

      NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2

      CaseAddInfo: Variant is asserted novel, Daughter of II:II-2

      CasePreviousTesting: Calcium levels (10.2 mg/dL), Decreased serum phosphate levels (2.1 mg/dL; reference 3.8-6.5), Elevated serum ALP (531 IU/L; reference 90-325), 25OHD3 levels (31.1 ng/ml), PTH levels (52.5 ng/L), TPR levels (62.3), Decreased TmP/GFR levels (1.31; reference 2.9-6.1)

      CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.

      Variant: NM_000444.5:c.979_983dup (p.His329Thrfs*4)

      CAID: CA913187410 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913187410

      gnomAD: Not in gnomAD

    1. Among the 1,348 patients with PD, we identified a single man of French origin with parkinsonism who harbored a novel nonsense mutation (c.557G>A in exon 2 [p.Trp186stop] of RAB39B) that was not found in 530 unrelated control individuals of European origin

      Case#: Lesage_Proband

      Demographics: Male, 39y at report, France

      CasePresentingHPOs: HP:0001300, HP:0002322, HP:0001256, HP:0100660, HP:0002451, HP:0100710,

      Proband was diagnosed with early-onset Parkinsonism. Proband had asymmetric rest tremor, akineto-rigid syndrome, and showed good response to Levodopa and normal brain MRI. He required sheltered employment due to intellectual disability. 8y after disease onset, patient developed treatment-related complications including motor fluctuations. Proband showed good global cognitive performance but difficulty concentrating and subcortico-frontal signs. Psychiatric interview revealed dysthymic disorder. Proband died at 55y, after apomorphine treatment was initiated.

      CaseNotHPOs: No pyramidal, cerebellar, or ocular disorders

      CasePreviousTesting: Exome analysis in the patient excluded variants in all other known PD genes.

      CaseMethod1: WES

      CaseMethod2:

      CaseGenotypingMethod: The variant was identified by data mining exomes for coding and splice site variants in RAB39B.

      Variant: NM_171998.4:c.557G>A (p.Trp186Ter)

      ClinVar:

      CAID: CA414923761

      gnomAD:

      VariantEvidence: The proband was hemizygous for the null variant, Trp186Ter in exon 2/2. NMD is not predicted. The evidence is scored reduced points. (0.5)

      CaseAddInfo: No family history of PD is reported.

      CasePMIDs:

    1. One is a novel 5-bp insertion between the thymidine at nt 704 and a cytosine at nt 705 (704ins5), which is seen only in the Japanese population.

      annotating here since this is a PDF

      Case#: Yamagishi Case 5, female, 1y at clinical dx, 20y at enzymatic dx, 31y at death

      DiseaseAssertion: Hurler/Scheie

      FamilyInfo: n/a

      CasePresentingHPOs: HP:0002240

      CaseHPOFreeText: height=117cm at 21yo. cardiac involvement. CHF caused death

      CaseNotHPOs:

      CaseNotHPOFreeText: mental delay

      PreviouslyPublished: n/a

      Variant: 704ins5; R89Q

      ClinVar: 11921; 11922

      CAID: CA256123; CA256124

      SupplementalData: n/a

    1. SAL-399-073

      Case# SAL-399-073, Female, 46yo, French, Hispanic

      CasePresentingHPOs HP:0002385, HP:0011448, HP:0001260, HP:0002066, HP:0002015, HP:0002650, HP:0001272

      CaseMethod1 Exome

      CaseMethod2 Sanger

      Variant NM_005186.3:c.463C>T(p.Q155X), NM_005186.3:c.1142C>T(p.R512C)

      CAID CA381242841, CA381248914

      gnomAD 0.00003567

      VariantEvidence nonsense, missense in trans with null variant

      CaseAddInfo in article supplement

    1. Family 1

      Family#PresentingHPOs HP:0000639, HP:0007256, HP:0001251

      FamilyNotHPOs HP:0001260, HP:0000486, HP:0001310

      CountryOrigin Sweden

      Family#Method1 WES

      Family#Method2 Sanger

      Family#GenotypingMethod expanded pedigree confirmed to have SAMD9L variants with Sanger

      Affected 5

      Unaffected 9

      Segregations 3*

      AddSegregationInfo not to score

      ProbandLabel Fam1:IV-3, Female, 38yo reported

      Variant NM_152703.4(SAMD9L):c.2956C>T (p.Arg986Cys), NM_152703.3:c.689A>C(p.Asn230Thr)

      ClinVar 446530(c.2956), CA368201553(c.689)

      FamilyAddInfo at least one member with the variant who is unaffected, but likely due to age (4yo)

      FamilyPMIDs 28202457

    1. 1

      Case1: Female, Italy, Birth onset

      CasePresentingHPOs: HP:0003798, HP:0002033, HP:0100703, HP:0000218, HP:0000689, HP:0000297, HP:0003325 (Nemaline bodies, Poor suck, Tongue thrusting, High-arched palate, Dental malocclusion, Facial hypotonia, Limb-girdle muscle weakness)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0003560, HP:0003715, HP:0001557, HP:0001270, HP:0002093, HP:0001627, HP:0000602, HP:0001283, HP:0002650, HP:0003306 (Muscular dystrophy, Myofibrillar myopathy, Prenatal movement abnormality, Motor delay, Respiratory impairment, Cardiac abnormality, Ophthalmoplegia, Bulbar palsy, Scoliosis, Spinal rigidity)

      NotHPOsFreeText: Congenital myasthenic syndromes

      CaseAddInfo: Typical NM presentation, Parental segregation was confirmed

      CasePreviousTesting: ACTA1, TPM2 and TPM3 mutations were ruled out via amplification and direct sequencing

      CaseGenotypingMethod: Genomic DNA was extracted from peripheral blood leukocytes or fibroblasts. 183 exons of NEB, the relative introns, and the full promoter region was captured via litigation-mediated PCR and high-throughput sequencing of resulting fragments. These were then aligned and filtered for inheritance and pathogenicity. Variants were evaluated for amino acid conservation and confirmed by Sanger sequencing.

      Variant1: NM_001164507.1:c.8899A>C (p.Thr2967Pro)

      CAID: CA348807784 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_001271208.2%3Ac.8899A%3EC

      gnomAD: Not in gnomAD

      Variant2: NM_001164507.1:c.23803_23806del (p.Arg7935Serfs*48)

      CAID: CA758865527 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_001271208.2%3Ac.23908_23911del

      gnomAD: Not in gnomAD

    1. Myasthenia gravis, T2DM, HepC, PVC, PACs, PSVT, SND59MYOZ2: c.488T>C p.(Leu163Ser)#905 (M)30NAYesYes/noH-txNAMYH7: c.2302G>C p.(Gly768Arg) MYOM1: c.1655G>A p.(Gly552Asp)#906 (F)5815NoNo/noNoneNAMYBPC3: c.3617G>A p.(Gly1206Asp)#907 (M)37<15aNoNo/noECG abnormalities60MYOM1: c.432-1G>T#908 (M)20<15bNoYes/noH-tx, T2DM50MYH6: c.5111C>T p.(Ala1704Val)#909 (M)31<15aNoYes/noNone75MYBPC3: c.1409G>A p.(Arg470Gln)#910 (F)1723NoNo/noNone76MYBPC3: c.639C>A p.(Tyr213*)#913 (M)1219NoNo/noAngiokeratomas right ear hearing loss Visual impairment hypothyroidism, AF, NSVT60MYBPC3: c.649A>G p.(Ser217Gly) GLA: c.718_719delAA p.(Lys240Glufs*9) MYH6: c.3883G>C p.(Glu1295Gln)914 (M)2234YesNo/noHOCM, LGE at CMR imaging, NSVT65MYBPC3: c.506-2A>C { label (or @symbol) needed for fn[@id='tfn12-ijmm-38-04-1111'] } Bold font indicates mutations in MYH6 and in genes encoding non-TTm proteins that would not been identified without NGS analysis. a Diagnosis of borderline HCM; b original diagnosis of borderline HCM has been modified in dilated cardiomyopathy. PAC, premature atrial contractions; H-tx, heart transplantation; T2DM, type 2 diabetes mellitus; LVWT, left ventricular wall thickness; SND, sinus node dysfunction; AF, atrial fibrillation; hep C, hepatitis C; LBBB, left bundle branch block; AICD, automatic implantable cardioverter defibrillator; LVEF, left ventricular ejection fraction; SCD, sudden cardiac death; LGE, late gadolinium enhancement; CMR, cardiac magnetic risonance; NSVT, non-sustained ventricular tachycardia; PVC, premature ventricular contractions; HOCM, hypertrophic obstructive cardiomyopathy; PSVT, paroxysmal supraventricular tachycardia; NA, not available; NGS, next generation sequencing; HCM, hypertrophic cardiomyopathy.

      Case: Cecconi_Patient#903, female, 52 yrs old at onset of HCM

      CasePresentingHPOs:

      CasePresentingHPOsFreeText: In adults, a maximal LV wall thickness (LVWT) ≥15 mm; the maximal LVWT between 10 and 14 mm, in conjunction with other features (i.e., family history, electrocardiogram abnormalities) prompted the diagnosis of borderline HCM.

      CaseNOTHPOs:

      CaseNOTHPOSFreeText:

      CasePreviousTesting: The clinical diagnosis of primary HCM was based on medical history, a physical examination and on the echocardiographic demonstration of a hypertrophied left ventricle (LV) that could not be explained by another cardiac or systemic disease.

      CaseGenotypingMethod: NGS, Sanger Targeted NGS panel to simultaneously analyze a total of 19 genes encoding not only TTm proteins, but also other sarcomeric proteins and some non-sarcomeric proteins that cause HCM phenocopies. Sanger sequencing to ensure a depth of coverage >20X for each target nucleotide.

      Variant: c.488T>C p.(Leu163Ser)

      ClinVarID: or CAID: 45784, CA282614

      gnomAD: MAF=0.001724 in African/African Americans (43/24948 alleles), total allele frequency=0.0001521. No homozygotes. v2.1.1

      AddCaseInfo: Pt has LVWT of 18, LVEF of 59%, and other medical issues (myasthenia gravis, T2DM, HepC, PVC, PACs, PSVT, and SND

      PreviouslyPublished: no

      VariantEvidence: none

    1. SD1 M I 185.5 60.5 c.534delAGTT (p.L178fs27X) c.534delAGTT (p.L178fs27X)

      Case: Zampieri SD1, Male

      DiseaseAssertion: Sandhoff Disease

      FamilyInfo: patient's genotype was confirmed in parents

      CasePresentingHPOs: HP:0000007, HP:0033978

      CaseHPOFreeText: neurological symptoms (unspecified)

      CaseNOTHPOs:

      CaseNOTHPOFreeText:

      CasePreviousTesting: Patients presented with neurological symptoms and diagnosis was confirmed by the demonstration of reduced Hex A and Hex B activity in peripheral white blood cells or cultured fibroblasts.

      GenotypingMethod: PCR

      PreviouslyPublished: n/a

      SupplementalData: n/a

      Variant: c.534delAGTT (p.L178fs27X) in both alleles

      CAID: CA560766108

      gnomAD: MAF 0.000008937, European (non-Finnish), gnomAD variant ID: 5-73992535-CAGTT-C

      VariantEvidence: PMID:11292324 previously reported this variant to be associated with the infantile form of SD. Genomic DNA amplification, heteroduplex analysis, cloning and sequencing revealed a 4-bp deletion in exon 4 at position 178. The result is a frameshift mutation that leads to a stop codon in exon 5. This mutation is associated with a dramatic decrease of HEXB mRNA levels.

    1. There is little information about MPS I-related complications during laronidase therapy. We describe the first autopsy report of a young male MPS I patient who died of infection-induced cardiopulmonary failure following 2 years of weekly treatment with laronidase.

      Annotating here since the article is a PDF.

      Case#: Lin ERT Proband, 3yo at dx, male, Taiwan

      DiseaseAssertion: MPS1 H/S

      FamilyInfo:

      CasePresentingHPOs: HP:0002094, HP:0030828, HP:0002870, HP:0001640, HP:0001712, HP:0005133, HP:0001654, HP:0005145, HP:0008155, HP:0002653, HP:0002829, HP:0001376, HP:0002751, HP:0004348, HP:0007957, HP:0007663, HP:0002167, HP:0032341, HP:0410042

      CaseHPOFreeText: Positive urine MPS screening test, blood IDUA activity=0.4 umol/h per mg protein (normal range 10-35). ERT improved cardiopulmonary status, joint range of motion, mobility, bone and joint pain, kyphoscoliosis, bone mineral density, sleep quality, corneal clouding and visual acuity, speech fluency, forced vital capacity and liver size, and resulted in 80.2% reduction in urinary GAG excretion. Cardiopulmonary failure

      CaseNotHPOs:

      CaseNotHPOFreeText:

      PreviouslyPublished: n/a

      Variant: T364M homozygous

      ClinVar: 11925

      CAID: CA256126

      SupplementalData: n/a

    1. On gene analysis thereafter, two missense mutations were verified in exons 3 and 11 of transmembrane protein 43 (TMEM43) in this patient and her mother (Fig. 3). The mutations were c. 265 g > a, p.V89M and c.896 g > c, p.R299T.

      Case# HondaF, female, newborn

      CasePresentingHPOs HP:0001640, HP:0006682, HP:0011713, HP:0100572

      CaseGenotypingMethod "gene analysis"

      Variant NC_000003.10:g.14147425G>A

      CAID CA052413

      gnomAD 0.001044 link

      CaseAddInfo 2 mutations in cis from mom, phenotypes described at birth (usually adult onset)

    1. RESULTS Gene and mutation identification Analysis of the single nucleotide polymorphism (SNP) microarray genotypes from six patients with PHID identified a single common 1.4 Mb region of shared homozygosity within cytogenetic band 10q22.1, between SNPs rs10509321 and rs1900515 (Fig. 1A). Inspection of the Ensembl and UCSC Genome Browsers demonstrated that the region included 14 known and predicted genes: ADAMTS14, C10orf27, CDH23, EIF4EBP2, LRRC2, KIAA1274, NODAL, NPFFR1, PCBD1, PPA1, PRF1, SLC29A3, SGPL1, UNC5B. Positional candidate genes were selected for sequencing in order to identify pathogenic mutations (Fig. 1B). Five different homozygous mutations were identified in the SLC29A3 gene encoding the equilibrative nucleoside transporter 3 (Fig. 1C, Table 1). Human ENT3 has been shown recently to be the cause of H syndrome, an autosomal recessive disorder with overlapping skin features to PHID (6), indicating that these are allelic disorders. hENT3 belongs to a structurally unique protein family of nucleoside and/or nucleobase transporters (13,14). The five homozygous mutations identified segregated with the disease within each family and were not present in over 100 Lebanese and Pakistani control chromosomes. Figure 1.Open in new tabDownload slideHomozygosity mapping and mutation results in five PHID families. (A) Homozygosity mapping of chromosome 10. Red bars indicate heterozygous single nucleotide polymorphisms (SNPs); blue bars, an extended run of homozygous SNPs greater than would be predicted by chance; green bars, a run of homozygous SNPs but insufficient to meet criteria for significance. (B) Genes within the 1.4 Mb interval bounded by heterozygous SNPs rs10509321 (CII.3) and rs1900515 (DII.1). (C) SLC29A3 sequence electrophoretograms demonstrating homozygous mutations in five PHID families. (D) Protein structure prediction of hENT3 by SVMTM software. (E) Multispecies alignment of the second transmembrane and the C-terminal cytoplasmic domains of ENT3 protein (accession numbers: Homo sapiens, NP_060814.4; Canis lupus, XP_546152.2; Bos taurus, XP_580640.3; Mus musculus, NP_076085.1; monodelphus domesticus, XP_001344438.1; Gallus gallus, XP_421594.2; Gasterosteus aculeatus, ENSGACP00000006741; Takifugu rubipens, ENSTRUP00000028258; Drosophila melangaster, FBpp0077753; Caenorhabditis elegans, NP_501807.3). Table 1.Mutation summary Mutation NM_018344.4 . Protein CCDS7310.1 . Protein domain . Predicted . Mutation predictions . Grantham . SIFT . c.347T>Gp.Met116ArgTransmembrane Domain 2Missense Hydrophobic to large basic910.03c.940delTp.Tyr314ThrfsX91Transmembrane Domain 7Frameshift––c.1309G>Ap.Gly437ArgIntra-cytoplasmic DomainMissense Small hydrophobic to large basic12512.0c.1330G>Tp.Glu444XIntra-cytoplasmic DomainNonsense––c.1346C>Gp.Thr449ArgIntra-cytoplasmic DomainMissense Small polar to large basic710.03Mutation NM_018344.4 . Protein CCDS7310.1 . Protein domain . Predicted . Mutation predictions . Grantham . SIFT . c.347T>Gp.Met116ArgTransmembrane Domain 2Missense Hydrophobic to large basic910.03c.940delTp.Tyr314ThrfsX91Transmembrane Domain 7Frameshift––c.1309G>Ap.Gly437ArgIntra-cytoplasmic DomainMissense Small hydrophobic to large basic12512.0c.1330G>Tp.Glu444XIntra-cytoplasmic DomainNonsense––c.1346C>Gp.Thr449ArgIntra-cytoplasmic DomainMissense Small polar to large basic710.03 Open in new tab Table 1.Mutation summary Mutation NM_018344.4 . Protein CCDS7310.1 . Protein domain . Predicted . Mutation predictions . Grantham . SIFT . c.347T>Gp.Met116ArgTransmembrane Domain 2Missense Hydrophobic to large basic910.03c.940delTp.Tyr314ThrfsX91Transmembrane Domain 7Frameshift––c.1309G>Ap.Gly437ArgIntra-cytoplasmic DomainMissense Small hydrophobic to large basic12512.0c.1330G>Tp.Glu444XIntra-cytoplasmic DomainNonsense––c.1346C>Gp.Thr449ArgIntra-cytoplasmic DomainMissense Small polar to large basic710.03Mutation NM_018344.4 . Protein CCDS7310.1 . Protein domain . Predicted . Mutation predictions . Grantham . SIFT . c.347T>Gp.Met116ArgTransmembrane Domain 2Missense Hydrophobic to large basic910.03c.940delTp.Tyr314ThrfsX91Transmembrane Domain 7Frameshift––c.1309G>Ap.Gly437ArgIntra-cytoplasmic DomainMissense Small hydrophobic to large basic12512.0c.1330G>Tp.Glu444XIntra-cytoplasmic DomainNonsense––c.1346C>Gp.Thr449ArgIntra-cytoplasmic DomainMissense Small polar to large basic710.03 Open in new tab Two novel homozygous mutations predicted to cause premature protein truncation were identified, a 1 bp deletion c.940delT and a nonsense mutation c.1330G>T. The deletion causes a frame shift mutation p.Y314Tfs in transmembrane domain 7 and is predicted to result in the substitution of transmembrane domains 8–11 with an irrelevant protein sequence of 91 amino acids derived from an alternate reading frame. The nonsense mutation p.E444X is predicted to lead to premature protein truncation with loss of part of the final cytoplasmic domain and transmembrane domain 11 of hENT3. It would appear unlikely that the either residual protein would be capable of nucleoside transport function.Three homozygous missense mutations of SLC29A3 were identified to involve conserved amino acids (Table 1). The first missense mutation involves Methionine116 in transmembrane domain 2, which is a hydrophobic amino acid in species as distantly related as humans and nematodes, with a large basic amino acid, Arginine (p.M116R; Fig. 1C and E). The Grantham score for this substitution is 91, which is classified as a moderate change (15). Analysis using the SIFT prediction software also classifies this as a likely deleterious change (16). The introduction of a large basic amino acid into a transmembrane domain would likely result in significant disruption of the hydrophobic nature of the domain and result in retention of the transporter protein within the endoplasmic reticulum, as has been demonstrated for other membrane proteins (17).The second missense change is a recently reported Glycine to Arginine substitution at hENT3 amino acid 437 (p.G437R Fig. 1C), which is located in the putative cytoplasmic domain between transmembrane domains 10 and 11. This is the only mutation in the PHID cohort that is shared with the known mutations in H syndrome. Of particular interest is the observation that this is the sole individual in the PHID cohort who has not developed insulin-dependent DM. The p.G437R change involves the substitution of a large basic amino acid at a position where 41 members of the ENT family as distantly related as humans and Arabidopsis thaliana encode a small hydrophobic amino acid (Fig. 1E) (18). The Grantham difference for this change is 125 and is classified as a moderately radical change.The third missense change occurs at hENT3 amino acid residue 449, which is also located in the final putative intracellular domain between transmembrane domains 10 and 11, and involves the substitution of a Threonine by an Arginine (p.T449R). The amino acids encoded at this position in hENT3 orthologs are small polar/uncharged or small hydrophobic residues (Fig. 1E). Substitution by arginine is associated with a Grantham score of 71 and is predicted by SIFT as not to be tolerated.

      Case: Family C/Prendiville Patient 2, Lebanese-Australian, 11yo at report

      Not scoring this proband since this variant has been reported many times already and parents are consanguineous, from Lebanon which is near many of the other cases

    1. The proband had first presented aged 14 years

      Case# II-4, Female, 14, Ireland

      CasePresentingHPOs HP:0002506, HP:0002497, HP:0002061, HP:0011448, HP:0001347

      CasePreviousTesting Initial genetic testing (with patient consent) included a screening panel for HSP, as well as SCA 1, 2, 3 and 6, all of which were negative.

      CaseMethod1 WES

      Variant NM_005186.3:c.1534C>T(p.Arg512Cys)

      CAID CA6093457

      gnomAD 0.000008977

    1. patient with congenital-onset pure spastic paraplegia caused by novel pathogenic variants in CAPN1

      Case# Travaglini 1, Male, 16 report, Italian

      CasePresentingHPOs HP:0006895, HP:0040083, HP:0001347, HP:0003487

      CasePreviousTesting Sanger of SPG4 and 89 other known/candid genes by Nextera Custom Enrichment panel

      CaseMethod1 Sanger Sequencing

      CaseGenotypingMethod CAPN1 variants found in same panel screen

      Variant NM_005186.3:c.221G>A (p.G74D), NM_005186.3:c.911C>T(p.T304M), NM_005186.3:c.1418G>T (p.R473L)

      CAID CA6092976, CA6093221, CA6093432

      gnomAD 0.0006904 , 0.0003415, 0.00003952

      CaseAddInfo nonconsanguineous family

    1. Indeed, in contrast to fibroblasts bearing the I382M mutation, which displayed mild mitochondrial network fragmentation, fibroblasts with the p.R445H and p.S545R mutations were marked by the disappearance of filamentous mitochondria in favour of fragmented and punctuated mitochondria (patients 1–3) (Fig. ​(Fig.2B2B and Fig. S1). Quantification of the ratio of mitochondrial to cellular volume showed a 20% decrease of mitochondrial content in fibroblasts with the dominant‐negative p.R445H and p.S545R mutations (patients 1–3), compared to control fibroblasts, whereas no significant loss of mitochondrial volume was observed in the haploinsufficient OPA1 mutated fibroblasts (patients 4–7) (Fig. ​(Fig.2C).2C).

      Cultured patient fibroblasts showed disappearance of filamentous mitochondria in favor of fragmented and punctuated mitochondria and a 20% decrease of mitochondrial content in fibroblasts.

    1. 4

      Case4: Male, Spain, Post-birth onset

      CasePresentingHPOs: HP:0003798, HP:0001324, HP:0000297, HP:0003701, HP:0001252, HP:0001284, HP:0002307, HP:0000218, HP:0001382 (Nemaline bodies, Muscle weakness, Facial hypotonia, Proximal muscle weakness, Muscular hypotonia, Areflexia, Drooling, High palate, Joint hypermobility)

      HPOsFreeText: Cephalic support, Sedestation

      CaseNotHPOs: HP:0000602, HP:0001249, HP:0001627, HP:0002093, HP:0002307, HP:0003722, HP:0002460, HP:0001283, HP:0002650, HP:0002540, HP:0006466, HP:0011471 (Ophthalmoplegia, Intellectual disability, cardiac abnormality, Ankle contracture, Drooling, Neck flexor weakness, Distal muscle weakness, Bulbar palsy, Respiratory insufficiency, Inability to walk, Scoliosis, PEG-fed in infancy)

      NotHPOsFreeText: Bimodal communication, Wheelchair dependence, Mechanic ventilation

      CaseAddInfo: Typical variant, Paternity/maternity was confirmed, cDNA analysis confirmed that Variant 1 results in a splice-site donor mutation which skips exon 24 which was confirmed by Sanger sequencing and leads to this deletion: p.His738_Asp770del (c.2212_2310del)

      CasePreviousTesting: N/A

      CaseGenotypingMethod: A research panel with 751 genes relating to neurological disorders, including the coding and intronic flanking regions of ACTA1, CFL2, KBTBD13, NEB, TNNT1, TNNT3, TPM2 and TPM3, was used to locate any variants in the proband. These variants were then prioritized and confirmed by Sanger sequencing in the probands and their relatives.

      Variant1: NM_001164507.1:c.2310+5G>A (p.=)

      CAID: CA913203562 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913203562

      gnomAD: Not in gnomAD

      Variant2: NM_001164507.1:c.17779_17780del (p.Tyr5927Hisfs*17)

      CAID: CA913203561 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913203561

      gnomAD: Not in gnomAD

    1. The effects of a previously identified T364M mutation and R619G mutation on IDUA activity were examined by transfection into COS-7 cells of the IDUA cDNA construct. When compared to that of wild type cDNA, the two point mutations showed only trace amounts of IDUA activity (1.2 and 1.5% respectively, Table 2). Table 2. Expression of α- l-iduronidase in transfected COS-7 cells Transfected vector α- l-Iduronidase activity (nmol mg−1 protein−1 h−1) Total (% of wild type) pcDNA3 20.9 0.0 pcDNA3-IDUA 90.2 100.0 pcDNA3-IDUA/T364M 21.7 1.2 pcDNA3-IDUA/R619G 21.9 1.5 The activity of endogenous α- l-iduronidase in COS-7 cells was subtracted before the percentage of wild type was calculated. Efficiency of transfection was similar in all dishes by 3′ IDUA cDNA PCR amplification of transfected genomic DNA (data not shown).

      Transfection into COS-7 cells showed that this variant has 1.2% IDUA activity compared to WT

    1. marked exon 2 skipping in these assays, but also yielded a large fraction of normal transcripts.

      Cell transfection assays showed marked exon 2 skipping in these assays, but also yielded a large fraction of normal transcripts.

      c.51+3A>G mutation cosegregates with low C1 inhibitor protein levels in one family. alternative splicing of exon 3, found in peripheral blood cell mRNA but not in the liver or in hepatoma cell lines and we show that, in cultured monocytes of a patient carrying the c.51+3A>G mutation, this alternative splicing is shifted from exon 3 exclusion to skipping of both exons 2 and 3

      Variants: c.51+3A>G; c.51+5G>A

      CAIDs: CA2579981804; error in CAR-unable to register

    1. Family-11COQ5c.933delCp.(Tyr311*)0.00001760Disease causingP (PVS1, PM2, PP3)–This study(GC21390)c.682-7 T > Gp.(Gln230*); p.(Leu193Phefs*27)0.001434See suppl. Table 1VUS (PM2, PM3, BP4)–This study

      Case: Family 11 GC21390 Proband II:1, 49yo at onset (incidental finding), 56yo at report

      CasePresentingHPOs:

      CasePresentingHPOsFreeText: Prolonged dark adaptation, peripheral visual field loss, BCVA= 6/9, 6/5, retinitis pigmentosa, hypertension, plasma coQ10 level=582.28nmol/L (Reference range: 227- 1432 nmol/L)

      CaseNOTHPOs:

      CaseNOTHPOSFreeText:

      CasePreviousTesting: negative IRD gene panel analysis

      CaseGenotypingMethod: genome sequencing, direct Sanger

      Variant: c.933delC p.(Tyr311); c.682-7 T > G p.(Gln230); p.(Leu193Phefs*27)

      ClinVarID: or CAID: CA6828694; CA6828747

      gnomAD: This nonsense variant, Tyr311Ter in exon 7/7, is present in gnomAD v4.1.0 with a MAF=0.00002627 (31/1179996 alleles) in the European NF population with 0 homozygotes. The score has been reduced since NMD is not expected to occur.

      This non-canonical splice site variant, c.682-7T>G, is present in gnomAD v4.1.0 with a MAF=0.001031 (66/64040 alleles) in the European Finnish population with 0 homozygotes.

      AddCaseInfo: only family member noted to be affected, mother was unaffected and heterozygous for tyr311ter but father is deceased and not genotyped

      PreviouslyPublished: n/a

      VariantEvidence: RT-PCR of patient blood derived mRNA using oligonucleotide primers targeting COQ5 (Supplementary Table 6) followed by agarose gel electrophoresis showed definite altered transcript length and mis-splicing for the COQ5 c.682-7 T > G variant. ONT sequencing of the full COQ5 transcript from whole blood of individual family 11, II:1 showed skipping of exon 5 to be the predominant effect of the c.682-7 T > G variant leading to early termination and probable nonsense-mediated decay (p.(Gln230)) (Fig. ​(Fig.4).4). In addition, exon 4–5 skipping was identified in a low proportion of reads (3%) leading to a reading-frame shift and early termination (p.(Leu193Phefs27)).

    1. Patient 1

      Case: Patient 1, female, AOR 2 years, Turkish

      CasePresentingHPOs: HP:0001561, HP:0003265, HP:0001270, HP:0000924, HP:0000253, HP:0002007, HP:0000520, HP:0005280, HP:0003196, HP:0000463, HP:0005306, HP:0000212, HP:0000347, HP:0005619, HP:0002938, HP:0000960, HP:0009826, HP:0001156, HP:0004060, HP:0100543, HP:0008936, HP:0007340, HP:0001265, HP:0005193, HP:0002063, HP:0002240, HP:0001407, HP:0100625, HP:0004565, HP:0005619, HP:0002867, HP:0100865, HP:0003016, HP:0003416, HP:0002176, HP:0006532, HP:0000670, HP:0004315, HP:0002850,

      CaseNOTHPOs: HP:0000365, HP:0000504

      CasePreviousTesting: Lab examines including urine organic acid analysis (urine glycosaminoglycan/ GAG and lysosomal enzymes), tandem mass screening, chromosome analysis, electroencephalogram were unremarkable. Negative for mutations in SLC35D1 (Schneckenbecken dysplasia MIM 269250), and INPPL1 (opsismodysplasia; MIM 258480) .

      CaseGenotypingMethod: WES

      Variant: NM_001440.3: c.953C>T(p.P318L)

      CA ID: CA370858101

      Homozygous

      gnomAD: no homozygotes, only 2 hets in Euro-ND populatin CA370858101

      AddCaseInfo: Parents were also tested by WES and were both found to be carriers of the mutation.

      VariantEvidence: WEstern blot analysis of EXTL3 from patinet 1 cells shows expression of hte P318L variant (Figure 1B), indicating the protein is still produced. However, a glycosyltransferase assay using the wildtype EXTL3 and th eP318L variant showed reduced enzyme activity in the P318L variant compared to wildtype, and simiar levels of activity as untransfected/ mock controls. This indicates the P318L mutation acts as a loss of protein function of the enzyme activity.

    1. 184I.OL.0,01 leukocytes {"type":"entrez-nucleotide","attrs":{"text":"NM_000203.5","term_id":"1450641494","term_text":"NM_000203.5"}}NM_000203.5:c.[1882C>T];[1882C>T] SevereUzbek/Uzbekistan

      This variant was found in homozygosity in patient #184 from Uzbekistan. The maximum point total for homozygosity has already been reached for this variant.

    1. c.463+

      PatientID: VHL 11

      KindredID: VHL 11

      Case: Sex, Age, Ethnicity unknown

      DiseaseAssertion: hemangioblastoma

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0010797 (hemangioblastoma)

      CaseHPOFreeText: Three samples of VHL hemangioblastomas were represented here (.1, .2, .3). They are recorded as both germline and somatic, involving the VHL- and C3ORF10-gene.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A - This sample was likely duplicated in 24132471

      SupplementalData: Yes - See Supplementary Table 1

      Variant: c.463+3A>C

      LegacyVariant: N/A

      CaseProblemVariantFreeText: Supplemental data records this as a c.463+3A>C (p.(?)) mutation. The only time the text mentions a splice site mutation however is at: c.463+2T>C p.(?). Will go by supplemental data but be cautious of this discrepancy.

      ClinVarID: N/A

      CAID: CA645525016 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.463%2B3A%3EC

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: splice_site_variant

      CivicName: Splice Region (c.463+3A>C) 

      MultipleGeneVariants: N/A

    2. c.462A>C p.Pro154Pro

      All patients that were operated on between 1995 and 2010 in the University Medical Center Groningen from who frozen hemangioblastoma tissue was available in the tissue bank of the Department of Pathology were eligible. Through PCR (MSP) and MLPA, one patient sample was confirmed with a germline mutation (c.462A>C) in the VHL gene. The patients' manifestations was thus only stated as hemangioblastoma; No other phenotypic or demographic information was available. Note: This sample was likely duplicated in 24132471

    3. c.259_260-insA p.Val87Aspfs*45

      All patients that were operated on between 1995 and 2010 in the University Medical Center Groningen from who frozen hemangioblastoma tissue was available in the tissue bank of the Department of Pathology were eligible. Through PCR (MSP) and MLPA, one patient sample was confirmed with a germline mutation (c.259_260insA) in the VHL gene. The patients' manifestations was thus only stated as hemangioblastoma; No other phenotypic or demographic information was available. Note: This sample was likely duplicated in 24132471

    1. deletion of exon 1

      A 39 year old man was confirmed to have a germline exon 1 deletion of the VHL gene at age 26. Details regarding genotyping methods are not specified. He presented with epistaxis at age 34 and CT scans showed an ethmoid mass later identified as a primary microcystic adenoma. He underwent endoscopic transsphenoidal resection of the legion and he was negative for metastatic disease. Analysis of tumour DNA showed it to be heterozygous for an intron 1 polymorphism (c.341-50G>A). He had a history of cerebellar haemangioblastoma and ccRCC.

    1. Ninety-eight individuals were tested for VHL mutations--23 symptomatic and 75 asymptomatic individuals belonging to 16 families. Seven of the families had definite clinical criteria of VHL disease, five had sporadic hemangioblastoma, and four had CNS hemangioblastoma combined with minor visceral signs. Molecular genetic testing identified five germline mutations in six of the definite VHL families (sensitivity 85%), but none in the possible VHL and sporadic hemangioblastoma cases; four of these mutations had been previously described and one is a novel mutation present in two unrelated families. After patients carrying the mutation were identified, they underwent clinical screening and asymptomatic VHL-related lesions were identified in 43%.

      PatientID: 22

      KindredID: C

      Case: Sex unknown, 30Y0M, Mexican (Latino/Admixed American)

      DiseaseAssertion: assumed VHL

      FamilyInfo: At least 13 members in this family presented with the mutation. 5 were asymptomatic (ages 9, 12, 13, 17, and 29Y). Other family manifestations include: cerebellar, spinal, retinal HBs, pancreatic, hepatic, suprarenal and kidney cysts, epididymal cystadenoma, and RCC. Fig 1 displays family pedigree.

      CasePresentingHPOs: HP:0006880; HP:0001737; HP:0000107 (cerebellar hemangioblastoma, pancreatic cysts, renal cyst)

      CaseHPOFreeText: Patient had 1 cerebellar HB, pancreatic and kidney cysts.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: 20064270 (Here, the family cohort is given with a reportedly different variant of: p.G34Rfs*98 (c.99_100insA). Unclear of why this is or which most correctly corresponds to the family).

      SupplementalData: N/A

      Variant: p.T100Nfs*32 (c.298dupA)

      LegacyVariant: c.1012_1013insA

      CaseProblemVariantFreeText: The ‘1012_1013insA’ mutation is out-of-frame, leading to a modification of 31 amino acids downstream and a premature stop codon at nucleotides 5441-5443 (amino acid residue 131).

      ClinVarID: N/A

      CAID: CA2573129737 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.298dupA

      gnomAD: N/A

      VariantEvidence: The modified amino acids are located in a domain common to all pVHL isoforms, the highly conserved cctbinding domain of the protein, involved in the formation of the pVHL elongin complex that is crucial for tumor suppression. Furthermore, the mutant protein is prematurely truncated and lacks the C-terminal half of exon 2 and exon 3 completely, which includes the nuclear export signal and the elongin C binding site of pVHL. Thus, this truncated protein would affect the two functional isoforms of pVHL: the major isoform pVHL30 and pVHL19, but not isoform 2, which lacks exon 2 but is not functional

      MutationType: plus_1_frameshift_variant; duplication

      CivicName: T100Nfs*32 (c.298dupA)

      MultipleGeneVariants: N/A

    1. c.309_322del14a

      Of 31 Brazilian patients, one was found to harbour the c.309_322del14(p.G104Hfs*23) mutation of the VHL gene. Genomic DNA was extracted and all VHL coding regions were analyzed by Sanger sequencing. MLPA was performed to investigate large deletions using SALSA® MLPA® P016 VHL probe mix. Data analysis was performed with Genescan 3.7. This patient, age 15, presented with renal and pancreatic cysts, CNS and retinal hemangioblastoma. It is not clear if this mutation is familial.

    1. 3'

      Complete molecular analysis of the VHL gene on genomic DNA was conducted on 4 patients and some of their relatives. Peripheral blood lymphocytes were collected and the VHL gene dosage was evaluated by quantitative Southern blot or real-time quantitative PCR analysis. The coding region was studied via direct sequencing. One patient (4), a 16 year old female, was found to harbour a polymorphic variant on the 3' UTR of the VHL gene (c.*1149 A>G). This patient also harboured the promoter region mutation c.–65_–55dup11 of the VHL gene. She presented with an isolated retinal angioma and an unremarkable family history although the dup11 variant was inherited from an nonsymptomatic parent. ACMG evidence codes: 'PP4' since the patient presents phenotypes highly specific for a disease with a single genetic etiology.

    1. IV/16 (16)-----Ser80Ile

      PatientID: IV-16

      KindredID: 1

      Case: M, 16Y0M, Hungarian

      DiseaseAssertion: Asymptomatic

      FamilyInfo: The patient had two unaffected siblings who did not carry the mutation. The patient's father (III-8) carried the mutation and had brain hemangioblastoma, pheochromocytoma, and retina hemangioblastoma. His paternal aunt (III-7) harboured the same mutation and had a brain hemangioblastoma and retina hemangioblastoma. Her children, this patient's cousins, also harboured the mutation and had clinical presentations of VHL. His other paternal aunt (III-6) carried a different VHL mutation, Pro25Leu, but was asymptomatic. The patient's paternal grandmother (II-5) also harboured the same mutation and presented with renal cell carcinoma. This patient's great aunt (II-1) carried two different VHL mutations; the Ser80Asn and Pro25Leu but herself was asymptomatic. She passed the Ser80Asn mutation to her daughter, the proband (III-1), who had renal cell carcinoma, brain hemangioblastoma, and pheochromocytoma. Refer to figure 1 for pedigree.

      CasePresentingHPOs: N/A

      CaseHPOFreeText: N/A

      CaseNotHPOs: HP:0005584, HP:0002666, HP:0010797, HP:0009711 (renal cell carcinoma, pheochromocytoma, hemangioblastoma, retinal capillary hemangioma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.S80N (c.239G>A)

      LegacyVariant: p.S80I (c.239G>A) *author mistake

      CaseProblemVariantFreeText: N/A

      ClinVarID:N/A

      CAID: CA70046108 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.239G%3EA

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: S80N (c.239G>A)

      MultipleGeneVariants: N/A

    2. IV/13 (27)-+ (22)-+ (23)renal cysts (20)Ser80Ile

      PatientID: IV-13

      KindredID: 1

      Case: F, 27Y0M, Hungarian

      DiseaseAssertion: VHL

      FamilyInfo: The patient had an affected brother (IV-14) who carried the Ser80Asn mutation and presented with pheochromocytoma and retina hemangioblastoma. The patient's mother (III-7) carried the same mutation and had a brain hemangioblastoma and retina hemangioblastoma. The uncle (III-8) harboured the same mutation and had brain hemangioblastoma, pheochromocytoma, and retina hemangioblastoma. He had three kids, out of which only one carried the mutation but was asymptomatic (IV-16). The patient's grandmother (II-5) also harboured the same mutation and presented with renal cell carcinoma. This patient's great aunt (II-1) carried two different VHL mutations; the Ser80Asn and Pro25Leu but herself was asymptomatic. She passed the Ser80Asn mutation to her daughter, the proband (III-1), who had renal cell carcinoma, brain hemangioblastoma, and pheochromocytoma. Refer to figure 1 for pedigree.

      CasePresentingHPOs: HP:0010797, HP:0009711, HP:0000107 (hemangioblastoma, retinal capillary hemangioma, renal cyst)

      CaseHPOFreeText: The patient presented with brain hemangioblastoma at age 22, retina hemangioblastoma at age 23, and renal cysts at age 20.

      CaseNotHPOs: HP:0005584, HP:0002666 (renal cell carcinoma, pheochromocytoma )

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.S80N (c.239G>A)

      LegacyVariant: p.S80I (c.239G>A) *author mistake

      CaseProblemVariantFreeText: N/A

      ClinVarID:N/A

      CAID: CA70046108 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.239G%3EA

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: S80N (c.239G>A)

      MultipleGeneVariants: N/A

    1. PatientID: N/A

      KindredID: 21

      Case: Sex, Age, Ethnicity Unknown

      DiseaseAssertion: pheochromocytoma

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0002666 (pheochromocytoma)

      CaseHPOFreeText: Nonsyndromic pheochromocytoma.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: RET, SDHB, SDHD

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.Q195* (c.583C>T)

      CaseProblemVariantFreeText: N/A

      LegacyVariant: p.Q195* (c.796C>T)

      ClinVarID: 428794 https://www.ncbi.nlm.nih.gov/clinvar/variation/428794/

      CAID: CA70052558 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.583C%3ET

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: stop_gained

      CivicName: Q195* (c.583C>T)

      MultipleGeneVariants: N/A

    1. Patient 1

      PatientID: 1

      KindredID: 1

      Case: M, 51Y0M, Arab

      DiseaseAssertion: VHL

      FamilyInfo: Patient 2 (the patient’s brother) presented with the same mutation and was diagnosed with VHL at age 45. The two brothers had very similar VHL clinical manifestations including cerebellar hemangioblastomas, renal cell carcinoma, and cysts in the pancreas. However, patient 1 had testicular and epididymal cysts, as well as lesions in the spine, which were absent in Patient 2. No other family history was noted. Immediate family members were recommended to genetically test for the relevant variant or monitor for VHL-related symptoms.

      CasePresentingHPOs: HP:0005584; HP:0009713; HP:0006880; HP:0000107; HP:0001737; HP:0030424; HP:0033608; HP:0000541; HP:0012215 (renal cell carcinoma; spinal hemangioblastoma; cerebellar hemangioblastoma; renal cyst; pancreatic cysts; epididymal cyst; pulmonary nodule; retinal detachment; testicular microlithiasis)

      CaseHPOFreeText: At 44Y, Patient 1 exhibited cerebellar and spinal hemangioblastomas, as well as retinal detachment. He also had renal cell carcinoma in both kidneys and multiple cysts in one kidney, testis, and pancreas. He also reported a history of headaches and vertigo, leading to a diagnosis of VHL disease type 1. At 49Y, multiple nodules were found in his lungs and a year later, a nodule in the testis and scrotal lithiasis were detected. At 51Y, renal cell carcinoma was identified in the left kidney and his left epididymis was enlarged. Patient continued to present with left testicular and scrotal lithiasis, right retinal detachment, and multiple nodules in both lungs. However, tMutation:Germlinehe lung phenotype was asymptomatic (see table 1).

      CaseNotHPOs: HP:0001392; HP:0005264; HP:0001743 (abnormality of the liver; abnormality of the gallbladder; abnormality of the spleen)

      CaseNotHPOFreeText: No lesions were observed in the liver, gallbladder, and spleen.

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData:  N/A

      Variant: p.F76del (c.227_229del)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA357012, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.227_229delTCT

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: inframe_deletion

      CivicName: F76del (c.227_229del)

      MultipleGeneVariants: N/Av

    1. c.340+563C>T

      Recently, Lenglet et al., 2018 identified a new VHL cryptic exon termed E1' deep in intron 1 that is naturally expressed in many tissues, and found E1' mutations in eight families with either erythrocytosis or VHL disease. The goal of this study was to determine the prevalence of E1' germline mutations from two cohorts, 221 patients with a single or multiple tumours, suggestive of VHL disease, and 946 patients with a Pheochromocytoma/paraganglioma (PPGL) but without an identified mutation in the three VHL exons or in the main PPGL susceptibility genes. They identified a rare germline genetic variant (maf <1%) in the E1’ VHL cryptic exon in 1% of patients (12/1167). Patient 1 was diagnosed at the age of 47 with follow up of a 5 year duration due to a Carotid body paraganglioma (PGL) and was found to have a germline c.340+563C>T E1' variant. Tumor analysis was performed for patient 1 since there was a paraffin embedded sample. Patient 1 did not have loss of heterozygosity, but the mutated allele was lost in the tumor. Immunostaining was negative for detection of CA9 expression. CA9 is a protein reported to influence regulation cell proliferation and tumor progression and is known to be expressed at the membrane of tumour cells in the case of VHL inactivation.

    1. 136G→T Ts Exon 1 46 GAG E E46X

      GroupID: 1

      Case: Age unknown, Sex unknown, French

      DiseaseAssertion: VHL

      FamilyInfo: None - one member documented here

      CasePresentingHPOs: HP:0009711 (retinal capillary hemangioma)

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: Possibly published in PMID:15300849

      SupplementalData: N/A

      Variant: p.E46* (c.136G>T)

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVarID: N/A

      CAID: CA351748085 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.136G%3ET

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: stop_gained

      CivicName: E46* (c.136G>T)

      MultipleGeneVariants: N/A

    2. 462A→C Tv Exon 2 154 CCA P P154P

      A study of 103 patients with VHL retinal manifestations and 108 patients without VHL retinal manifestations extracted from the French VHL database revealed that the number of hemangioblastomas appeared higher in patients who had a substitution when compared with patients with a truncated protein. Detected by PCR and SSCP, this synonymous mutation (p.P154= (c.462A>C)) was found in a VHL patient with retinal hemangioblastomas. Other manifestations are not clearly stated. No family information was provided.

    1. 2 small deletions leading to a frameshift

      PatientID: 20

      KindredID: 900

      Case: Sex unknown, Age unknown, French

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0030405 (pancreatic endocrine tumour)

      CaseHPOFreeText: N/A

      CaseNotHPOs: HP:0002666; HP:0005584 (pheochromocytoma, renal cell carcinoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.P95Rfs*64 (c.284delC)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA2497030172 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA2497030172

      gnomAD: N/A

      VariantEvidence:N/A

      MutationType: minus_1_frameshift_variant

      CivicName: P95Rfs*64 (c.284del)

      MultipleGeneVariants: N/A

    1. PatientID: 194

      KindredID: 194

      Case: Sex Unknown, 46Y0M, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0010797; HP:0001732; HP:0002666; HP:0000107 (Hemangioblastoma, Abnormality of the pancreas, Pheochromocytoma, Renal cyst)

      CaseHPOFreeText: CNS hemangioblastoma, pancreatic cyst or tumor, pheochromocytoma and renal cystic lesion.

      CaseNotHPOs: HP:0009711; HP:0006770 (Retinal capillary hemangioma, Clear cell renal cell carcinoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: Table S1, S2 and S3

      Variant: p.P59Rfs*8 (c.176del)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA432536374, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.176del

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: deletion; minus_1_frameshift_variant

      CivicName: P59fs (c.176delC)

      MultipleGeneVariants: N/A

    2. PatientID: 259

      KindredID: 259

      Case: Sex Unknown, 29Y0M, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: None.

      CasePresentingHPOs: HP:0001737, HP:0009711 (pancreatic cysts, retinal capillary hemangioma)

      CaseHPOFreeText: N/A

      CaseNotHPOs:HP:0002666, HP:0006770, HP:0000107, HP:0010797 (pheochromocytoma, clear cell renal cell carcinoma, renal cyst, hemangioblastoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: Table S1, S2, S3.

      Variant: p.R167Q(c.500G>A)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 2216 https://www.ncbi.nlm.nih.gov/clinvar/variation/2216/

      CAID: CA020454 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.500G%3EA

      gnomAD: 0.000003977 https://gnomad.broadinstitute.org/variant/3-10191507-G-A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: R167Q(c.500G>A)

      MultipleGeneVariants: N/A

    3. 80 23 c.422_440del19 p.Asn141IlefsX12 x x De novo Parents -

      PatientID: 80

      KindredID: 80

      Case: Sex Unknown, 23Y0M, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: Parents were negative for the mutation. No phenotype details are noted for these family members.

      CasePresentingHPOs: HP:0010797; HP:0000107 (Hemangioblastoma, Renal cyst)

      CaseHPOFreeText: CNS hemangioblastoma and renal cystic lesion.

      CaseNotHPOs: HP:0002666; HP:0006770; HP:0001732; HP:0009711 (Pheochromocytoma, Clear cell renal cell carcinoma, Abnormality of the pancreas, Retinal capillary hemangioma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: Table S1, S2 and S3

      Variant: p.N141Ifs*12 (c.422_440del)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA16621933, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.422_440del

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: deletion; minus_1_frameshift_variant

      CivicName: N141fs (c.422_440del)

      MultipleGeneVariants: N/A

    1. VHL c.499C>T.

      This paper presented a pheochromocytoma detected by autopsy. The index case was a 26-year-old male who presented to the emergency department complaining of obstipation, severe headache and abdominal pain. The family background of the parents and siblings history is unavailable since the patient was an orphan. An autopsy revealed bilateral pheochromocytoma and acute myocardial infarction. Molecular genetic analyses for germline mutations of the VHL gene were performed after DNA extraction from normal liver tissue using standard methods. A mutation in VHL gene R167W (c.499C>T) was detected.

    1. 645 G insertion

      PatientID: cousin 1

      KindredID: B

      Case: M, 35Y0M, Chinese

      DiseaseAssertion: assumed VHL

      FamilyInfo: Family history is positive. A total of 7 members were genetically tested for this mutation. 5 were asymptomatic and non-VHL (no mutation was found). This patient's cousin also had HB and the mutation was found in them.

      CasePresentingHPOs: HP:0010797 (hemangioblastoma)

      CaseHPOFreeText: Patient had multiple hemangioblastoma of the CNS diagnosed at 35Y

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.Q145Tfs*29(c.431dup)

      LegacyVariant: p.Q145Tfs*29 (c.645insG)

      CaseProblemVariantFreeText: AF010238.1:c.645insG translates to an updates NM_000551.3:c.432_433insG; or c.431dupG

      ClinVarID: N/A

      CAID: CA2573106040 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA2573106040

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: plus_1_frameshift_variant; duplication

      CivicName: Q145fs (c.431dup)

      MultipleGeneVariants: N/A

    1. 41 non-related patients with retinal capillary hemangioma presenting in the Benjamin Franklin University Eye Clinic between 1988 to 1999 Germany were evaluated for the presence of other VHL lesions. VHL disease was diagnosed in 33 patients based on the presence of other severe VHL lesions (spinal hemangioblastoma, cerebellar hemangioblastoma, renal cysts, pancreatic cyst, renal carcinoma, and pheochromocytoma), molecular genetic testing, and/or family history. VHL germline mutations were identified in 27 out of 29 VHL families screened with molecular genetics. Blood samples were genetically tested using PCR-SSCP sequencing. One patient with VHL-related retinal angiomatosis was found to have germline frameshift deletion (c.210delG) mutation in the VHL gene. This variant was reported as c.423delG (AF010238.1) and mapped to p.E70Dfs*89 (c.210del) (NM_000551.3). It's unclear which other VHL-related lesions were identified in this patient.

    2. GroupID: None (9)

      DiseaseAssertion: VHL

      GroupSize: 1

      GroupNumberMales: N/A

      GroupNumberFemales: N/A

      GroupEthnicity: N/A

      GroupAgeRange: N/A

      GroupInfo: This family group of 1 individual has clinically confirmed VHL disease presenting with retinal angiomatosis. This individual was found to harbor a c.210del variant causing a Glu70Asp frameshift mutation (noted in the paper as c.423delG due to Latif reference transcript being used).

      GroupPresentingHPOs: HP:0009711 (Retinal capillary hemangioma)

      GroupHPOFreeText: Patients within this family were found to have a clinical diagnosis of VHL disease. No VHL clinical phenotypes were explicitly stated other than retinal angiomatosis.

      GroupNotHPOs: N/A

      GroupNotHPOFreeText: N/A

      GroupPreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.E70Dfs*89 (c.210del)

      LegacyVariant: c.423del

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA2573320434, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA2573320434

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: minus_1_frameshift_variant; deletion

      CivicName: E70Dfs*89 (c.210del)

      MultipleGeneVariants: N/A

    1. We have described the development and validation of a new gene-expression diagnostic test called Pheo-type for classification of PPGL tumors based on the underlying genetic driver of the disease. Our assay confirms that the predominant gene-expression subtypes of PPGL are closely linked to tumor genotype and for the first time show that classification can be achieved using a relatively small gene set. Pheo-type is similar to other clinical assays developed on the Nanostring platform for subtyping of solid tumors (50–52). As with these other studies, we have shown that robust gene-expression analysis can be achieved from small amounts of FFPE tissue material generating data that are comparable to other gene-expression platforms. The assay is rapid, largely automated, and cost effective, enabling the generation of results in 2 days from RNA extraction to data analysis, facilitating its implementation in a routine diagnostic laboratory.
    1. Genotype-phenotype correlations of 573 VHL patients from 200 kindreds were analyzed and confirmed that higher risk of pheochromocytoma is associated with missense mutations that result in substitution of a surface amino acid or that disrupt the structural integrity of the VHL gene product (pVHL). Age-related risks of retinal hemangoblastomas and renal cell carcinoma were higher in patients with nonsense or frameshift mutations. Southern blot and/or MLPA analysis by whole blood detected this mutation (c.562delC) was found in 2 family members with renal cell carcinomas, one with retinal angiomas (diagnosed at 25Y), and one with cerebellar hemangioblastoma (diagnosed at 24Y).

    2. GroupID: 50

      DiseaseAssertion: assumed VHL

      GroupSize: 5

      GroupNumberMales: N/A

      GroupNumberFemales: N/A

      GroupEthnicity: N/A

      GroupAgeRange: N/A

      GroupInfo: 5 of the 573 patients discussed in this paper were found to have the following mutation belonging to 1 family

      GroupPresentingHPOs: HP:0005584; HP:0006880; HP:0009711 (renal cell carcinoma; cerebellar hemangioblastoma; retinal capillary hemangioma)

      GroupHPOFreeText: 4 patients had retinal angiomas diagnosed at a mean age of 27Y, and 3 had cerebellar hemangioblastomas diagnosed at a mean age of 32Y

      GroupNotHPOs: HP:0002666 (pheochromocytoma)

      GroupNotHPOFreeText: N/A

      GroupPreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: Supplementary Table S1.

      Variant: p.R82_V84del (c.243_251delGCGCGTCGT)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA658820713 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.243_251del

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: inframe_deletion

      CivicName: R82_V84del (c.243_251del)

      MultipleGeneVariants: N/A

    3. Genotype-phenotype correlations of 573 VHL patients from 200 kindreds were analyzed and confirmed that higher risk of pheochromocytoma is associated with missense mutations that result in substitution of a surface amino acid or that disrupt the structural integrity of the VHL gene product (pVHL). Age-related risks of retinal hemangoblastomas and renal cell carcinoma were higher in patients with nonsense or frameshift mutations. Southern blot and/or MLPA analysis by whole blood detected this mutation. c.182_185del was found in a VHL patient with retinal angiomas diagnosed at 31Y, and hemangioblastomas of the cerebellum at 30Y.

    1. Here, we report imaging findings in a VHL patient and in 3 consecutive family members

      Four patients from the same family carrying missense VHL mutation c.509 T>G were screened for VHL related lesions. Patient 1, 30Y F, had undergone treatment for pancreatic endocrine tumors and pheochromocytoma. Patient 2, 30Y M, was affected by retinal angioma, bilateral adrenal pheochromocytoma and sacral, intercarotid paraganglioma. Patient 3 underwent treatment for pheochromocytoma. Investigations revealed additional pancreatic endocrine tumor and a pheochromocytoma. Patient 4 had an endocrine pancreatic tumor and a pheochromocytoma. ACMG: 'PP4' because the patients' phenotypes and family history are highly specific for a disease with single genetic etiology.

    1. PatientID: 1

      KindredID: 1

      Case: Sex Unknown, 40Y0M, Chinese

      DiseaseAssertion: VHL

      FamilyInfo: None.

      CasePresentingHPOs: HP:0006770, HP:0001732, HP:0010797 (clear cell renal cell carcinoma, abnormality of the pancreas, hemangioblastoma)

      CaseHPOFreeText: The patient presented with a hemangioblastoma at age 34, clear cell renal cell carcinoma at age 37, and abnormality of the pancreas at age 37.

      CaseNotHPOs: HP:0009711, HP:0002666, HP:0030424, HP:0030393 (retinal capillary hemangioma, pheochromocytoma, epididymal cyst, endolymphatic sac tumor)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.S65W(c.194C>G)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 43597 https://www.ncbi.nlm.nih.gov/clinvar/variation/43597/

      CAID: CA020099 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.194C%3EG

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transversion

      CivicName:S65W(c.194C>G)

      MultipleGeneVariants: N/A

    2. germline mutations

      Mutational analysis for 16 patients with clinically diagnosed VHL disease, revealed 12 germline mutations. This missense mutation was found in a 43-year-old VHL type 1 patient with renal cell carcinoma, pancreatic cysts, an endolymphatic sac tumor, and an epididymal /ovarian cystadenoma (proband no. 5) and no family history. HPO terms: renal cell carcinoma, multiple pancreatic cysts, epididymal cysts, endolymphatic sac tumors.

    1. Germline mutations were identified in 300/469 (63%) of the families tested; 137 distinct intragenic germline mutations were detected.

      GroupID/ KindredID: 40CA

      DiseaseAssertion: VHL

      GroupSize: N/A

      GroupNumberMales: N/A

      GroupNumberFemales: N/A

      GroupEthnicity: N/A

      GroupAgeRange: N/A

      GroupInfo: This germline familial VHL mutation was taken from the Cambridge, Department of Pathology database, with an unknown number of members belonging to Family ID 40CA. Table 4 lists all ID and mutations associated with individuals with pheochromocytoma.

      GroupPresentingHPOs: HP:0002666 (pheochromocytoma)

      GroupHPOFreeText: Described as a VHL family with pheochromocytoma. Other phenotypes are likely, including renal cell carcinoma, however not detailed here.

      GroupNotHPOs: N/A

      GroupNotHPOFreeText: N/A

      GroupPreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.G114C (c.340G>T)

      LegacyVariant: p.G114C (c.553G>T)

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA351751376 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.340G>T

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant; transversion

      CivicName: G114C (c.340G>T)

      MultipleGeneVariants: N/A

    2. Germline mutations were identified in 300/469 (63%) of the families tested; 137 distinct intragenic germline mutations were detected.

      GroupID/ KindredID: 146CA

      DiseaseAssertion: VHL

      GroupSize: N/A

      GroupNumberMales: N/A

      GroupNumberFemales: N/A

      GroupEthnicity: N/A

      GroupAgeRange: N/A

      GroupInfo: This germline familial VHL mutation was taken from the Cambridge, Department of Pathology database, with an unknown number of members belonging to family ID Family 146CA. Table 5 lists all ID and mutations associated with individuals without detailed clinical information.

      GroupPresentingHPOs: N/A

      GroupHPOFreeText: Described as multiple VHL families without detailed clinical information. Other phenotypes are possible, however not detailed here.

      GroupNotHPOs: N/A

      GroupNotHPOFreeText: N/A

      GroupPreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.A56Sfs*76 (c.165_166insA)

      LegacyVariant: FS (c.378insA)

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA645524648 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.165_166insA

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: plus_1_frameshift_variant

      CivicName: A56fs (c.165_166insA)

      MultipleGeneVariants: N/A

    3. Germline mutations were identified in 300/469 (63%) of the families tested; 137 distinct intragenic germline mutations were detected.

      Germline mutational data on VHL was gathered from various countries to assess variation in germline mutations that produce disease within different populations. Families were grouped according to three possible outcomes of disease: renal cell carcinoma without pheochromocytoma, renal cell carcinoma with pheochromocytoma, or pheochromocytoma alone. SSCP and denaturing gradient gel electrophoresis identified mutations in 300/469 (63%) of families affected with VHL. This germline familial VHL mutation (c.468T>G) was taken from the Neuro Olcologie database in Paris, with an unknown number of members belonging to Family ID 41F. It was reported in the paper as c.681T>G due to a difference in transcript reference. As reported in Table 3, this mutation is found in VHL families without pheochromocytoma, and with renal cell carcinoma.

    4. Germline mutations were identified in 300/469 (63%) of the families tested; 137 distinct intragenic germline mutations were detected.

      Germline mutational data on VHL was gathered from various countries to assess variation in germline mutations that produce disease within different populations. Families were grouped according to three possible outcomes of disease: renal cell carcinoma without pheochromocytoma, renal cell carcinoma with pheochromocytoma, or pheochromocytoma alone. SSCP and denaturing gradient gel electrophoresis identified mutations in 300/469 (63%) of families affected with VHL. This germline familial VHL mutation (L188fs (c.563delT)) was taken from the Cambridge, Department of Pathology database, with an unknown number of members belonging to Family ID 141CA. It was reported in the paper as c.776delT due to a difference in transcript reference. As reported in Table 3, this mutation is found in VHL families without pheochromocytoma, and with renal cell carcinoma.

    1. PatientID: 18

      KindredID: N/A

      Case: Sex Unknown, Age Unknown, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CohortInfo: The authors evaluated 64 VHL patients (32 women and 32 men) with renal involvement of whom 54/64 had undergone renal surgery or a radiofrequency thermal ablation procedure for RCC. In 10/64 VHL patients, at least one or more RCC were diagnosed, however at the time of diagnosis an indication for treatment was not yet present. For all patients several CT/MRI scans existed for retrospective description of tumour growth kinetics.

      CasePresentingHPOs: HP:0005584 (Renal cell carcinoma)

      CaseHPOFreeText: This is a tumor resolution study (VHL patients were investigated based on the presence of renal tumors.) No other phenotypic information is available.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: Supplementary Table S5 describes 8 patients with frameshift or in-frame deletions, including this patient.

      Variant: p.F76del(c.224_226del)

      LegacyVariant: c.437_439delTCT

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA357012, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.224_226del

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: deletion

      CivicName: F76del(c.224_226delTCT)

      MultipleGeneVariants: N/A

    1. GroupID/ KindredID: F41

      Case: Sex unknown, 22Y0M, Spanish

      DiseaseAssertion: assumed VHL

      FamilyInfo: familial antecedents found; unknown of any additional features to index case relatives

      CasePresentingHPOs: HP:0009711; HP:0006770; HP:0006880; HP:0000107; HP:0001737 (retinal capillary hemangioma, clear cell renal cell carcinoma, cerebellar hemangioblastoma, renal cysts, pancreatic cysts)

      CaseHPOFreeText: Multiple lesions were found with the patient’s cerebellar hemangioma. Unilateral ccRCC. Age of onset is 22Y0M.

      CaseNotHPOs: HP:0002666 (pheochromocytoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.L128R (c.383T>G)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA351753891 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.383T%3EG

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant; transversion

      CivicName: L128R (c.383T>G)

      MultipleGeneVariants: N/A

    2. Thirty-five unrelated patients suspected of having von Hippel-Lindau disease were analyzed and 32 VHL gene variants were found in 35 patients using PCR and SSCP by peripheral blood leukocytes. An association of clear cell renal carcinoma development with a relatively high loss of structural stability in VHL protein missense mutations was discovered. This nonsense mutation was found in a patient with retinal hemangioblastoma, cerebellar hemangioblastoma, and pancreatic cysts (patient no. F3). Patient has family history of paragangliomas, epididymial cysts, and clear cell renal carcinoma. Paper gives variant by protein sequence: L135*. NM_000551.3:c.404T>A and NM_000551.3:c.404T>G both could result in this protein change. Unclear which is correct to the given patient.

    1. missense

      A cohort of 314 patients with pheochromocytoma and functional paraganglioma had blood samples collected and all five major pheo-pgl susceptibility genes (RET, VHL, SDHB, SDHD, and SDHC) were screened for mutations. 25 patients had germline VHL mutations, 16 of which had a family history and 9 patients had an apparently sporadic presentation, 11 were male and 14 were female, the median age of diagnosis is 23.9 and range of diagnosis was 4-49. Out of the 25 patients 23 had adrenal tumours, 4 had para-adrenal tumours, and 9 had other VHL lesions (renal tumours and hemangioblastomas). 1 patient with positive family history and/or a syndromic presentation was found with pheochromocytoma or functional paraganglioma and a germline missense VHL mutation (p.L184H (c.551T>A), referred to in the paper by c.608T>A due to a difference in transcript sequence). Other phenotypes unique to the patient are unknown. ACMG: PP4

    1. The remaining two families without RET mutations were subsequently shown to have a mutation within the VHL gene.

      GroupID: None

      DiseaseAssertion: VHL

      GroupSize: 9

      GroupNumberMales: Unknown

      GroupNumberFemales: Unknown

      GroupEthnicity: Unknown

      GroupAgeRange: Unknown

      GroupInfo: Nine individuals from 2 different families initially diagnosed with MEN-IIA were investigated. All were found to have the same (c.562C>G) missense mutation in the VHL gene.

      GroupPresentingHPOs: HP:0002666; HP:0006737; HP:0002865; HP:0011781 (pheochromocytoma, extra adrenal pheochromocytoma, medullary thyroid carcinoma, thyroid C cell hyperplasia)

      GroupHPOFreeText: All 9 patients had pheochromocytoma, 2 of the 9 patients (unspecified) also had thyroid C-cell tumors, 1 (unspecified) had medullary thyroid carcinoma, and 1 (unspecified) had C-cell hyperplasia. 3 of the 9 patients (unspecified) also developed extra-adrenal pheochromocytoma.

      GroupNotHPOs: HP:0000843; HP:0009711; HP:0010797; HP:0000107; HP:0001737 (Hyperparathyroidism, retinal capillary hemangioma, hemangioblastoma, renal cysts, pancreatic cysts.

      GroupNotHPOFreeText: None of the patients had any clinical signs of renal cancer. Two patients (unspecified) were screened for retinal, CNS, and abdominal lesions; neither had occult VHL lesions.

      GroupPreviousTesting: RET

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.L188V (c.562C>G)

      LegacyVariant: c.775C>G

      CaseProblemVariantFreeText: N/A

      ClinVarID: 2225, https://www.ncbi.nlm.nih.gov/clinvar/variation/2225/

      CAID: CA020488

      gnomAD: 0.00002121, https://gnomad.broadinstitute.org/variant/3-10191569-C-G?dataset=gnomad_r2_1

      VariantEvidence: N/A

      MutationType: missense_variant;transversion

      CivicName: L188V (c.562C>G)

      MultipleGeneVariants: N/A

    1. GroupID: III (from Hemangioma VHL Associated Group)

      Case: Sex Unknown, Age Unknown, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CohortInfo: Studied 36 VHL-related pheochromocytoma by comparative genomic hybridization. In addition, we compared their genetic profiles with those of (1) multiple endocrine neoplasia type 2 (MEN 2)-related pheochromocytomas; (2) previously reported sporadic pheochromocytomas; and (3) VHL-related CNS hemangioblastomas.

      CasePresentingHPOs: HP:0010797 (hemangioblastoma)

      CaseHPOFreeText: The patient had VHL associated hemangioblastoma (table 1).

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: MEN1 and SDHD

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.C77_N78insL (c.230_231insTCT)

      CaseProblemVariantFreeText: N/A

      LegacyVariant: p.C77_N78insL (c.443_444insTCT)

      ClinVarID: N/A

      CAID: CA2499214029, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.230_231insTCT

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant; transversion

      CivicName: C77_N78insL (c.230_231insTCT)

      MultipleGeneVariants: N/A

    2. 36 VHL-related pheochromocytomas (from 21 patients) and 10 VHL-related CNS hemangioblastomas (from 6 patients) were studied using comparative genomic hybridization (CGH) to detect genetic imbalances. Patient I with VHL-Associated hemangioblastoma was found with a germline insertion mutation (c.316insGCC) in the VHL gene. (stated as c.529insGCC in the paper which used the Latif sequence as reference) in the VHL gene. All patients have familial VHL.

    1. GroupID/ KindredID: 1

      Case: Age, Sex, Swedish

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0005584; HP:0002666 (renal cell carcinoma; pheochromocytoma)

      CaseHPOFreeText: N/A

      CaseNotHPOs: HP:0009711; HP:0010797 (retinal capillary hemangioma; hemangioblastoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.S38P (c.112T>C)

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVarID: N/A

      CAID: CA351747824 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.112T%3EC

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant; transition

      CivicName: S38P (c.112T>C)

      MultipleGeneVariants: N/A

    1. Von Hippel-Lindau (VHL) is a tumor suppressor that negatively regulates the production of angiogenic factors. Mutations in the VHL gene cause VHL syndrome, which is characterized by highly vascularized tumors. Here we report a c.464T>A mutation of the VHL gene in three patients with hemangioblastoma from a Chinese family. This mutation was not reported previously and was absent in the unaffected family members. The mutation is predicted to cause Val to Glu substitution at VHL protein residue 155 in a conserved region. Previous biochemical studies demonstrated that residue Val-155 was critical for VHL protein binding to chaperonin TRiC/CCT, an essential step for proper VHL protein folding. Our finding of naturally occurring VHL V155E mutation in patients with VHL syndrome supports the functional importance of Val-155 residue in VHL protein and illustrates the diversity of VHL gene defects underlying VHL syndrome.

      PatientID: III-1

      KindredID: 1

      Case: F, 26Y0M, Chinese

      DiseaseAssertion: assumed VHL

      FamilyInfo: 10 members of this Chinese family were tested, and 3 were found with the same genetic mutation (c.464T>A). The proband’s grandmother (I-1, 79Y), and father (II-1, 53Y) had hemangioblastomas, and tested positive for the mutation. This mutation was not found in the other unaffected members in the family.

      CasePresentingHPOs: HP:0006880; HP:0030405; HP:0002666 (cerebellar hemangioblastoma, endolyphmatic sac tumor, pheochromocytoma)

      CaseHPOFreeText: patient suffered with dizziness and headache and frequent vomiting since 25Y (CT and MRI identified occupying lesions and obstructive hydrocephalus in the cerebellar vermis). The cerebellar tumor nodes were removed surgically. Abdominal CT showed multiple lesions in the liver, pancreas and posterior peritoneum. The tumors in the proband’s pancreatic tail and retroperitoneal space also were removed subsequently. Histological analysis indicated the tumors to be pancreatic isletcell tumor and phaeochromocytoma, respectively.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: patient was negative in the bilateral Babinski’s sign test

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.V155E (c.464T>A)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA351756032 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.464T%3EA

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transversion

      CivicName: V155E (c.464T>A)

      MultipleGeneVariants: N/A

    1. a deleting mutation in the first exon (nt. 394-406) of the VHL locus, truncating 16 amino acids (N61-77) from the first beta sheet in the VHL protein.

      The patient presented at age 43 with a new left varicocele having already suffered one episode of gross hematuria. An abdominal ultrasonography revealed the presence of a left renal mass and a 2-cm renal mass in his right kidney. CT scan demonstrated two small 4-mm lung lesions. This was followed by a left radical nephrectomy. Pathological examination of the mass demonstrated a clear-cell RCC. A 1-cm isolated metastatic nodule was also found in the adrenal gland. Two years later, the lung lesions had increased to 5 mm, a further three 2-mm nodular lesions had appeared in the lungs and no growth in the small right renal lesion was found. Following this, MR imaging demonstrated an intradural intramedullary lesion (later confirmed to be consistent with a hemangioblastoma from the inferior portion of the T-5 to T-6) with a prominent feeding vessel. The patient underwent a T5–8 laminectomy. Clinical diagnosis of VHL was reached at this point. Genetic analysis found a deleting mutation in the first exon (nt. 394-406) of the VHL locus, truncating 16 amino acids (N61-77) from the first beta sheet in the VHL protein. This mutation was translated to the updated reference sequence (NM_000551.3) as p.P61_C77del (c.181_231del). This mutation was not present in any of the family members tested including the patient’s two children. At this point, MRI showed no masses, ophthalmological examination showed normal results and a congenital malformation with C-1 occipitalization and C2–3 fusion were identified. The patient underwent resection of the right renal mass, which was consistent with a clear-cell carcinoma. One year later, two cerebral lesions were diagnosed and were consistent with RCC metastases in the right occipital lobe for which he received radiation therapy. No new lesions had appeared in the spinal cord and his chest disease was found to be stable. ACMG evidence codes: 'PM6' since this mutation was declared to be non-familial but kindred testing was not specified (assumed de novo), 'PP4' since the patients phenotypes are highly specific for a disease with a single genetic etiology.

    1. Patient 2 A 17-year-old girl with a history of primitive headache, intense nocturnal sweating and 2-month-long amenorrhoea and elevated blood pressure presented a 7-cm-diameter right adrenal mass at abdominal sonography, confirmed by MRI. The mass showed inhomogeneous density: hypodensity in T1 and hyperdensity in T2 and after Gadolinium contrast. Immunometric assays indicated very high levels of chromogranin A (242 UI/L; NR 2–18) and catecholamines: noradrenaline levels were 14·460 nmol/day (NR: 90–470), and adrenaline and dopamine levels were in the normal range. A 123I-MIBG scintigraphy showed a high tracer uptake in right adrenal gland, as expected. The patient underwent surgical removal of the mass, which was 8 × 6 × 5 cm in size. Immunohistochemical assays indicated that the tumour was positive for chromogranin A and synaptophysin, compatible with a diagnosis of PHEO. Follow-up blood test after 2 years was within normal limits, except for a still moderate elevated CgA (67 UI/L, NR 2–18). The family history was negative for PHEO or other neuroendocrine tumours.

      PatientID: 2

      KindredID: 2

      Case: F, 17Y0M, Ethnicity Unknown

      DiseaseAssertion: adrenal pheochromocytoma

      FamilyInfo: None - The family history was negative for PHEO or other neuroendocrine tumours. Their parents however, decided not to be tested neither to extend the test to other family members

      CasePresentingHPOs: HP:0006748 (adrenal pheochromocytoma)

      CaseHPOFreeText: Apparently sporadic pheo. She had a history of primitive headache, intense nocturnal sweating and 2-month-long amenorrhoea and elevated blood pressure presented a 7-cm-diameter right adrenal mass at abdominal sonography, confirmed by MRI.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: RET, SDHB, SDHD

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.D197N (c.589G>A)

      LegacyVariant: p.D197N (g.13,278)

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA351756524 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.589G%3EA

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: D197N (c.589G>A)

      MultipleGeneVariants: N/A

    1. 33 patients diagnosed with VHL disease, according to (Maher et al. 1990), were tested for germline VHL mutations. Genetic testing was performed on high-molecular-weight DNA from peripheral blood using Southern analysis and PCR. One patient was found to harbour the 508G>T (Val170Phe) VHL gene mutation, documented in the paper as 721G>T due to a difference in transcript sequence. This patient presented with a cerebellar hemangioblastoma. As well, a somatic mutation presenting in their tumor as p.N193M*9 (c.576del13). ACMG evidence codes: 'PP4' since the patient presents phenotypes highly specific for a disease with a single genetic etiology.

    1. PatientID: V89

      KindredID: V89

      Case: Sex Unknown, Age Unknown, French

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0002666 (Pheochromocytoma)

      CaseHPOFreeText: Diagnosed with VHL Type 2B.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.G106Tfs*54 (c.315_316insAC)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA2573130208, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.315_316insAC

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: insertion; plus_2_frameshift_variant

      CivicName: G106Tfs*54 (c.315_316insAC)

      MultipleGeneVariants: N/A

    1. c.292 T>Cap.Y98H

      GroupID: 7A

      DiseaseAssertion: VHL

      GroupSize: 2

      GroupNumberMales: N/A

      GroupNumberFemales: N/A

      GroupEthnicity: N/A

      GroupAgeRange: N/A

      GroupInfo: 2 VHL patients with the given VHL mutation were grouped in this study.

      GroupPresentingHPOs: HP:0030405 (pancreatic endocrine tumor)

      GroupHPOFreeText: Patients have islet cell tumors (ICTs), or listed as pancreatic endocrine tumor. Other clinical manifestations outside of a pancreatic neuroendocrine tumor are possible, but were not discussed.

      GroupNotHPOs: N/A

      GroupNotHPOFreeText: N/A

      GroupPreviousTesting: N/A

      PreviouslyPublished: 7987306

      SupplementalData: N/A

      Variant: p.Y98H (c.292T>C)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 2223 https://www.ncbi.nlm.nih.gov/clinvar/variation/2223/

      CAID: N/A

      gnomAD: 0.00001343 https://gnomad.broadinstitute.org/variant/3-10183823-T-C

      VariantEvidence: N/A

      MutationType: missense_variant; transition

      CivicName: Y98H (c.292T>C)

      MultipleGeneVariants: N/A

    1. We observed 10 different intragenic mutations in 10/15 (66.7%) patients: five missense mutations

      PatientID: 7

      KindredID: 7

      Case: F, 30Y0M, Korean

      DiseaseAssertion: VHL

      FamilyInfo: None. Sporadic

      CasePresentingHPOs: HP:0010797; HP:0009711; HP:0005584 (hemangioblastoma, retinal capillary hemangioma, renal cell carcinoma)

      CaseHPOFreeText: Bilateral involvements of renal cell carcinomas (See table 1). 'Other' phenotypes found in patient. These are noted in the paper to include: pancreatic neuroendocrine tumors (PNETs), renal and pancreatic cysts and central nervous system tumors, although it is not clearly stated that patient has all. (See Table 1).

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.C162R (c.484T>C)

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVar: 496067 https://www.ncbi.nlm.nih.gov/clinvar/variation/496067/

      CAID: CA351756117 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.484T%3EC

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant; transition

      CivicName: C162R (c.484T>C)

      MultipleGeneVariants: N/A

    1. In patient 9, sequencing of the VHL gene revealed a missense mutation at codon 167 (Arg to Gln). Previous data suggested that germline codon 167 mutations (Arg167Glu, Arg167Trp) convey a high risk for the development of pheochromocytoma and renal cell carcinoma.2 However in patient 9, neither tumor had appeared so far at the age of 58.

      PatientID: 9

      KindredID: V

      Case: Sex Unknown, 58Y0M, Chinese

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0010797 (hemangioblastoma)

      CaseHPOFreeText: The patient had two CNS hemangioblastomas.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.R167Q (c.500G>A)

      LegacyVariant: p.R167Q (c.713G>A)

      CaseProblemVariantFreeText: N/A

      ClinVarID: 2216 https://www.ncbi.nlm.nih.gov/clinvar/variation/2216/

      CAID: CA020454 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.500G%3EA

      gnomAD: 0.000003977 https://gnomad.broadinstitute.org/variant/3-10191507-G-A

      VariantEvidence: Mutation was predicted to compromise the elongin-binding region. Refer to table 3 for LOH information.

      MutationType: missense_variant;transition

      CivicName: R167Q (c.500G>A)

      MultipleGeneVariants: N/A

    1. One hundred and sixteen unrelated VHL disease patients have been investigated by molecular genetic analysis. Twenty-two of these were previously shown to have germline deletions on Southern analysis, and in the present study the remaining 94 patients were screened for intragenic mutations via SSCP and heteroduplex analysis of 855 bp of the VHL coding sequence and 800 bp of the 3' UTR. An intragenic mutation was identified in 55 (59%) out of 94 patients without germline deletions on Southern analysis. In all patients with multiple affected family members the missense mutation segregated with the disease. Large deletions or intragenic mutations predicted to cause a truncated protein were found in 36 of 53 families without pheochromocytoma (VHL type 1) and 2 of 12 families with pheochromocytoma (VHL type 2). This study also investigated the frequency of different mutation classes between kindreds with and without pheochromocytoma. The p.R79P (c.236G>C) variant (noted as p.R150P (c.449G>C) in the paper due to a difference in reference transcript used) was found in at least one patient in kindred 150. No familial phenotypic information could be inferred from the paper.

    1. 031Fnt 713 G to A, Arg to GlnP, 13488

      PatientID: 40

      KindredID: 3488

      Case: F, 31Y0M, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0030405 (pancreatic endocrine tumour)

      CaseHPOFreeText: She presented with one pathologic pancreatic endocrine tumour.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.R167Q (c.500G>A)

      LegacyVariant: p.R167Q (c.713G>A)

      CaseProblemVariantFreeText: N/A

      ClinVar: 2216 https://www.ncbi.nlm.nih.gov/clinvar/variation/2216/

      CAID: CA020454 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.500G%3EA

      gnomAD: 0.000003977 https://gnomad.broadinstitute.org/variant/3-10191507-G-A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: R167Q (c.500G>A)

      MultipleGeneVariants: N/A

    2. 2231Mnt 553 G to C, Gly to Arg

      PatientID: 22

      KindredID: 3816

      Case: M, 31Y0M, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0030405 (pancreatic endocrine tumour)

      CaseHPOFreeText: He presented with one pathologic pancreatic endocrine tumour.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.G114R (c.340G>C)

      LegacyVariant: p.G114R (c.553G>C)

      CaseProblemVariantFreeText: N/A

      ClinVar: 223193 https://www.ncbi.nlm.nih.gov/clinvar/variation/223193/

      CAID: CA357101 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.340G%3EC

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transversion

      CivicName: G114R (c.340G>C)

      MultipleGeneVariants: N/A

    1. 226_228delTTC

      GroupID/ KindredID: 6

      Case: Age unknown, Sex unknown, Polish

      DiseaseAssertion: VHL

      FamilyInfo: This mutation was found in Family No. 6 with 1 member affected.

      CasePresentingHPOs: HP:0009711; HP:0010797 (retinal capillary hemangioma, hemangioblastoma)

      CaseHPOFreeText: N/A

      CaseNotHPOs: HP:0005584 (renal cell carcinoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: 32179488

      SupplementalData: N/A

      Variant: p.F76del (c.226_228delTTC)

      CaseProblemVariantFreeText: NM_000551.3:c.226_228delTTC automaps to updated c.227_229delTCT

      LegacyVariant: N/A

      ClinVarID: N/A

      CAID: CA357012 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.226_228delTTC

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: inframe_deletion

      CivicName: F76del (c.227_229del)

      MultipleGeneVariants: N/A

    1. and 9

      PatientID: None

      KindredID: 1

      Case: F, 9Y0M, Ethnicity Unknown

      DiseaseAssertion: Asymptomatic

      FamilyInfo: This patient had an older brother who at 7-years-old, presented with multiple retinal haemangiomas. At the age of 9, he underwent a left adrenalectomy for a phaeochromocytoma. At the age of 13, a 9 mm solid lesion consistent with a pNET. This patient also had a renal cell carcinoma. They also had a 12-year old younger brother who had a retinal hemangioma. The patients father was diagnosed with VHL at 31 years-old and had multiple cerebellar haemangioblastomas, retinal angiomas, a phaeochromocytoma, a ccRCC and a small pNET. Pedigree: See Figure 1.

      CasePresentingHPOs: N/A

      CaseHPOFreeText: N/A

      CaseNotHPOs: HP:0002666, HP:0005584, HP:0009711, HP:0030405 (pheochromocytoma, renal cell carcinoma, Retinal capillary hemangioma, Pancreatic endocrine tumor)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.Arg120* (c.358A>T)

      LegacyVariant: N/A

      ClinVarID: N/A

      CAID: CA351753732 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA351753732

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: stop_gained

      CivicName: R120*(c.358A>T)

      MultipleGeneVariants: N/A

    1. 32 c.341-2A>C IVS2-2A>C Familial VHL

      Between 1994 and 2001, the Dutch VHL working group conducted DNA analysis on 146 probands with VHL-associated manifestations. DNA of probands was extracted from peripheral blood samples. Exons 1, 2 and 3 of the VHL gene and their flanking untranslated and intronic coding sequences were amplified by PCR and subjected to semi-automated sequence analysis. Screening for structural rearrangements, including deletions, involving the VHL gene was performed by Southern blot analysis and the multiplex ligation-dependent probe amplification (MLPA) assay. Deletions encompassing the entire VHL gene were confirmed by FISH analysis on lymphocytes from affected individuals. VHL mutations were identified in 43 families. This splice mutation c.341-2A>C was found in a VHL patient with hemangioblastomas of the retina and central nervous system, renal cysts and RCC, and pancreatic cysts (family no. 32). They were described as being familial VHL however no other members were described. ACMG evidence codes: 'PSV1' because they observe a splice-site variant in a gene where loss-of-function is known mechanism of disease, 'PP4' because the patients' phenotypes or family history are highly specific for a disease with single genetic etiology.

    1. PatientID: 11

      KindredID: 1

      Case: M, Age Unknown, German

      DiseaseAssertion: Asymptomatic

      FamilyInfo: The patient's father (patient 8) was had both mutations and presented with pheochromocytoma. The patient's brother (patient 10) did not carry the mutation and was unaffected. The patient's maternal grandfather (patient 3) presented with pheochromocytoma and carried both mutations. The patient's materal grandmother (patient 4) was unaffected and did not carry either mutation. The patient's great aunt (patient 2) presented with pheochromocytoma and had both mutations. Her husband (patient 1) was unaffected and did not carry either mutation. They had four children; one died and presented with pheochromocytoma, two (patient 5 and 7) had both mutations and presented with pheochromocytoma, and one child (patient 6) was unaffected and carried neither mutation. Patient 7 had a child (patient 9) who also carried both mutations and presented with pheochromocytoma. See Figure 3 for family pedigree.

      CasePresentingHPOs: N/A

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.P81S (c.241C>T)

      LegacyVariant: P81S (c.454C>T)

      CaseProblemVariantFreeText: N/A

      ClinVar: 2233 https://www.ncbi.nlm.nih.gov/clinvar/variation/2233/

      CAID: CA020148 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.241C%3ET

      gnomAD: 0.0002179 https://gnomad.broadinstitute.org/variant/3-10183772-C-T

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: P81S (c.241C>T) and L188V (c.562C>G)

      MultipleGeneVariants: Germline, VHL, c.562C>G (p.Leu188Val)

    1. Meanwhile, it was also found that the guanine replaced the 559th cytosine on one patient and two carriers from the third family, which made the 116th leucine replaced by valine.

      PatientID: III-1

      KindredID: 3

      Case: M, Age Unknown (deceased), Chinese

      DiseaseAssertion: CNS Hemangioblastoma

      FamilyInfo: The transition mutation was found and confirmed in 1 patient (II-3) and 2 carriers (III-7, IV-2). 5 members, including III-1, had hemangioblastomas of the CNS, but had all passed away before genetic testing. Could be assumed and deduced the genetics due to pedigree showing future linear relations of this mutation.

      CasePresentingHPOs: HP:0010797 (hemangioblastoma)

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.L116V (c.346C>G) [assumed]

      LegacyVariant: p.L116V (c.559C>G) [assumed]

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA351753642 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.346C%3EG

      gnomAD: N/A

      VariantEvidence: No genetic testing was done prior to death, however family history and presentation leads to this deduction

      MutationType: missense_variant;transversion

      CivicName: L116V (c.346C>G)

      MultipleGeneVariants: N/A

    1. detected point germline vhl mutations in 14 patients

      PatientID: 11

      KindredID: 11

      Case: 31Y0M, sex unknown, ethnicity unknown

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0010797; HP:0009711 (hemangioblastoma; retinal capillary hemangioma)

      CaseHPOFreeText: See Table 1&2 for retinal capillary hemangioma information

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.F76del (c.226delTTC)

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVarID: N/A

      CAID: CA357012 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.224_226del

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: inframe_deletion

      CivicName: F76del (c.226_228delTTC)

      MultipleGeneVariants: N/A

    1. Case report A 6-year-old girl was brought into the ED by her parents in the late evening with a 5 week history of colicky, peri-umbilical pain and general malaise. Her mother reported that they had been to the family doctor repeatedly since the onset of symptoms and trialled a number of medications (including antispasmodics and various analgesics) without success. On further questioning, the patient described several episodes of spontaneous vomiting without obvious cause or association over the past month. Her appetite was poor and she had been losing weight. There were no other gastrointestinal or urinary symptoms. There was no history of fever, although she did report ‘sweating for no reason’ on occasion. She had also been suffering from intermittent, generalized headaches without any other focal symptoms over the same time period. She had been previously well, the only noteworthy point in her medical history being her conception through in vitro fertilization. There were no developmental concerns or family history of note. On examination, the patient appeared pale, tired, mildly dehydrated, but apyrexial and comfortable at rest. She was profoundly tachycardic, with a heart rate of 170 beats per minute, and had a BP of 203/157 mmHg on repeat measurements (normal systolic range 90–110 mmHg in this age group). Crucially, as the patient arrived in the early evening, she was triaged in the adult ED and not the paediatric ED (which was closed at this time), where BP would not have been part of routine observations in this age group. Urinary dipstick showed raised protein and blood. General examination was otherwise normal. In discussion with paediatric cardiology, the patient was started immediately on oral nifedipine to control the malignant hypertension prior to further investigation. Blood tests revealed low potassium of 3.0 mmol/L (normal 3.3–4.6) with raised urea (10.0 mmol/L; 2.5–6.5) and creatinine (81 mmol/L; 25–60). Routine haematology and biochemistry bloods (including liver and thyroid function tests) were otherwise unremarkable. An abdominal ultrasound scan demonstrated a 3 × 2.5 cm mass at the upper pole of the left kidney without a distinctly identifiable adrenal gland, a finding confirmed on CT (Fig. 1), which also showed some low attenuation suggestive of cystic change within the mass. Serial urinary metanephrines were subsequently found to be grossly elevated (17.0, 18.1 and 14.7 µmol/mmol creatinine; normal <1.74) with a predominant normetanephrine fraction, suggesting a diagnosis of phaeochromocytoma. Figure 1Open in figure viewerPowerPoint Ultrasound image (above) of the patient's left kidney (between the two crosses) clearly showing an abnormal mass associated with the organ. The adrenal cannot be distinctly identified. The mass was further characterized on CT (below, the mass having been circled). Sympathetic blockade was established first using gradually increasing doses of oral phenoxybenzamine (switched to i.v. dosing in the 5 days prior to surgery), then adding propranolol, aiming for a systolic BP of 80 mmHg with postural drop of 10 mmHg in order to facilitate safe removal of the tumour. Concurrent investigations identified raised serum renin and aldosterone levels consistent with secondary hyperaldosteronism. Serum calcitonin and urinary steroid profiles were normal, as was retinal screening for abnormalities associated with von Hippel-Lindau (vHL) disease, including retinal haemangiomas and hypertensive retinopathy. A laparoscopic left adrenalectomy took place 6 weeks after initial presentation, and priority was placed on close cardiovascular monitoring perioperatively. The patient was fit for discharge 3 days after surgery histology subsequently confirming the diagnosis of phaeochromocytoma.

      PatientID: 1

      KindredID: 1

      Case: F, 6Y0M, Ethnicity Unknown

      DiseaseAssertion: pheochromocytoma

      FamilyInfo: No history - the only noteworthy point in her medical history being her conception through in vitro fertilization, however no noted concerns. This mutation was not present in either parent, indicating a de novo.

      CasePresentingHPOs: HP:0002666 (pheochromocytoma)

      CaseHPOFreeText: patient presented with a prolonged history of general malaise, headaches and abdominal pain. She was noted to have malignant hypertension. Subsequent imaging of the abdomen demonstrated a left adrenal mass (diagnosis of phaeochromocytoma confirmed by serial raised urinary metanephrines). Sympathetic blockade was established prior to definitive surgical treatment, resulting in complete resolution of the patient’s symptoms and hypertension.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.N90H (c.268A>C)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA351750708 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.268A%3EC

      gnomAD: N/A

      VariantEvidence: Neurofibromatosis type (NF) 1 was excluded on clinical grounds as she had none of the cutaneous features. Mutational analysis of the RET proto-oncogene was normal, making MEN2 unlikely. Sequencing of exons 1–3 of the VHL gene revealed a novel single base pair substitution (A268C).

      MutationType: missense_variant;transversion

      CivicName: N90H (c.268A>C)

      MultipleGeneVariants: N/A

    1. Poorer survival has been associated with loss of function events (frameshift or nonsense mutations) compared with wild-type, missense mutations, and mutations of unknown biological consequence (25, 32) although numbers of cases in the LOF group were very small. We found no prognostic effect of VHL mutation but a trend (although not quite statistically significant) was seen for increased frequency of microvascular invasion in tumors where the presumed deletion would occur essentially from the elongin binding region onwards, possibly indicating a role for either HIF-regulated factors or other VHL substrates in this aspect of tumorigenesis. The largest previous study also found no relationship between clinicopathologic factors and VHL mutation/LOH in cRCC (26, 35). In marked contrast, however, is that 0 of 11 cRCC cases with methylation had an intragenic mutation whereas we found 14 of 19 methylated cases to have a confirmed mutation, although their mutation and methylation frequencies overall were much lower (51% and 5.4%, respectively). However, a significantly better cancer-free and overall survival was seen in patients with stage I to III cancer with VHL alteration (mutation or methylation) but wasn't seen in stage IV disease (35). Our data fails to confirm this although when stage IV patients were included a similar trend was seen. Differences between studies might reflect samples sizes, length of follow-up, and postoperative treatment.
    1. 1 Germany c.339delA p.Gly114Valfs*45

      GroupID: 13

      Case: Sex unknown, Age unknown, German

      DiseaseAssertion: VHL

      FamilyInfo: Unknown. 1 registrant was found with this variant; no family info was mentioned

      CasePresentingHPOs: HP:0030393 (Endolymphatic sac tumor)

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.G114Vfs*45 (c.339delA)

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVarID: N/A

      CAID: CA645509026 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.339delA

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: minus_1_frameshift_variant

      CivicName: G114Vfs*45 (c.339delA)

      MultipleGeneVariants: N/A

    2. 1 France c.473T>C p.Leu158Pro

      GroupID: 23

      Case: Sex, Age, Ethnicity unknown

      DiseaseAssertion: VHL

      FamilyInfo: Unknown. 1 registrant from France was found with this variant; no family info was mentioned

      CasePresentingHPOs: HP:0030393 (Endolymphatic sac tumor)

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.L158P (c.473T>C)

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVarID: 182980 https://www.ncbi.nlm.nih.gov/clinvar/variation/182980/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant; transition

      CivicName: L158P (c.473T>C)

      MultipleGeneVariants: N/A

    1. Molecular and clinical analysis of 126 French VHL families tested for renal involvement revealed 92 different mutations. 90 of these families had renal involvement. The p.K159delinsI* (c.475_476insTTT) germline variant of the VHL gene was detected in a family (ID 43). Member 3207 had no renal involvement. Members 3206 and 3203 presented with mild renal disease. Member 3189 presented with severe renal disease (RCC). The paper states that this family is previously reported in PMID 12202531 and/or 9829912.

    2. Molecular and clinical analysis of 126 French VHL families tested for renal involvement revealed 92 different mutations. 90 of these families had renal involvement. The p.N67_V74del (c.197_221del) germline variant of the VHL gene was detected in a family (ID 287). Member 6396 presented with mild renal disease. Member 6611 presented with severe renal disease (RCC). The paper states that this family is previously reported in PMID 9829912, where 1 patient with this mutation is reported but relation to this patient is unclear. The variant is reported as c.197_220del which was mapped to c.198_221del.

    1. 40.

      Case#: 40

      DiseaseAssertion: Hemophilia B, severe

      FamilyInfo: NA

      ParentalTesting: NA

      CasePresentingHPOs: HP:0011858

      CaseHPOFreeText: FIX:C < 1%

      CaseNotHPOs: NA

      CaseNotHPOFreeText: NA

      CasePreviousTesting: All relevant sequences of F9 were PCR amplified and analyzed by DNA sequencing

      Gene: F9

      Variant: NM_000133.3:c.892C>T

      LegacyVariant:

      ClinVar: No

      CAID: CA255370

      gnomAD:

    2. 4.

      Case#: 4

      DiseaseAssertion: Hemophilia B, severe

      FamilyInfo: NA

      ParentalTesting: NA

      CasePresentingHPOs: HP:0011858

      CaseHPOFreeText: FIX:C < 1%

      CaseNotHPOs: NA

      CaseNotHPOFreeText: NA

      CasePreviousTesting: All relevant sequences of F9 were PCR amplified and analyzed by DNA sequencing

      Gene: F9

      Variant: NM_000133.3:c.160G>C

      LegacyVariant:

      ClinVar: No

      CAID: CA414435755

      gnomAD:

    3. 24.

      Case#: 24

      DiseaseAssertion: Hemophilia B, severe

      FamilyInfo: NA

      ParentalTesting: NA

      CasePresentingHPOs: HP:0011858

      CaseHPOFreeText: FIX:C < 1%

      CaseNotHPOs: NA

      CaseNotHPOFreeText: NA

      CasePreviousTesting: All relevant sequences of F9 were PCR amplified and analyzed by DNA sequencing

      Gene: F9

      Variant: NM_000133.3:c.1193G>A

      LegacyVariant:

      ClinVar: No

      CAID: CA414446384

      gnomAD:

    4. 29.

      Case#: 29

      DiseaseAssertion: Hemophilia B, severe

      FamilyInfo: NA

      ParentalTesting: NA

      CasePresentingHPOs: HP:0011858

      CaseHPOFreeText: FIX:C < 1%

      CaseNotHPOs: NA

      CaseNotHPOFreeText: NA

      CasePreviousTesting: All relevant sequences of F9 were PCR amplified and analyzed by DNA sequencing

      Gene: F9

      Variant: NM_000133.3:c.1279G>A

      LegacyVariant:

      ClinVar: No

      CAID: CA414447040

      gnomAD:

    5. 11.

      Case#: 11

      DiseaseAssertion: Hemophilia B, severe

      FamilyInfo: NA

      ParentalTesting: NA

      CasePresentingHPOs: HP:0011858

      CaseHPOFreeText: FIX:C < 1%

      CaseNotHPOs: NA

      CaseNotHPOFreeText: NA

      CasePreviousTesting: All relevant sequences of F9 were PCR amplified and analyzed by DNA sequencing

      Gene: F9

      Variant: NM_000133.3:c.677G>A

      LegacyVariant:

      ClinVar: No

      CAID: CA121128

      gnomAD:

    6. 39.

      Case#: 39

      DiseaseAssertion: Hemophilia B, severe

      FamilyInfo: NA

      ParentalTesting: NA

      CasePresentingHPOs: HP:0011858

      CaseHPOFreeText: FIX:C < 1%

      CaseNotHPOs: NA

      CaseNotHPOFreeText: NA

      CasePreviousTesting: All relevant sequences of F9 were PCR amplified and analyzed by DNA sequencing

      Gene: F9

      Variant: NM_000133.3:c.892C>T

      LegacyVariant:

      ClinVar: No

      CAID: CA255370

      gnomAD:

    1. 20

      Case#: 20

      DiseaseAssertion: Hemophilia B, severe

      FamilyInfo: NA

      ParentalTesting: NA

      CasePresentingHPOs: NA

      CaseHPOFreeText: FIX:C < 1%

      CaseNotHPOs: NA

      CaseNotHPOFreeText: NA

      CasePreviousTesting: All exons, UTRs, exon-intron junction regions, and the promotor of F9 were amplified by PCR and analyzed by direct DNA sequencing

      Gene: F9

      Variant: NM_000133.3:c.252+1G>A

      LegacyVariant:

      ClinVar: No

      CAID: CA414436412

      gnomAD:

    2. 2

      Case#: 2

      DiseaseAssertion: Hemophilia B, severe

      FamilyInfo: NA

      ParentalTesting: NA

      CasePresentingHPOs: NA

      CaseHPOFreeText: FIX:C < 1%

      CaseNotHPOs: NA

      CaseNotHPOFreeText: NA

      CasePreviousTesting: All exons, UTRs, exon-intron junction regions, and the promotor of F9 were amplified by PCR and analyzed by direct DNA sequencing

      Gene: F9

      Variant: NM_000133.3:c.391+1G>C

      LegacyVariant:

      ClinVar: No

      CAID: CA414438024

      gnomAD:

    1. genetic defects

      Case#: Taipei_1 & Taipei_2 (assumed male; Chinese)

      DiseaseAssertion: Severe Hemophilia B

      FamilyInfo: Mothers of both families were found to be carriers as well as several other females in the family

      ParentalTesting: Mothers were carriers

      CasePresentingHPOs: HP:0011858

      CaseHPOsFreeText: reduced factor IX activity (Patient 1: FIX:C: <1% FIX:Ag: 38 ; Patient 2: FIX:C: <1% ; FIX:Ag: 55)

      CaseNotHPOs: None

      CasePreviousTesting: N/A

      Gene: F9

      Variant: NM_000133.4:c.128G>A (p.Arg43Gln)

      ClinVar: 810864

      CAID: CA414435539

      gnomAD: Absent/Not Reported

    1. R46S

      Case#: N/A

      DiseaseAssertion: Severe Hemophilia B

      FamilyInfo: None

      ParentalTesting: None

      CasePresentingHPOs: HP:0001929

      CaseHPOsFreeText: reduced factor IX activity

      CaseNotHPOs: N/A

      CasePreviousTesting: N/A

      Gene: F9

      Variant: NM_000133.4:c.138G>T (p.Arg46Ser)

      ClinVar: Absent

      CAID: CA414435596

      gnomAD: Absent/Not Reported

    2. K45N

      Case#: N/A

      DiseaseAssertion: Severe Hemophilia B

      FamilyInfo: None

      ParentalTesting: None

      CasePresentingHPOs: HP:0001929

      CaseHPOsFreeText: reduced factor IX activity

      CaseNotHPOs: N/A

      CasePreviousTesting: N/A

      Gene: F9

      Variant: NM_000133.4:c.135G>T (p.Lys45Asn)

      ClinVar: Absent

      CAID: CA414435576

      gnomAD: Absent/Not Reported

    1. Case#: Calgary 4

      DiseaseAssertion: Hemophilia B

      FamilyInfo: 9 carrier females, 3 affected males, 1 female obligate carrier

      ParentalTesting: N/A

      CasePresentingHPOs: HP:0001929

      CaseHPOsFreeText: reduced factor IX activity

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      Gene: F9

      Variant: c.19A>T (p.Ile7Phe)

      LegacyVariant: c.48A>T (p.Ile-40Phe)

      ClinVar: Absent

      CAID: CA10529708

      gnomAD: Filtering AF: 0.0007752 (no homozygotes)

      Variant: NM_000133.3:c.1150C>T (p.Arg384Ter)

      LegacyVariant: c.31133C>T (p.Arg338Ter)

      ClinVar: Absent

      CAID: CA255399

      gnomAD: Absent/Not Reported

    1. Factor IX San Dima

      Case#: Factor IX San Dimas Case

      DiseaseAssertion: Severe Hemophilia B

      FamilyInfo: None

      ParentalTesting: N/A

      CasePresentingHPOs: HP:0011858

      CaseHPOsFreeText: reduced factor IX activity (FIX:Ag 98%; FIX:C: <0.01)

      CaseNotHPOs: N/A

      CasePreviousTesting: DNA Seq analysis of the Factor IX gene (FIX:Ag 98%; FIX:C: <0.01)

      Gene: F9

      Variant: NM_000133.4:c.128G>A (p.Arg43Gln)

      LegacyVariant: p.Arg-4Gln

      ClinVar: 810864

      CAID: CA414435539

      gnomAD: Absent/Not Reported

    1. (6372)

      Case#: Patient E (assumed male)

      DiseaseAssertion: Severe, Familial Hemophilia B

      FamilyInfo: Mothers were heterozygous, but patient E’s sister and aunt were non-carriers (homozygous for the cleavage)

      ParentalTesting: Mothers were heterozygous, but patient E’s sister and aunt were non-carriers (homozygous for the cleavage)

      CasePresentingHPOs: HP:0011858

      CasePresentingHPOsFreeText: reduced factor IX activity (FIX:C: <1; FIX:Ag:37/38)

      CaseNotHPOs: N/A

      CasePreviousTesting: N/A

      Gene: F9

      Variant: NM_000133.4:c.135G>T (p.Lys45Asn)

      ClinVar: Absent/Not Reported

      CAID: CA414435576

      gnomAD: Absent/Not Reported