Proband KH7 was 10yo at report, has the Hurler/Scheie phenotype, and has this variant but a second variant does not appear to have been detected.

Case19: Male, 4 yrs onset

CasePresentingHPOs: HP:0006785, HP:0003236, HP:0003458, HP:0008981, HP:0031322, HP:0032019, HP:0003701 (Limb-girdle muscular dystrophy, Elevated serum creatine kinase, EMG: myopathic abnormalities, Calf muscle hypertrophy, Myocardial lymphocytic infiltration, Muscle eosinophilia, Proximal muscle weakness)

HPOsFreeText: N/A

CaseNotHPOs: HP:0100543 (Cognitive impairment)

NotHPOsFreeText: N/A

CaseAddInfo: Proband is homozygous for this deletion, Parents are confirmed heterozygous and consangeuinous

CasePreviousTesting: Peak CPK at 25,000 IU/l, Partially absent α- and β-sarcoglycan staining, Normal dystrophin content, Totally absent γ-sarcoglycan staining

CaseGenotypingMethod: Total mRNA was isolated from muscle biopsies and cDNA was synthesized from it via reverse transcriptase. PCR and SSCP analysis was performed and excised, amplified, and sequenced. After finding the mutations, DNA from peripheral blood leukocytes or muscle biposies was isolated, PCR amplified, and sequenced to confirm the results.

ClinVar: 2004 https://www.ncbi.nlm.nih.gov/clinvar/variation/2004/

Also Reported As

Variant: NM_000231.2(SGCG):c.525del (p.Phe175fs)

ClinVar: 189243 https://www.ncbi.nlm.nih.gov/clinvar/variation/189243/

gnomAD: 0.00009671, https://gnomad.broadinstitute.org/variant/13-23869568-CT-C

Case44: Female, 7 yrs onset

CasePresentingHPOs: HP:0006785, HP:0003236, HP:0040083, HP:0003307, HP:0002527, HP:0003701, HP:0003323, HP:0009042, HP:0003458, HP:0100305, HP:0031542 (Limb-girdle muscular dystrophy, Elevated serum creatine kinase, Toe walking, Hyperlordosis, Falls, Proximal muscle weakness, Progressive muscle weakness, Marked muscular hypertrophy, EMG: myopathic abnormalities, Ring fibers, Myelin-like whorls in vacuolated fibers)

HPOsFreeText: Wheelchair at 14 yrs

CaseNotHPOs: HP:0003115, HP:0100543 (Abnormal EKG, Cognitive impairment)

NotHPOsFreeText: N/A

CaseAddInfo: Proband is homozygous for this duplication, Parents are confirmed heterozygous

CasePreviousTesting: Peak CPK at 20,000 IU/l, Partially absent α- and β-sarcoglycan staining, Normal dystrophin content, Totally absent γ-sarcoglycan staining

CaseGenotypingMethod: Total mRNA was isolated from muscle biopsies and cDNA was synthesized from it via reverse transcriptase. PCR and SSCP analysis was performed and excised, amplified, and sequenced. After finding the mutations, DNA from peripheral blood leukocytes or muscle biposies was isolated, PCR amplified, and sequenced to confirm the results.

Variant: NM_000231.2(SGCG):c.87dup (p.Gly30fs)

ClinVar: 2008 https://www.ncbi.nlm.nih.gov/clinvar/variation/2008/

gnomAD: 0.000008805, https://gnomad.broadinstitute.org/variant/13-23777919-A-AT

Case# A4, Male, UK

CasePreviousTesting re-sequenicing of genome

CaseGenotypingMethod genotyped for five microsatellite markers spanning TMEM43 on chromosome 3p25

Variant NM_024334.2(TMEM43):c.424G>A (p.Glu142Lys)

ClinVar 46147

gnomAD 0.001121 link

Case#: Family 1, Individual III-2, Male, 23 yo, dx at 5 years

CasePresentingHPOs: HP:0002355, HP:0001260, HP:0001251, HP:0025402, HP:0000640, HP:0002544, HP:0012036, HP:0002451, HP:0007256

CaseNotHPOs: HP:0100543, HP:0012547, HP:0007108

CasePreviousTesting: MRI

CaseGenotypingMethod: combination of homozygosity mapping and WES, haplotype analysis

Variant: NM_177400.2(NKX6-2):c.121A>T (p.Lys41Ter)

ClinVar: 430622, https://www.ncbi.nlm.nih.gov/clinvar/variation/430622/

gnomAD: n/a

VariantEvidence: fibroblast cell line used to determine variant as null.

CaseAddInfo: Walked at 12mo, but at 8yo required walking assistance. Disease did not significantly progress until teen years.

CasePMIDs:

Case#: Family 1, Individual III-1, Female, 27 yo, dx at 3 months old

CasePresentingHPOs: HP:0000639, HP:0001332, HP:0001270, HP:0002497, HP:0001272, HP:0002062, HP:0000571, HP:0002540, HP:0000511, HP:0012547, HP:0001260, HP:0030187, HP:0001332, HP:0000473

CaseNotHPOs: HP:0003474, HP:0007108

CasePreviousTesting: MRI showing brain hypomyelination

CaseGenotypingMethod: combination of homozygosity mapping and WES, haplotype analysis

Variant: NM_177400.2(NKX6-2):c.121A>T (p.Lys41Ter)

ClinVar: 430622, https://www.ncbi.nlm.nih.gov/clinvar/variation/430622/

gnomAD: n/a

VariantEvidence:

CaseAddInfo: Wheelchair bound at 27 yo

CasePMIDs:

Case: Family III-I:2

CaseHPOs: HP:0003563, (decreased LDL cholesterol)

CaseNotHPOs: HP:0000819 (Diabetes)

CasePreviousTesting: Heterozygous (Chr2:21,230,941; c.8799 G > T; APOBp.Cys2933*) TC 145 mg/dl, LDL-C 55 mg/dl, HDL-C 81 mg/dl, TG 45 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.8799C>A (p.Cys2933*), heterozygous

CAID: CA345993342

AddInfo: Mother of Family III-II:2. Other daughter (II-1) also has low LDL-C, but no genetic testing results available.

Case: Family IV-III:2, 19 year old female

CaseHPOs: HP:0003563 (decreased LDL cholesterol)

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

CasePreviousTesting: TC 124 mg/dl, LDL-C 49 mg/dl, HDL-C 62 mg/dl, TG 65 mg/dl (see additional values in Table 1)

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.

CaseAddInfo: Daughter of Family IV-II:1

CaseJO: Female, 56 yrs onset

CasePresentingHPOs: HP:0002326, HP:0003236, HP:0001712, HP:0003458, HP:0012548, HP:0030197, HP:0003557, HP:0031237 (Transient ischemic attack, Elevated serum creatine kinase, Left ventricular hypertrophy, EMG: myopathic abnormalities, Fatty replacement of skeletal muscle, Fatigable weakness of skeletal muscles, Increased variability in muscle fiber diameter, Internally nucleated skeletal muscle fibers)

HPOsFreeText: N/A

CaseNotHPOs: HP:0030972, HP:0030177 (Abnormal systemic blood pressure, Abnormal nerve conduction study)

NotHPOsFreeText: N/A

CaseAddInfo: Proband is homozygous for this variant

CasePreviousTesting: No family history suggestive of neuromuscular or cardiac disorders

CaseGenotypingMethod: Leukocyte-derived DNA was examined via NGS sequencing with 265 genes and shown to carry a homozygous nonsense mutation in TRIM63. TRIM54 was examined and no variants were found.

Variant: NM_032588.3(TRIM63):c.739C>T (p.Gln247Ter)

ClinVar: 222849, https://www.ncbi.nlm.nih.gov/clinvar/variation/222849/

gnomAD: 0.008100, https://gnomad.broadinstitute.org/variant/1-26384973-G-A

Case3: Female, Birth onset

CasePresentingHPOs: HP:0001558, HP:0008947, HP:0002643, HP:0011470, HP:0001270, HP:0001349, HP:0001488, HP:0007941, HP:0010628, HP:0003327, HP:0003722, HP:0003391, HP:0030051, HP:0002938, HP:0002943, HP:0008081, HP:0003273, HP:0012785, HP:0012432, HP:0010300, HP:0001611, HP:0002792, HP:0003458, HP:0003557, HP:0003803, HP:0003715 (Reduced fetal movements, Infantile hypotonia, Neonatal respiratory distress, Nasogastric tube feeding in infancy, Motor delay, Facial diplegia, Bilateral ptosis, Limited extraocular movement, Facial muscle weakness, Axial muscle weakness, Neck flexor weakness, Gowers sign, Tip-toe gait, Lumbar hyperlordosis, Thoracic scoliosis, Pes valgus, Hip contracture, Flexion contracture of finger, Chronic fatigue, Abnormally low-pitched voice, Nasal voice, Reduced vital capacity, EMG: myopathy, Increased fiber size variation, Type 1 muscle fiber predominance, Myofibrillar myopathy)

HPOsFreeText: Nocturnal ventilation started at 2 yrs, Tracheostomy performed, Hypermobility of the upper extremities, Spinal contracture, Intermyofibrillar network was coarse and irregular, Cap structures, Jagged z-lines

CaseNotHPOs: HP:0001627, HP:0040081, HP:0040129 (Cardiac abnormality, Abnormal levels of creatine kinase in blood, Abnormal nerve conduction)

NotHPOsFreeText: 24-hour Holter-EKG recording and cardiac ultrasound were normal

CaseAddInfo: Healthy parents and 3 healthy siblings, Mutation is de novo

CasePreviousTesting: N/A

CaseGenotypingMethod: PCR and sequencing analysis were performed on genomic DNA, specifically the entire coding sequence of TPM2. TPM2 was sequenced in both parents and all siblings with negative results.

Variant: NM_003289.3:c.606C>G (p.Asn202Lys)

ClinVar: 12467 https://www.ncbi.nlm.nih.gov/clinvar/variation/12467/

gnomAD: Not in gnomAD

FamilyName: Family 1

FamilyPresentingHPOs: HP:0000685

FamilyNotHPOs:

CountryOrigin: Pakistan

Ethnicity: Pakistani

Race: Asian

FamilyPreviousTesting:

FamilyMethod1: WES

FamilyMethod2:

FamilyGenotypingMethod: Whole exome sequencing identified 27 regions of homozygosity for Family 1, specifically from WES of the proband IV:3 (Supplemental Table 3).

Affected: 2

Unaffected: 1

Segregations: 1

Consanguineous: yes

PublishedLOD: n/a The minimum requirement for segregation inclusion is not met according to the ClinGen SOP version 6.

eLOD: n/a

AddSegregationInfo:

ProbandLabel: Family 1-IV:3, female

Variant: NM_033068.2(ACP4):c.746C>T (p.Pro249Leu)

Homozygous

ClinVar: 375694

gnomAD: n/a

FamilyAddInfo: WES identified 27 regions of homozygosity for Family 1 (Supplemental Table 3).

Variant deposited into the Leeds AI repository in LOVD, variant #0000000186.

FamilyPMIDs:

CasePresentingHPOs: Hypermineralization of dentine

CaseNOTHPOS: HP:0010299

CasePreviousTesting: n/a

CaseGenotypingMethod: WES identified 27 regions of homozygosity in which 2 genes, other than ACPT were flagged. These 2 genes/ variants are ZNF534:c.118A>C(p.N40H) (gnomAD AF= 0.00025 62 hets, 1 homo) and TCOF1:c.431C>T(p.T144I) (gnomAD AF= 8.12E-4, 2 hets, no homozygous; Gene Associated with Treacher collins syndrome). These variants segregated with disease along with the ACPT variation.

VariantEvidence: n/a

Case#: Consequence 30 Table 1 in Data Supplement (2 cases)

DiseaseAssertion: HCM

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Cardiac magnetic resonance imaging, BSA, NYHA functional class, obstructive HCM, atrial fibrillation, coronary artery disease, NSVT, Syncope, SCD family hitory, wall thickness

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Additional oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing for MYBPC3, TMP1, TNNC1, TNNI2, TNNI3, TNNT2, ACTC1, MYL3

CaseGenotypingMethod: oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing

Variant: NM_000257.4(MYH7):c.1988G>A (p.Arg663His)

ClinVar: 42875 https://www.ncbi.nlm.nih.gov/clinvar/variation/42875/

CAID: n/a

gnomAD: 0.00003097 European (non-Finnish) https://gnomad.broadinstitute.org/variant/14-23896042-C-T

Case#: Consequence 11 Table 1 in Data Supplement (4 cases)

DiseaseAssertion: HCM

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Cardiac magnetic resonance imaging, BSA, NYHA functional class, obstructive HCM, atrial fibrillation, coronary artery disease, NSVT, Syncope, SCD family hitory, wall thickness

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Additional oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing for MYBPC3, TMP1, TNNC1, TNNI2, TNNI3, TNNT2, ACTC1, MYL3

CaseGenotypingMethod: oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing

Variant: NM_000257.4(MYH7):c.2779G>A (p.Glu927Lys)

ClinVar: 42932 https://www.ncbi.nlm.nih.gov/clinvar/variation/42932/

CAID: n/a

gnomAD: absent

Case# Arno P2, German, Female

CasePresentingHPOs HP:0007675, HP:0000486, HP:0007663

CaseNotHPOs HP:0031605

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod Sanger of RBP3 exons

Variant NM_002900.2:c.3454G>T

CAID CA376677245

CaseAddInfo nonsense variant

Case: Family C Proband CII-2, male, Arabic, Israeli, 32yo at report

CasePresentingHPOs: HP:0000953, HP:0030053, HP:0000998, HP:0008064, HP:0001433, HP:0001634, HP:0001935, HP:0033211, HP:0003565, HP:0000027, HP:0100324, HP:0002716, HP:0100727, HP:0001084

CasePresentingHPOsFreeText: scrotal masses, Testicular ultrasound examination done in patient C2 revealed echogenic thickening of both the spermatic cords and the scrotal sac, normal-sized testes with a few microcalcifications; extreme infiltration of the subcutis in the lower abdominal wall and thighs was noted in patient C2 by computed tomography scan; nonspecific inflammatory infiltrates in the portal spaces on liver biopsy; nonspecific pathological deviations on bone marrow biopsy

CaseNOTHPOs: HP:0000054, HP:0002619, HP:0000365, HP:0000520, HP:0012385, HP:0007380

CaseNOTHPOSFreeText: dilated scleral vessels

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: 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, heterozygous parents. brother (CII-4) is also genotype/phenotype +

PreviouslyPublished: PMID: 18410979

VariantEvidence: Kang et al. (2010; PMID: 20595384) 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.

Case: Family D Proband DII-2, male, Arabic, Israeli, 33yo at report

CasePresentingHPOs: HP:0000953, HP:0030053, HP:0000998, HP:0008064, HP:0000054, HP:0000771, HP:0001433, HP:0002619, HP:0001684, HP:0001634, HP:0000365, HP:0000520, HP:0007380, HP:0001935, HP:0003565, HP:0008734, HP:0000027, HP:0002716, HP:0100727, HP:0100324

CasePresentingHPOsFreeText: scrotal masses, thickened scrotal sac, retracted penis, nonspecific inflammatory infiltrates in the portal spaces on liver biopsy

CaseNOTHPOs: HP:0012385

CaseNOTHPOSFreeText: Dilated scleral vessels

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: 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, heterozygous parents. brothers (DII-5 and DII-7) are also genotype/phenotype +. brothers (DII-8, DII-9, and DII-11) are het and unaffected. brother DII-10 was affected but deceased so no genotype recorded

PreviouslyPublished: PMID: 18410979

VariantEvidence: Kang et al. (2010; PMID: 20595384) 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.

Case: Alonso-Perez_Patient 1, Male, 46yo, Spanish

DiseaseAssertion: Sandhoff Disease

CasePresentingHPOs: HP:0000007, HP:0002380, HP:0001260, HP:0001324, HP:0003202

CaseHPOFreeText:

CaseNOTHPOs:

CaseNOTHPOFreeText: No signs of cerebellar involvement, cranial nerves appeared normal

CasePreviousTesting: Nerve conduction studies and EMG were performed with normal results from nerve conduction studies but active and chronic denervation revealed by EMG. 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, but whole-body MRI revealed fatty replacement along with areas of healthy muscles in both quadriceps. Muscle biopsy showed neurogenic changes with angulated and atrophic fibers. Results from all previous tests suggested a diagnosis of lower motor neuron disease. 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

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

MONDO: MONDO:0005144 for FALS

Case#6: Smith 2014 FALS A383T, M, 71 y.o. onset, Italy

CasePresentingHPOs: HP:0007354

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

CasePreviousTesting: All FALS were screened for known causative mutations/repeat expansions in SOD1, C9orf72, TARDBP, FUS, PFN1, UBQLN2, OPTN, VCP and ANG and removed from cohort if positive for variant.

CaseMethod1: This case identified through case-control study

CaseGenotypingMethod: Exome sequencing, confirmed with Sanger sequencing.

Variant: NM_006000.3(TUBA4A):c.1147G>A (p.Ala383Thr)

ClinVar: 180186

gnomAD: 2-220115274-C-T; Total overall AF (non-neuro) = 0.000009611; TUBA4A_p.Ala383Thr_gnomAD

CaseAddInfo: This variant found in 1/13023 control samples.

Case8: Female, 65 yrs report

CasePresentingHPOs: HP:0001263, HP:0030051, HP:0003326, HP:0003731, HP:0002540, HP:0003236, HP:0006466, HP:0005830, HP:0012785, HP:0009600, HP:0003798, HP:0031237, HP:0003555, HP:0001761 (Delayed milestones, Tip-toe gait, Myalgia, Quadriceps weakness, Non-ambulatory, Elevated serum creatine phosphokinase, Ankle contracture, Toe contractures, Flexion contracture of finger, Contracture of thumb, Nemaline bodies, Internally nucleated skeletal muscle fibers, Muscle fiber splitting, Pes cavus)

HPOsFreeText: Tendo-achilles release performed, NCPAP from 54 yrs, Jaw contractures, Nuclei clumps, Fiber type grouping, Required non-invasive nocturnal ventilatory support at age 54 years

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Parental testing not performed

CasePreviousTesting: ACTA1 was sequenced and returned negative.

CaseGenotypingMethod: The TPM2 gene was sequenced and variants identified. No other information is provided.

Variant: NM_003289.3:c.14_16delAGA (p.Lys7del)

ClinVar: 140486 https://www.ncbi.nlm.nih.gov/clinvar/variation/140486/

gnomAD: Not in gnomAD

Case1: Female, 45 yrs report

CasePresentingHPOs: HP:0008994, HP:0002015, HP:0003236, HP:0003273, HP:0031237, HP:0003555, HP:0100295, HP:0012548 (Proximal muscle weakness in lower limbs, Dysphagia, Elevated serum creatine phosphokinase, Hip contracture, Internally nucleated skeletal muscle fibers, Fiber splitting, Muscle fiber atrophy, Skeletal muscle fatty infiltration)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband of Family 1, Mother of Case 2, Variant is de novo

CasePreviousTesting: N/A

CaseGenotypingMethod: The TPM2 gene was sequenced and variants identified. No other information is provided.

Variant: NM_003289.3:c.14_16delAGA (p.Lys7del)

ClinVar: 140486 https://www.ncbi.nlm.nih.gov/clinvar/variation/140486/

gnomAD: Not in gnomAD

Case1118: 11 yrs onset, United States, Hispanic

CasePresentingHPOs: HP:0006785, HP:0003236, HP:0001644, HP:0002540 (Limb-girdle muscular dystrophy, Elevated serum creatine kinase, Dilated cardiomyopathy, Inability to walk)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parental testing not performed

CasePreviousTesting: Serum CK levels 3,000 - 4,000 UI/l; Genetic testing also included DSG

CaseGenotypingMethod: DNA was collected from peripheral blood or saliva samples. WES was performed and processed though a pipeline before aligning the reads and analyzing the candidate gene list for any variants using the various inheritance patterns. Screening was performed based on in silico predictors with a liberal threshold to filter variants before PCR amplification and Sanger sequencing confirmed the pathogenic mutations.

Variant: NM_000231.2(SGCG):c.787G>A (p.Glu263Lys)

ClinVar: 2009 https://www.ncbi.nlm.nih.gov/clinvar/variation/2009/

gnomAD: 0.00006193, https://gnomad.broadinstitute.org/variant/13-23898591-G-A

Note: Variant-level evidence found in PMID: 16832103. Immunohistochemistry showed absent γ-sarcoglycan in this proband.

CaseF4:II-1: Male, Italy

CasePresentingHPOs: N/A

CaseAddInfo: Proband for F4

CaseF6:II-1: Male, Italy

CasePresentingHPOs: N/A

CaseAddInfo: Proband for F6

Case: Family B/Prendiville Patient 3, Lebanese-Australian, 11yo at report

CasePresentingHPOs: HP:0000343, HP:0030084, HP:0001953, HP:0100651, HP:0003237, HP:0030166, HP:0003326, HP:0002829, HP:0002315, HP:0002027, HP:0000998, HP:0000520, HP:0001433, HP:0002594, HP:0002171, HP:0100578, HP:0001999, HP:0100534, HP:0001763, HP:0003565

CasePresentingHPOsFreeText: Inflammatory symptoms. Decreased IgM. Onset of hyperpigmentation at 2-3mo; located on upper thigh and scrotum. Right frontal lobe gliosis. Lipoatrophy of lower legs.

CaseNOTHPOs: HP:0004322, HP:0001738, HP:0002926

CaseNOTHPOSFreeText: Autoantibodies to pancreatic islet cells.

CasePreviousTesting: ADAMTS14, C10orf27, CDH23, EIF4EBP2, LRRC2, KIAA1274, NODAL, NPFFR1, PCBD1, PPA1, PRF1, SLC29A3, SGPL1, UNC5B were sequenced since they were positional candidate genes

CaseGenotypingMethod: homozygosity mapping (50K SNP array), candidate gene sequencing

Variant: c.940del (p.Tyr314fs) "c.940delT"

ClinVarID: or CAID: CA351489

gnomAD: This frameshift variant, Tyr314fs, is absent from gnomAD v4.0.0 and occurs in exon 6/6. Downscoring since NMD is not expected to occur.

AddCaseInfo: first-cousin parents

PreviouslyPublished: 17461801

VariantEvidence: Functional in Xenopus oocytes demonstrated transport activity that was approximately one-fourth that of WT SLC29A3. Studies in NIH 3T3 fibroblasts showed mistrafficking of the mutant protein to the ER or Gogli apparatus (Kang et al. 2010; PMID: 20595384).

Case# Postma 2:2, female, 6yo, white

CasePresentingHPOs HP:0004758

CasePreviousTesting no

CaseMethod1 PCR

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

Variant NM_001232.3(CASQ2):c.62delA (p.Glu21Glyfs)

ClinVar 41042 link

VariantEvidence not in this article

CaseAddProband2 Male, African-Caribbean

CasePresentingHPOs HP:0012125 (Prostate cancer)

CaseNotHPOs n/a

CasePreviousTesting Screened nonsense and missense variants in 202 candidate genes comprising ~15.5Mb. Established evidence of linkage of 17q21-22.

Variant NM_006361.5:c.646G>T(p.Gly216Cys)

ClinVar n/a

CAID CA8633934

gnomAD MAF= 0.00006152(African), no homozygotes

CaseAddInfo Affected half-brother with same variant genotyped positive. G216C variant not observed in 110 African-American subjects in Exome Sequencing Project.

CasePMIDs 17120048

CaseAddProband1 Male, African-American

CasePresentingHPOs HP:0012125 (Prostate cancer)

CaseNotHPOs n/a

CasePreviousTesting Screened nonsense and missense variants in 202 candidate genes comprising ~15.5Mb. Established evidence of linkage of 17q21-22.

Variant NM_006361.5:c.685C>G(p.Arg229Gly)

ClinVar n/a

CAID CA400106634

gnomAD MAF= 0.0001148(African), no homozygotes

CaseAddInfo Affected brother with same variant genotyped positive. R229G variant not observed in 110 African-American subjects in Exome Sequencing Project.

CasePMIDs 17120048

Case: Cecconi_Patient#692, female, 65 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.36A>C, p.(Lys12Asn)

ClinVarID: or CAID: 1493383, CA104969015

gnomAD: MAF=0.0001635 in (1/6118 alleles), total allele frequency=0.000003986. No homozygotes. v2.1.1

AddCaseInfo: Pt has LVWT of 22, family history of HCM, LVEF% of 65, and history of hypertension. Pt also has a variant in MYBPC3 (c.1624G>C p.Glu542Gln)

PreviouslyPublished: no

VariantEvidence: none

CURATE AS FAMILY

Case2: Male, Birth onset, Bosnia

CasePresentingHPOs: HP:0008872, HP:0006829, HP:0001270, HP:0010628, HP:0006466, HP:0000486, HP:0012630, HP:0012240 (Feeding difficulties in infancy, Severe muscular hypotonia, Motor delay, Facial muscle weakness, Ankle contracture, Squint, Abnormality of the trabecular meshwork, Increased muscle lipid droplets)

HPOsFreeText: Predominance of Type 1 muscle fibres, Broad z-band

CaseNotHPOs: HP:0002795, HP:0002540, HP:0003798 (Abnormal respiration, Inability to walk, Nemaline bodies)

NotHPOsFreeText: N/A

CaseAddInfo: Affected Mother had myopathic facies and high-arched palate, weak neck flexors, and asymmetric limb involvement, Healthy grandparents and the father did not have any mutations present

CasePreviousTesting: N/A

CaseGenotypingMethod: Genomic DNA and RNA was extracted from blood or lymphoblastoid cell lines. SSCP was used to analyze all 10 exons of TPM2. After locating the mutations, RT-PCR was used to confirm the mutated allele expression and haplotype analysis was performed on the probands and their family.

Variant: NM_003289.3:c.349G>A (p.Glu117Lys)

ClinVar: 12462 https://www.ncbi.nlm.nih.gov/clinvar/variation/12462/

gnomAD: Not in gnomAD

Case# Baskin EK, Female, 47

CasePresentingHPOs HP:0010872, HP:0100660

CasePreviousTesting patients referred to our high-risk hereditary heart disorders clinic for assessment of possible ARVC, as well as DNA-bearing blood or tissue samples sent for clinical ARVC gene-testing from other physicians, clinics or institutions to our CLIA-approved molecular genetics laboratory at the Hospital for Sick Children (listed on www.genetests.org).

CaseMethod1 PCR

CaseGenotypingMethod direct sequence analysis of all exons and flanking intron sequences of DSP (MIM 125647), PKP2 (MIM 602861), DSC2 (MIM 125645), DSG2 (MIM 125671) and TMEM43.

Variant NM_024334.2(TMEM43):c.424G>A (p.Glu142Lys)

ClinVar 46147

gnomAD 0.001121 link

Case# Baskin YH, Male, 12

CasePreviousTesting patients referred to our high-risk hereditary heart disorders clinic for assessment of possible ARVC, as well as DNA-bearing blood or tissue samples sent for clinical ARVC gene-testing from other physicians, clinics or institutions to our CLIA-approved molecular genetics laboratory at the Hospital for Sick Children (listed on www.genetests.org).

CaseMethod1 PCR

CaseGenotypingMethod direct sequence analysis of all exons and flanking intron sequences of DSP (MIM 125647), PKP2 (MIM 602861), DSC2 (MIM 125645), DSG2 (MIM 125671) and TMEM43.

Variant NM_024334.2(TMEM43):c.1111T>C (p.Tyr371His)

ClinVar 46140

gnomAD 0.01076 link

Case: Patient #F061-male, Italy, 2 months old at onset, died at 6 months

CasePresentingHPOs: HP:0002014, HP:0002570, HP:0003270, HP:0001903, HP:0001433, HP:0001508, HP:0008221

CasePresentingHPOsFreeText: Anemia (RBC 3.02 × 106/μL; Hb 7.7 g/dL), increased liver enzymes (AST 86 IU/L—n.v. 10–40; ALT 38 IU/L—n.v. 5–35), hypoproteinemia (4.8 g/dL—n.v. 6.1–7.9). Presence of vacuolated leukocytes. Bone marrow biopsy showed vacuolization in histiocytes suggesting intralysosomal and cytoplasmic accumulation of lipids (foam cells). Adrenal glands seeded with calcific deposits. LAL activity in skin fibroblasts was 1.4 nmol/mg protein/min (n.v. 55.8 ± 15.6 nmol/mg protein/min). Hepatic and adrenal failure at 6 months of age. LAL activity is 2.5% of normal.

CaseNOTHPOs:

CaseNOTHPOSFreeText:

CasePreviousTesting: peripheral blood smear, bone marrow biopsy

CaseGenotypingMethod: LIPA gene exons and exon–intron boundaries were PCR amplified using sets of primers designed according to the LIPA genomic sequence. Putative mutations were confirmed by sequencing duplicate PCR products.

Variant: c.229+1G>A homozygous

ClinVarID: or CAID: CA211323057

gnomAD: This proband is homozygous for a splice site variant, c.229+1G>A in intron 3, which is predicted to cause out-of-frame skipping of exon 3, generating a transcript with a PTC which would rapidly undergo degradation by NMD. The variant is not reported in gnomAD. This proband is scored reduced points due to alternative splicing.

AddCaseInfo: consanguineous parents

PreviouslyPublished: no

VariantEvidence: predictive

Case# Gamundi II:6, female, Spanish

CasePresentingHPOs HP:0007843, HP:0007791, HP:0007675

CasePreviousTesting no

CaseMethod1 PCR

CaseGenotypingMethod scanned cDNA

Variant NM_004698.3(PRPF3):c.1466C>A (p.Ala489Asp)

ClinVar 3354

gnomAD n/a

VariantEvidence n/a

Case# 135, Male, Chinese

CasePresentingHPOs HP:0007737, HP:0007843, HP:0007924, HP:0007675, HP:0000543, HP:0007994

CaseGenotypingMethod Sanger

Variant NM_000087.3(CNGA1):c.472delC(p.L158FfsX3)

ClinVar 225315

gnomAD 0.001378 link

CaseAddInfo homozygous

CaseP840: Female, 11 yrs onset,

CasePresentingHPOs: HP:0002078, HP:0002015, HP:0001152, HP:0000639, HP:0007340, HP:0007210, HP:0002495 (Truncal ataxia, Dysphagia, Saccadic smooth pursuit, Nystagmus, Lower limb muscle weakness, Lower limb amyotrophy, Impaired vibratory sensation)

HPOsFreeText: Wheelchair-bound 25 yrs

CaseNotHPOs: HP:0000648, HP:0000365, HP:0001760, HP:0001639 (Optic atrophy, Hearing impairment, Abnormal foot morphology, Hypertrophic cardiomyopathy)

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CasePreviousTesting: 19.9% fratraxin protein levels

CaseGenotypingMethod: See Group

Variant1: FXN, (GAA)n REPEAT EXPANSION, IVS1

ClinVar: 561195, https://www.ncbi.nlm.nih.gov/clinvar/variation/561195/

gnomAD: Not in gnomAD

Variant2: NM_000144.5:c.101del (p.Pro35HisfsTer?)

CAID: CA193369020, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA193369020

gnomAD: Not in gnomAD

Individual

Case#: 14817

Caseprevioustesting: SSCP Scan

Casemethod1: PCR, Sanger

Variant: NM_000268.3:c.1396C>T (Arg 466X)

CAID: CA021327

CaseAddinfo: de novo

gnomad: no data

Case#: CM (II:3), deceased at age 18 years.

CaseHPOs: HP:0002024, HP:0002013, HP:0002570, HP:0001251, HP:0001260, HP:0002495, HP:0001284 (malabsorption, vomiting, steatorrhea, ataxia, dysarthria, impaired vibratory sensation, absent deep tendon reflexes)

CaseHPOsFreeText: Symptoms as early as 4 months of age. Diagnosed with FHBL at 10 month; treatment with medium chain triglycerides (MCT) led to weight gain and a decrease in steatorrhea. Abnormalities in liver function, micronodular cirrhosis at 30 months, thought to be caused by treatment with MCT, progression to portal hypertension and esophageal varices. Neurologic symptoms stabilized on vitamin E therapy. At age 15, hepatitis A and cholelithiasis. He developed seizures, had a cerebrovascular accident, recurrent massive gastrointestinal hemorrhages, and finally cardiac arrest at the age of 18 (further details in PMID: 4135110).

CasePreviousTesting: No detectable plasma apoB by radial immunodiffusion (PMID: 4135110), Total cholesterol 36 mg/dl, triglyceride 12 mg/dl, no detectable LDL-cholesterol, HDL-cholesterol 36 mg/dl at age 15 years. No genetic testing other than APOB sequencing.

CaseGenotypingMethod: See family method

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;<br /> Variant 2: 0.00002640 (Euro non-Finnish)

CasePMIDs: 4135110

Case1: Female, Austria, 18 yrs report

CasePresentingHPOs: HP:0010628, HP:0001558, HP:0002643, HP:0002015, HP:0040288, HP:0001260, HP:0003690, HP:0009046, HP:0003551, HP:0003798 (Facial weakness, Reduced fetal movement, Neonatal respiratory distress, Swallowing difficulties, Nasogastric tube feeding, Dysarthric speech, Limb weakness, Difficulty running, Difficulty climbing stairs, Nemaline bodies)

HPOsFreeText: 4/5/7 Apgar score

CaseNotHPOs: HP:0002015, HP:0002540, HP:0002650, HP:0002098 (Swallowing difficulties, Non-ambulatory, Scoliosis, Respiratory distress)

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CasePreviousTesting: N/A

CaseGenotypingMethod: Whole exome sequencing of the proband revealed this homozygous LMOD3 mutation.

Variant: NM_198271.4:c.1648C>T (p.Leu550Phe)

ClinVar: 374498 https://www.ncbi.nlm.nih.gov/clinvar/variation/374498/

gnomAD: Not in gnomAD

Case#: KMP 7, male, 36 yrs, East Slovakia

DiseaseAssertion: HCM

FamilyInfo: n/a

CasePresentingHPOs: n/a

CaseHPOFreeText: symptomatic; LVOTO yes; LVEF 60%; ECG; echocardiography;

CaseNotHPOs: n/a

CaseNotHPOFreeText: no ICD

CasePreviousTesting: Additional Sanger sequencing of exons 12, 24, 25 of MYBPC3, exon 12 NEBL, exons 12, 20, 21 of SCN5A, exon 7 of TNNI3, and exon 9 of TNNT2 gene

CaseGenotypingMethod: Sanger sequencing;

Variant: NM_000257.4(MYH7):c.2845G>A (p.Glu949Lys)

ClinVar: 14093 https://www.ncbi.nlm.nih.gov/clinvar/variation/14093/

CAID: n/a

gnomAD: absent

Case: Bottillo Patient 17, Female, 50 yrs at diagnosis

CasePresentingHPOs: copy from group

CasePresentingHPOsFreeText: NYHA functional class 2, maximal wall thickness=14mm, left ventricular mass (at CMRI)=91(mg/m2), LVEF=52%, maximal oxygen uptake=78%, diastolic dysfunction grade=3, QT interval corrected for heart rate=0.4ms, thoracic pains, met ECG hypertrophy criteria, left bundle branch block, heart failure, mild intramyocardial CMRI

CaseNOTHPOs:

CaseNOTHPOSFreeText: family history of HCM or SCD

CasePreviousTesting: copy from group

CaseGenotypingMethod: copy from group

Variant: c.4485-6T>C

ClinVarID: or CAID: CA2573331909

gnomAD: This proband has an intronic missense variant that is not present in gnomAD. Pt also has variants in TNNT2 (p.R84S), RBM20 (p.D20G), CAV3 (p.T78M), and MYPN (p.A135A) which are either not present in or have conflicting interpretations of pathogenicity in ClinVar. This proband is scored reduced points.

AddCaseInfo:

PreviouslyPublished: no

VariantEvidence: Predicted branch-point splice site broken.

Case# Katagiri094, Male, Japanese

CasePresentingHPOs HP:0007987, HP:0007675, HP:0000551, HP:0007737

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod PCR of exons 4-11 of CNGA1

Variant NM_000087.3(CNGA1):c.265delC (p.Leu89Phefs)

ClinVar 225315 link

gnomAD 0.001378 link

Case# Katagiri029, female, Japanese

CasePresentingHPOs HP:0007987, HP:0007675, HP:0000551, HP:0007737

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod PCR of exons 4-11 of CNGA1

Variant NM_000087.3(CNGA1):c.265delC (p.Leu89Phefs)

ClinVar 225315 link

gnomAD 0.001378 link

Case: Malicdan Proband III.4, Iraqi-Jewish, female

CasePresentingHPOs: Short stature (HP:0004322), Impulsivity (HP:0100710), Short attention span (HP:0000736), Motor delay (HP:0001270), Cognitive impairment (HP:0100543) , Nonprogressive cerebellar ataxia (HP:0002470), Dysarthria (HP:0001260), Myoclonus (HP:0001336), Bilateral tonic-clonic seizure with generalized onset (HP:0025190), Horizontal nystagmus (HP:0000666), Oculomotor apraxia (HP:0000657), HP:0000514, HP:0001152, Dysarthria (HP:0001260), Dysmetria (HP:0001310), HP:0002174, HP:0002080, Gait ataxia (HP:0002066), Impaired tandem gait (HP:0031629), HP:0002061, Brisk reflexes (HP:0001348), Cerebellar atrophy (HP:0001272)

CasePresentingHPOsFreeText: oppositional characteristics

CaseNOTHPOs: HP:0003487, HP:0030680

CaseNOTHPOSFreeText: dysmorphic features. Complete blood count, electrolyte levels, CPK, liver and renal function tests, carnitine and acyl-carnitine, copper, ceruloplasmin, thyroid function tests, lactate, pyruvate, ammonia, blood amino acid profile, VLCFA, phytanic acid, homocysteine, isoelectric focusing of transferrin, alpha –FP, quantitative immunoglobulin levels, vitamin E levels, as well as urine for protein and organic acids, were within normal limits.

CasePreviousTesting: copy from family

CaseGenotypingMethod: copy from family

Variant: copy from family

ClinVarID: or CAID: copy from family

gnomAD: absent from gnomAD v4.1.0

AddCaseInfo:

PreviouslyPublished: n/a

VariantEvidence:

Case#: Li Proband, US

DiseaseAssertion: MPS1 (Hurler)

FamilyInfo: n/a

CasePresentingHPOs: deficient IDUA activity in leukocyte, fibroblasts, or cultured trophoblasts. MPS IH defined as "organomegaly, heart disease, severe mental retardation, and death in childhood" but no individual phenotype information provided.

CaseHPOFreeText:

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: n/a

GenotypingMethod: mutation detection using reverse transcriptional polymerase chain reaction (RT-PCR) and genomic PCR sequencing. Polymorphism analyses were performed on controls by restriction enzyme assays of PCR amplicons flanking nine IDUA intragenic single nucleotide polymorphic alleles.

PreviouslyPublished: n/a

Variant: R628X; Q70X (path classification by LD VCEP). Also has Q33H(187G/T) polymorphism

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

Case1: Male, Spain, Birth onset

CasePresentingHPOs: HP:0003722, HP:0001324, HP:0000297, HP:0003701, HP:0001252, HP:0001284, HP:0001283, HP:0002540, HP:0002307, HP:0000218, HP:0011471 (Nemaline bodies, Muscle weakness, Facial hypotonia, Proximal muscle weakness, Muscular hypotonia, Areflexia, Bulbar palsy, Inability to walk, Drooling, High palate, PEG-fed in infancy)

HPOsFreeText: Bimodal communication, Wheelchair dependence, Cephalic support, Sedestation

CaseNotHPOs: HP:0002460, HP:0000602, HP:0001249, HP:0001627, HP:0002093, HP:0002650, HP:0006466, HP:0001382, HP:0003798 (Neck flexor weakness, Distal muscle weakness, Ophthalmoplegia, Intellectual disability, cardiac abnormality, Respiratory insufficiency, Scoliosis, Ankle contracture, Joint hypermobility)

NotHPOsFreeText: Mechanic ventilation

CaseAddInfo: Intermediate variant, Paternity/ maternity was confirmed

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.17779_17780del (p.Tyr5927Hisfs*17)

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

gnomAD: Not in gnomAD

Variant2: NM_001164507.1:c.11086A>C (p.Thr3696Pro)

CAID: CA348785269 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_001271208.2%3Ac.11086A%3EC

gnomAD: Not in gnomAD

CaseII:II-2: Female, 37 years, Turkey

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

HPOsFreeText: -3.95 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, Mother of II:II-3

CasePreviousTesting: Calcium levels (9.8 mg/dL), Decreased serum phosphate levels (2.1 mg/dL; reference 2.7-4.5), Normal serum ALP (111 IU/L; reference 41-120), 25OHD3 levels (10.5 ng/ml), 1,25(OH)2D3 levels (N/A pg/mL), PTH levels (73 ng/L), TPR levels (87), Decreased TmP/GFR levels (1.70; reference 2.2-3.6)

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

Case# F3-II1, female, 23yo report, Greek

CasePresentingHPOs HP:0008947, HP:0003155, HP:0010837, HP:0003124, HP:0003141, HP:0012347, HP:0012358, HP:0001263 (Infantile Hypotonia, Elevated alkaline phosphatase, Low ceruloplasmin, Elevated cholesterol, Elevated LDL-C, Abnormla N-glycosylation, Abnormal O-glycosylation, Psychomotor delay)

HPOsFreeText Elevated amino transferases

CaseNotHPOs n/a

CasePreviousTesting Serum ALT 36–172 U/l [normal range, 0–50 U/l], AST 31–119 U/l [normal range, 0–50 U/l], ALP 132–1,528 U/l [normal range, < 360 U/l], ceruloplasmin 17–24 mg/dl [normal range, 15–60 mg/dl], cholesterol 231–257 mg/dl [normal range, 120–200 mg/dl], LDL-C 161–171 mg/dl [normal range, 50–130 mg/dl], type 2 CDG

CaseMethod1 Sanger

CaseMethod2 n/a

CaseGenotypingMethod Sanger on patient and parents found variant in heterozygous state in both parents

Variant NM_152464.2(TMEM199):c.92G>C (p.Arg31Pro), homozygous

ClinVar 218964

gnomAD 0.00008933(Latino), 0.00004108(Overall), 10 heterozygotes

VariantEvidence n/a

CaseAddInfo nonconsanguineous

CasePMIDs n/a

Case# F2-II2, male, 41yo report

CasePresentingHPOs HP:0003155, HP:0010837, HP:0003124, HP:0001397, HP:0025321, HP:0003141, HP:0012347, HP:0006579, HP:0000023, HP:0003236 (Elevated alkaline phosphatase, Low ceruloplasmin, Elevated cholesterol, Steatosis, Copper accumulation in liver, Elevated LDL-C, Abnormal N-glycosylation, Neonatal jaundice, Inguinal hernia, Elevated CPK)

HPOsFreeText Inguinal hernia and increased CPK (11yo) minimal fibrosis (30yo), elevated amino transferases (11yo)

CaseNotHPOs HP:0200032 ( Kayser-Fleischer rings)

CasePreviousTesting serum ALT 190 U/l [normal range, 0–50 U/l], AST 153 U/l [normal range, 0–50 U/l], and ALP 718 U/l [normal range, < 360 U/l] (11yo), hepatic dry copper weight of 90 μg/g [normal range, <40 μg/g], ceruloplasmin 8.8 mg/dl [normal range, 15–60 mg/dl], cholesterol 204–337 mg/dl [normal range, 120–200 mg/dl], LDL-C 182–226 mg/dl [normal range, 50–130 mg/dl], type 2 CDG.

19067230: Laboratory tests excluded celiac disease, alpha1-antitrypsin deficiency, cystic fibrosis, galactosaemia and hypobetalipoproteinaemia. Liver iron concentration was normal, normal saturation of transferrin and ferriten, negative for hepatotrophic viruses. Serum anithrombin III (57%, normal range 80–120%) and clotting factor XI (42% , normal range 60–140%) were low.

CaseMethod1 WES

CaseMethod2 n/a

CaseGenotypingMethod WES in patient, sequenced father and mother found to be heterozygous for either variant

Variant NM_152464.2(TMEM199):c.[376-1G>A];[40G>C]

ClinVar 427819

gnomAD n/a for both

VariantEvidence Fig 2C, Western blot: reduced TMEM199 expression in patient fibroblasts

CaseAddInfo nonconsanguineous, father had history of hypercholesterolemia and ischemic heart disease.

CasePMIDs 19067230

***Note, this patient shows overlap of several homozygous regions and alterations with PAtient 1. Althgouh they state they are unrelated, it seems evident that they may be distantly related, the Parents of Patient 2 are consanguineous and the Turkish population. Patietn 1 is Turkish, and the parents are not marked as being consanguineous.

Case: Patient 2, female, Turkish

CasePresentingHPOs: 

CaseNOTHPOs:

CasePreviousTesting: 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:

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.

Case: Family 12 Proband, 5yo at onset, 38yo at report

CasePresentingHPOs:

CasePresentingHPOsFreeText: Muscle weakness (hyposthenia), followed by vision problems in the dark (14), BCVA=6/18, 6/7.5, retinitis pigmentosa, nystagmus, infantile appearance, hypertelorism, undeveloped fertile function, constricted visual field

CaseNOTHPOs:

CaseNOTHPOSFreeText:

CasePreviousTesting: negative IRD gene panel analysis

CaseGenotypingMethod: "genome-wide analysis" -exome or genome sequencing

Variant: c.367 C > T p.(Arg123Trp); c.682-7 T > G p.(Gln230); p.(Leu193Phefs27)

ClinVarID: or CAID: CA6828832; CA6828747

gnomAD: 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.

This missense variant, p.Arg123Trp, is present in gnomAD v4.1.0 with a MAF=0.00002665 (2/75052 alleles) in the African/African American population and 0 homozygotes.

AddCaseInfo: only family member noted to be affected, others do not have genotype information available

PreviouslyPublished: n/a

VariantEvidence:

Family Name: Family 6

FamilyPresentingHPOs: HP:0000705

FamilyNotHPOs:

CountryOrigin: Turkey

Ethnicity: Turkish

Race: n/a

FamilyPreviousTesting: candidate gene sequencing, array comparative genomic hybridization, or exome sequencing

FamilyGenotypingMethod: WES

Affected: 2

Unaffected: 3

Segregations: 1

PublishedLOD: n/a

eLOD: 1.0

AddSegregationInfo: non-consanguineous family

ProbandLabel: Family 6: III:1, female, 11 yo

Variant 1: NM_033068.2(ACP4):c.382G>C (p.Ala128Pro)

ClinVar or CAID: 374865, https://www.ncbi.nlm.nih.gov/clinvar/variation/374865/

genomAD: 2.449e-5, http://gnomad.broadinstitute.org/variant/19-51294991-G-C

Variant 2: NM_033068.2(ACP4):c.397G>A (p.Glu133Lys)

ClinVar: 374866, https://www.ncbi.nlm.nih.gov/clinvar/variation/374866/

genomAD: 8.196e-6, http://gnomad.broadinstitute.org/variant/19-51295006-G-A

FamilyAddInfo: parents unaffected

CasePresentingHPOs: HP:0006297, HP:0011077, HP:0000698

CasePresentingHPOTerm: hypoplastic enamel, destructed first molars, mandibular anterior teeth had incisal edges,

CaseNotHPOs: HP:0011073

AddCaseInfo: compound heterozygous mutations

VariantEvidence:

CaseB:III-2: Male, 2 years onset, China

CasePresentingHPOs: HP:0004912, HP:0003109, HP:0003155, HP:0006505, HP:0002753, HP:0002982, HP:0004349, HP:0000944, HP:0011849, HP:0002970, HP:0003170 (Hypophosphatemic rickets, Hyperphosphaturia, Elevated alkaline phosphatase, Abnormality of limb epiphysis morphology, Thin cortices, Tibial bowing, Reduced bone mineral density, Abnormality of the metaphysis, Abnormal bone ossification, Genu varum, Abnormality of the acetabulum)

HPOsFreeText: Fuzzy structures

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is hemizygous for this mutation, Has a mother and grandmother with the same mutation/disease at 141.3 cm and 142.8 cm respectively

CasePreviousTesting: For all probands: Decreased serum phosphorus levels (0.64–0.9 mM; normal range, 1.29–1.94 mM), Increased 24-h urinary phosphorus levels (49.8–68.4 mmol/day; normal range, 12.9–42.0 mmol/day), Elevated blood alkaline phosphatase levels (350–668.7 U/L; normal range, 42–390 U/L), Lower limit of normal serum 1,25-dihydroxyvitamin D3 levels, Normal blood PTH, serum calcium levels and urine calcium/creatinine ratio, Elevated serum FGF23 (>1500 pg/mL; lower than 28 pg/mL in healthy family members)

CaseGenotypingMethod: Peripheral blood from the probands and affected family members was collected and genomic DNA extracted and quantified. Next-generation sequencing was performed on the probands following PCR amplification and the results were examined with the TruSight One Sequencing Panel, with such genes as PHEX, FGF23, SLC34A3, DMP1 and ENPP1. The mutations were then compared to a reference sequence and filtered for pathogenicity. Sanger sequencing was performed on the probands and family members to confirm the detected mutations.

Variant: NM_000444.5:c.433G>T (p.Glu145Ter)

CAID: CA412571205 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000444.5%3Ac.433G%3ET

gnomAD: Not in gnomAD

Case19 Male, Finland

CasePresentingHPOs HP:0000347, HP:0002101, HP:0000238, HP:0001341, HP:0007370, HP:0010664, HP:0002126, HP:0007260

(Micrognathia, Defective lung lobation, Hydrocephalus, Olfactory lobe agenesis, Callosal agenesis, Fused thalami, Polymicrogyria, Type II lissencephaly)

HPOsFreeText Crown-heel body length 49cm, body weight 3864g, brain weight 286g, abnormal larynx/trachea, hydrocephalus/open-book, occipitotemporal hypoplasia, infratentorial hypoplasia, occipitoschisis/keyhole, leptomeningeal heterotopia, neuroepithelial rosettes, absent developed and identifiable mamillary bodies, absent anterior commissure, difficult to identify nucleus dentatus, (Fig6:) markedly narrowed basis pontis with minute corticospinal tract and a larger tg above, dysplastic dentate nucleus with irregular neuronal strands and intermingled matrix-like small cells is seen in the cerebellar hilus

CaseNotHPOs HP:0001161, HP:0001829, HP:0001627, HP:0000157, HP:0007165

(Hand polydactyly, Foot polydactyly, Congenital heart defect, Tongue abnormality, Periventricular neuronal heterotopia)

NotHPOsFreeText Uterus duplex, hydranencephaly/anencephaly, true alobar or semilobar holoprosencephaly

CasePreviousTesting n/a

Variant NM_145014.2(HYLS1):c.632A>G (p.Asp211Gly), homozygous

ClinVar 1143

gnomAD MAF= 0.009594(European(Finnish)), no homozygotes

CaseAddInfo died 1 minute after birth, 40+6wk gestational age

CasePMIDs n/a

Patient: H02

Variant: c.685 + 2_685 + 13del

CAID: CA2580612034

Functional effect: Normal exon inclusion (band A) *, exon 4 skipping (band B), exon 4 + 6 skipping. Observed in blood.

MonDO: MONDO:0032706

Case: 58-year-old male of Greek origin presenting with a progressive cerebellar syndrome starting at the age of 33 years with mild gait imbalance, ataxia and dysarthria. Apart from dyslipidaemia, type 2 diabetes, and chronic diarrhoea presenting at 37 years of age and attributed to irritable bowel syndrome, the rest of the patient’s medical history is unremarkable. Proband has NM_017686.4; c.134delC with mother as carrier.

DiseaseAssertion: Cerebellar ataxia

FamilyInfo: His relatives have reported personality changes with emotional lability, aggressive behaviour and depressive episodes. Family history is negative for neurological disorders. Both parents originated from the same small village but there was no known consanguinity in the family

CasePresentingHPOs: HP:0002141, HP:0002070, HP:0002066, HP:0001260, HP:0003119, HP:0005978, HP:0002028, HP:0000726 (Gait imbalance, Limb Ataxia, Gait Ataxia, Dysarthria, Abnormal circulating lipid concentration, Type II diabetes mellitus, Chronic diarrhea, Dementia)

CasePreviousTesting: Neurological examination at the age of 50, when the proband was first seen, showed severe gait ataxia with mild pyramidal features consisting of brisk reflexes, dysmetria, dysdiadochokinesia, cerebellar dysarthria, jerky pursuit and nystagmus, mild behavioural changes, and disturbances of short-term memory. Follow-up neurological examination at the age of 58, revealed severe gait disturbance, dysmetria, dysdiadochokinesia and brisk deep tendon reflexes with flexor plantar responses, as well as gaze-evoked nystagmus, jerky pursuit, hypermetric saccades, cerebellar dysarthria, and mild sensory loss in the lower limbs (Supplementary Video 1). Scale for the assessment and rating of ataxia (SARA) score at that time was 31/40 and Mini-Mental State Examination (MMSE) score was 24/30. A detailed neuropsychological assessment was performed, revealing widespread deficits in encoding, learning, and consolidating new verbal information. Overall, the patient exhibited prominent deficits in episodic memory, verbal working memory, and executive functions. A brain MRI scan, including susceptibility-weighted imaging (SWI), was performed and revealed marked cerebellar atrophy affecting the hemispheres and more significantly the vermis, as well as mild cortical atrophy, midbrain and pons atrophy. Nerve conduction studies (NCS), electromyography (EMG) and ophthalmological evaluation were all normal. Laboratory testing of alpha-fetoprotein levels, vitamin E, copper, and folic acid were also normal. To exclude the possibility of an underlying autoimmune disease, the patient’s serum was tested for binding to various markers, including a panel of paraneoplastic markers of autoimmunity, GAD, NMDA, AMPA, GABAB, DPPX and VGKC, as well as monkey cerebellum frozen tissue. No binding to any of these markers was detected.

GenotypingMethod: Blood samples from the proband and his mother were collected for whole exome sequencing ans Sanger confirmation. Initial screening for Friedreich’s ataxia, as well as spinocerebellar ataxia (SCA) types 1, 2, 3, 6 and 7 in the proband was negative.

Variant: GDAP2:c.134del, p.(Pro45Leufs*22)

CAID: CA2574039871

gnomAD: Total AF 0.000001866, gnomAD v4.1 (https://gnomad.broadinstitute.org/variant/1-117920223-AG-A?dataset=gnomad_r4)

Case: Zampieri SD2, 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.850C>T (p.R284X) on allele 1

CAID: CA116495

gnomAD: MAF: 0.0002286 South Asian, gnomAD variant ID: 5-74009409-C-T

VariantEvidence: PMID:8162015 previously reported this variant to be associated with the infantile form of SD. A fibroblast line from this patient with the infantile form of the disease was investigated for mutations by single strand conformation polymorphism analysis and direct sequencing of PCR products. A nonsense mutation was found which generated a stop codon at codon 284. The study investigated the steady-state level of mRNA produced by cells containing stop codons using a competitive polymerase chain reaction technique and found that at codon 284, the mRNA levels were 0.8%, as percent of normal per single gene dose.

MultipleGeneVariants: AR, different variant in second allele

GeneName: HEXB

Variant: c.1613+2T>G (p.E538ins4X5) on allele 2

CAID: CA3306214

gnomAD: MAF: 0.000008808, European (non-Finnish), gnomAD ID: 5-74016574-T-G

VariantEvidence: PMID: 8535449 previously reported this variant to be associated with the infantile form of SD. This study found the total Hex activity to be 8% of the normal level, with only 0.5% being hex B which was reported to be insignificant. This intronic mutation affects the 5' donor site of intron 13 and results in insertion of 48 nucleotides which shifts the reading frame and results in the generation of a PTC.

Case# Monnier 3:12, died age 30, male, French

CasePresentingHPOs HP:0001649, HP:0006682, HP:0012416, HP:0001695, HP:0001945

CasePreviousTesting N/A

CaseMethod1 PCR

CaseGenotypingMethod PCR and sequencing gel for CACNL1A3.PCR1 amplimer

Variant NM_000069.2(CACNA1S):c.3257G>A (p.Arg1086His)

ClinVar 17626

gnomAD 0.00002978 link

VariantEvidence N/A

Case# Subject 1, F, 4yo onset, Hispanic

CasePresentingHPOs HP:0002373, HP:0001260, HP:0006957, HP:0002913, HP:0007359, HP:0002104, HP:0003236, HP:0001987, HP:0001943, HP:0002058, HP:0000252, HP:0006801, HP:0003487, HP:0000577, HP:0002376, HP:0003236, HP:0001249, HP:0003201, HP:0000252

HPOcont: Febrile seizures, Dysarthria, loss of ability to walk, Myoglobinuria, Focal autonomic seizures, Apnea, Hyperammonemia, Hypoglycemia, Myopathic facies, Microcephaly, Brisk DTR, Babinski sign, Exotropia, Developmental regression, Elevated CPK, Hypoglycemia, Intellectual Disability, Rhabdomyolysis, Microcephaly

HPOFreeText: Febrile seizure at 1 year of age, developmental regression in the following 3 years with recurrent seizures, losing the ability to ambulate and speak, as well as right focal seizure, apnea, and unresponsiveness triggered by fever. On hospital admission she was noted to have elevated urine myoglobin, elevated creatine phosphokinase, aspartate aminotransferase, alanine aminotransferase, ammonia and hypoglycemia. MRI showed mild diffuse atrophy of the left cerebral hemisphere. "Ophthalmology evaluation showed intermittent exotropia. Echocardiogram and electrocardiogram (ECG) were unremarkable. Hysical examination was relevant for microcephaly (FOC 47.5 cm; <5th percentile for age), myopathic facies with drooling, increased tone in all extremities, and brisk deep tendon reflexes (DTRs) throughout with positive Babinski sign.

CaseNotHPOs HP:0011675

NotHPOcont: Arrhythmia

CasePreviousTesting "urine myoglobin of 94 ng/ml (normal range 10–65 ng/ml), serum creatine phosphokinase (CPK) of 205,000 U/l (normal range 75–230 U/l), elevated aspartate aminotransferase (AST) of 1,618 U/l (normal range 15–50 U/l), alanine aminotransferase (ALT) of 571 U/l (normal range 10–25 U/l), ammonia of 122 μmol/l (normal range 22–48 μmol/l), and hypoglycemia (blood glucose 30 mg/dl; normal range 70–110 mg/dl)."

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, mother tested heterozygous, father unavailable. cSNP data showed no evidence of deletion or uniparental isodisomy of the region.

CasePMIDs n/a

Case# Subject 4, M, 8yo onset, Hispanic

CasePresentingHPOs HP:0001249, HP:0001289, HP:0002066, HP:0009053, HP:0007340, HP:0001987, HP:0002925, HP:0005184, HP:0002058, HP:0002169, HP:0003201, HP:0001250, HP:0003236, HP:0000821, HP:0006801

HPOcont: Intellectual Disability, Confusion, Gait ataxia, Lower limb muscle weakness, Dysarthria, Hyperammonemia, Elevated TSH, Prolonged QTc interval, Myopathic facies, Clonus, Rhabdomyolysis, Seizures, Elevated CPK, Hypothyroidism, Brisk DTR

HPOFreeText: (2 years) uncoordinated gait and intellectual disability. (8 years) disorientation, ataxic gait, weakness in lower extremities, and dysarthria. (12 years) myopathic facies, brisk tendom reflexes, clonus, and impaired gait.

CaseNotHPOs HP:0001943, HP:0002151, HP:0002913

NotHPOcont: Hypoglycemia, Elevated Lactate, Myoglobinuria

CasePreviousTesting "lactate and glucose normal; elevated ammonia(111 μmol/l), elevated CPK (16,674 U/l). Urine was negative for myoglobin. TSH level was increased to 30.8 μIU/ml (range 0.32–5.00 μIU/ml), T3 was 166 ng/dl (range 90–260 ng/dl), and T4 was 5.2 μg/dl (range 6.4–13.3 μg/dl). Urine organic acids were normal."Muscle biopsy showed normal respiratory chain studies. Mitochondrial genome sequencing for common point mutations and deletions were normal."

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 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 nonsanguineous, confirmed heterozygosity of both parents

CasePMIDs n/a

Case#: Greenwood Genetic Center Molecular Diagnostic Laboratory Patient 6

DiseaseAssertion: MPS 1

FamilyInfo:

CasePresentingHPOs:

CaseHPOFreeText: N/A

CaseNotHPOs:

CaseNotHPOFreeText:

PreviouslyPublished: no

Variant: NM_000203.3 c.1728-1G>C (IVS12)/ c.1403-1G>T (IVS9) ‡

ClinVar:

CAID: CA355965306

SupplementalData: ESM 4 contains proband info

Case: Family 2 Kismet Proband, Turkish, male

CasePresentingHPOs: HP:0000407, HP:0002240, HP:0004322, HP:0025289, HP:0033176, HP:0100727

CasePresentingHPOsFreeText: Rapidly growing orbital mass with SHML histopathology. Retropharyngeal lymphadenopathy. Filling of lymph node sinuses with histiocytes, plasma cells and lymphocytes. Histiocytes had a benign appearance, were CD-1a negative but positive for CD68 and S-100.

CaseNOTHPOs:

CaseNOTHPOSFreeText:

CasePreviousTesting: direct sequencing of PRF1 and UNC5B

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

Variant: p.Gly437Arg; p.Phe103X

ClinVarID: or CAID: 565; 30947

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.

The nonsense variant, p.Phe103Ter found in exon 2/6, is present in gnomAD v4.0.0 with a MAF=0.0005201 (3/5768 alleles) in the Middle Eastern population and 0 homozygotes.

AddCaseInfo: 2 affected brothers

PreviouslyPublished: 16118898

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)

MonDO: MONDO:0032706

Case: Patient AW, Belgian female developed mild gait imbalance at age 38 years with progressive decline with clear dementia at age 53 years. She died at age 62 years due to infectious complications. Homozygous for GCAP2:c.1198_1199insG; p.(His400fs*15). The variant and its segregation were confirmed in the proband and her daughter using standard Sanger sequencing methodology.

DiseaseAssertion: Cerebellar ataxia

FamilyInfo: No consanguineous family. Her brother died from brain tumor, her father had epilepsy and died at 84 years old, her mother was alive without ataxia or gait disorder at age 85 years. Daughter is healthy.

CasePresentingHPOs: HP:0002141, HP:0007240, HP:0001348, HP:0033687, HP:0000708, HP:0002061, HP:0002540, HP:0001268, HP:0000741, HP:0000718, HP:0000716, HP:0002546, HP:0002015, HP:0002300, HP:0000726 (Gait imbalance, Progressive gait ataxia, Brisk reflexes, Short term memory impairment, Atypical behavior, Lower limb spasticity, Inability to walk, Mental deterioration, Apathy, Aggressive behavior, Depression, Incomprehensible speech, Dysphagia, Mutism, Dementia

CaseHPOFreeText: Speech problems, jerky eye movements, dysexecutive syndrome, bed ridden

CaseNOTHPOs: HP:0000639 (Nystagmus)

CasePreviousTesting: Brain MRI at age 53 years revealed severe atrophy of the cerebellum, both vermian and hemispheric, mainly of the superior aspect, and also global cerebral atrophy (cortical and central). Levels of alpha-fetoprotein, vitamin E, copper, and folic acid were normal. Screening for trinucleotide repeat expansions was negative for SCAs 1, 2, 3, 6, 7, 8, 10, 12, and 17, and for Friedreich’s ataxia. Post-mortem brain examination revealed cerebellar atrophy in combination with a mild atrophy of the pes pontis. Normal nerve conduction studies. Normal opthalmological evaluation.

GenotypingMethod: Exome sequencing. Sanger sequencing was performed for confirmation of the variants and for segregation analyses using standard techniques. 90 560 single-nucleotide variations and 8961 indels were called. No obvious variants in known ataxia genes were observed. Variants were filtered for variant type, rarirty (MAF <0.5%) and conservation (>0.75, phyloP). Trio-sequencing analysis to detect putativede novo variants was not possible because of the unavailability of paternal DNA for Patient NIJ and parental DNA for Patient AW.

Variant: c.1198_1199insG; p.(His400fs*15) Homozygous

ClinVarID: 624620

CAID: CA30125084

gnomAD: Total AF 0.000004342, gnomAD v4.1. https://gnomad.broadinstitute.org/variant/1-117883536-T-TC?dataset=gnomad_r4

Functional evidence: Drosophila fly GDAP2 model supports a role of GDAP2 in motor behaviour and suggests that cellular stress might be driving the neurodegenerative cascade. Ubiquitous Gdap2 RNAi-1 knockdown results in droopy wings. Gdap2 knockdown does not result in increased levels of apoptotic cell death in central brain upon 18 hours paraquat exposure.

CaseA032-IV-1 male, unknown age, Han Chinese

CasePresentingHPOs HP:0003251, HP:0012868, HP:0012207

(male infertility, sperm tail anomaly, reduced sperm motility)

HPOsFreeText Table S1: Sperm volume: 1.1mL, sperm concentration: 15.5million/mL, progressive motility: 1.5%, motility: 9.5%, normal spermatozoa: 7.0%, absent flagella: 12.0%, short flagella: 55.0%, coiled flagella: 23.0%, angulation: 1.0%, irregular caliber: 2.0%. Semen volume and sperm concentration were normal to the standards.

CaseNotHPOs n/a

CasePreviousTesting Ejaculation disorder, erectile dysfunction, and orchiatrophy not detected. Chromosomal karyotypes were normal (46; XY) and no deletion detected in the human Y chromosome. In addition, primary ciliary dyskinesia-related symptoms of sinusitis, bronchitis, pneumonia, and otitis media were also excluded.

Variant 1. NM_144668.5:c.415C>T(p.Gln139Ter), 2. NM_144668.5:c.1722del(p.Phe574LeufsTer3)

ClinVar 1. n/a, 2. n/a

CAID 1. CA387002758, 2. CA891834513

gnomAD 1. Maximum population minor allele frequency in gnomAD = 0.00005574 (East Asian); no homozygotes, 2. not in gnomAD

CaseAddInfo phase confirmed in parents, in trans in patient

CasePMIDs n/a

Family L has this variant segregating through

Case2: Female, Birth onset

CasePresentingHPOs: HP:0002093, HP:0002938, HP:0002015, HP:0003798, HP:0003200, HP:0003548 (Respiratory insufficiency, Lumbar hyperlordosis, Dysphagia, Nemaline bodies, Ragged-red fibers, Subsarcolemmal accumulations of abnormally shaped mitochondria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Mother of proband

CasePreviousTesting: N/A

CaseGenotypingMethod: See Family

Variant: NM_003289.3:c.397C>T (p.Arg133Trp)

ClinVar: 12463 https://www.ncbi.nlm.nih.gov/clinvar/variation/12463/

gnomAD: Not in gnomAD

Case1: Female, Birth onset

CasePresentingHPOs: HP:0008947, HP:0008872, HP:0002033, HP:0030043, HP:0001349, HP:0001488, HP:0010804, HP:0002650 (Infantile hypotonia, Feeding difficulties in infancy, Poor suck, Hip subluxation, Facial diplegia, Bilateral ptosis, Tented mouth, Scoliosis)

HPOsFreeText:Disorganized myofibrils and thickened Z bands

CaseNotHPOs: HP:0003798 (Nemaline bodies)

NotHPOsFreeText: N/A

CaseAddInfo: Proband of Family 1

CasePreviousTesting: N/A

CaseGenotypingMethod: See Family

Variant: NM_003289.3:c.397C>T (p.Arg133Trp)

ClinVar: 12463 https://www.ncbi.nlm.nih.gov/clinvar/variation/12463/

gnomAD: Not in gnomAD

Case#: Vazna Patient #15, female, Czech Republic or Slovakia, onset in infancy, 10mo at dx, 12yo at report

DiseaseAssertion: MPS1, H/S

FamilyInfo:

CasePresentingHPOs: HP:0008301, HP:0002159, HP:0000280, HP:0000943, HP:0007957, HP:0004322, HP:0000256, HP:0001387, HP:0001263, HP:0001433, HP:0031664, HP:0000023, HP:0000158

CaseHPOFreeText: Deficiency of IDUA activity in leukocytes showed either no or very low residual enzyme activity (no exact amount specified), systolic murmur 3–4/6. After ERT: decreased illness (obstructive bronchitis), decreased excretion of GAGs in the urine, decreased organomegaly, increased mobility

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: n/a

GenotypingMethod: Direct sequencing of PCR products

PreviouslyPublished: n/a

Variant: p.Q70X (pathogenic); p.R628X. Compound heterozygosity was confirmed by analysis of parental samples. Also has p.A8, p.A20, p.Q33H, p.L118

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

Case# Subject 2, male, 8mo report, Hispanic

CasePresentingHPOs HP:0001276, HP:0000341, HP:0000294, HP:0000316, HP:0000286, HP:0000494, HP:0000664, HP:0008589, HP:0005989, HP:0001257 (Hypertonia, Narrow forehead, Low anterior hairline, Hypertelorism, Downslanted palpebral fissures, Epicanthus, Synophrys, Hypoplastic helices, Redundant neck skin, Spasticity)

HPOFreeText: Hypertonic(postnatal), bifrontal narrowing, low anterior hairline, mild hypertelorism, bilateral epicanthal folds, downslanted palpebral fissures, synophrys, mild hypoplastic helices, redundant nuchal skin, and spasticity of all four extremities with upper limbs being more affected than lower limbs (8 months old)

CaseNotHPOs HP:0002194, HP:0001252, HP:0012443, HP:0012372, HP:0000453, HP:0001627, HP:0000077, HP:0002650 (Gross motor delay, Hypotonia, Abnormality of the brain, Abnormal eye morphology, Choanal atresia, Congenital heart defects, Renal anomaly, Scoliosis)

CasePreviousTesting Screen for BRAF, CBL, HRAS, KRAS, MAP2K1, NRAS, PTPN11, RAF1, SCHOC2, and SOS1 was normal.

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES confirmed with sanger in patient and parents

Variant NM_012102.3:c.248dup (p.Ser84ValfsTer4), de novo

ClinVar n/a

CAID CA658820860

gnomAD n/a

VariantEvidence n/a

CaseAddInfo n/a

CasePMIDs n/a

Family#PresentingHPOs HP:0001263, HP:0010864, HP:0002370, HP:0000664, HP:0000675, HP:0000545, HP:0001763, HP:0008763, HP:0000430, HP:0012471, HP:0000331, HP:0000303, HP:0000662, HP:0000529, HP:0011228

Absent or single-word speech, box-shaped face

FamilyNotHPOs

CountryOrigin Pakistani

Ethnicity

Race

Family#PreviousTesting None

Family#Method1

Family#Method2

Family#GenotypingMethod DNA samples from three affected (V-2, VI-2, VI-3) and two unaffected individuals (V-3, V-4), were genotyped using the Affymetrix Genome-Wide Human SNP 6.0 microarray.

homozygosity-by-descent (HBD) or autozygosity mapping and copy number variation (CNV) analysis was performed using dChip software.

direct Sanger sequencing of VPS13B was performed, based on homozygosity mapping results, for all 62 exons and splice junctions of VPS13B.

Potential candidate variants were further validated in Pakistani population controls through Sanger sequencing.

Affected 2

Unaffected 0

Segregations 1

PublishedLOD No

eLOD 0.6

AddSegregationInfo Pedigree in Figure 1. 5 affected and 3 unaffected individuals clinically determined.

ProbandLabel RQMR10_V-2

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

ClinVar

CAID CA4824093

gnomAD 0.00003250 (South Asian)

FamilyAddInfo Complete biochemical testing in affected and unaffected. neurological, psychological, ophthalmological, skeletal, behavioral, dental examinations in affecteds. RQMR10_VI-2 underwent fundoscopic examination.

Case# Tun66275, Female, 20, Tunisia

CasePresentingHPOs HP:0002066, HP:0001260, HP:0001257

CaseNotHPOs HP:0001272

CaseMethod1 Exome

CaseMethod2 Sanger

Variant NM_005186.3:c.1534C>T(p.R512C)

CAID CA6093457

gnomAD 0.000008977

VariantEvidence none

CaseAddInfo in supplement

Case#: 071-2003

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.4825dupA

LegacyVariant:

ClinVar: No

CAID: CA255152

gnomAD:

Case#: 001-1026,...

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%, Inhibitor present

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NA

LegacyVariant:

ClinVar: No

CAID: No

gnomAD:

Case#: 047-1004

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%, Inhibitor present

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant:

LegacyVariant:

ClinVar: No

CAID: No

gnomAD:

Case#: 080-2002

DiseaseAssertion: Hemophilia A, mild

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: 5% < FVIII:C < 40%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.1649G>A

LegacyVariant:

ClinVar: No

CAID: CA255115

gnomAD:

Case#: 048-1002

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%, Inhibitor present

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant:

LegacyVariant:

ClinVar: No

CAID: No

gnomAD:

Case#: 038-2002

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.5687_5690delCT

LegacyVariant:

ClinVar: No

CAID: No

gnomAD:

Case#: 016-2001

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.901C>T

LegacyVariant:

ClinVar: No

CAID: CA414917990

gnomAD:

Case#: 003-2005

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.5275delG

LegacyVariant:

ClinVar: No

CAID: No

gnomAD:

Case#: 071-2007

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.1208A>C

LegacyVariant:

ClinVar: No

CAID: CA414916134

gnomAD:

Case#: 060-2009

DiseaseAssertion: Hemophilia A, mild

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: 5% < FVIII:C < 40%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.1834C>T

LegacyVariant:

ClinVar: No

CAID: CA255129

gnomAD:

Case#: 016-2003

DiseaseAssertion: Hemophilia A, mild

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: 5% < FVIII:C < 40%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.2129G>A

LegacyVariant:

ClinVar: No

CAID: CA414904142

gnomAD:

Case#: 020-1011

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%, Inhibitor present

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant:

LegacyVariant:

ClinVar: No

CAID: No

gnomAD:

Case#: 004-2017

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant:

LegacyVariant:

ClinVar: No

CAID:

gnomAD:

Case#: 091-2004

DiseaseAssertion: Hemophilia A, moderate

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: 1% < FVIII:C < 5%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.5281T>C

LegacyVariant:

ClinVar: No

CAID: CA414911024

gnomAD:

Case#: 038-2025

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.514T>G

LegacyVariant:

ClinVar: No

CAID: CA414919550

gnomAD:

Case#: 016-2005

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.3531_3533delA

LegacyVariant:

ClinVar: No

CAID: No

gnomAD:

Case#: 004-2008

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.4379dupA

LegacyVariant:

ClinVar: No

CAID: CA645292749

gnomAD:

Case#: 035-2021

DiseaseAssertion: Hemophilia A, mild

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: 5% < FVIII:C < 40%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.5954G>A

LegacyVariant:

ClinVar: No

CAID: CA414905715

gnomAD:

Case#: 035-1005

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%, Inhibitor present

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.1271þ1G>C

LegacyVariant:

ClinVar: No

CAID: CA414915615

gnomAD:

Case#: 038-2011

DiseaseAssertion: Hemophilia A, severe

FamilyInfo: NA

ParentalTesting: NA

CasePresentingHPOs: HP:0003125

CaseHPOFreeText: FVIII:C < 1%

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: The 26 exons and their flanking regions of F8 were amplified by PCR using specific primers with a simple modification

Gene: F8

Variant: NM_000132.3:c.5252A>G