Case 16 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

Variant1: NM_015506.2(MMACHC):c.217C > T (p.Arg73Ter)

ClinVar: 203825

CAID: CA312728

gnomAD: 0.00005560 (East Asian)

CaseAddInfo: proband genotype, homozygous, no phenotypic info, sibling (fetus) is a carrier of variant

Case 5 (Level 2)

**CasePreviousTesting: ** same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

Variant1: NM_015506.2(MMACHC):c.626dupT (p.Thr210Aspfs*35)

ClinVar: not in ClinVar

CAID: Not in ClinGen

gnomAD: not in gnomAD

Variant2: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for c.626dupT maternal variant

Case 6 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

Variant1: NM_015506.2(MMACHC):c.658_660delAAG (p.Lys220del)

ClinVar: 95707

CAID: CA223197

gnomAD: 0.0003071 (East Asian)

Variant2: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for both variants

Case2: Female, 3 m at initiation of follow up, European ancestry

HPOsFreeText: NBS C4-acylcarnitine 2.5 umol/L, plasma C4-acylcarnitine 10.00 umol/L, isoC4-acylcarnitine 0.120 umol/g protein, in vitro prob C4-acylcarnitine 0.220 umol/ g protein

CaseAddInfo: no data for urine excretion, unremarkable clinical condition

Case2 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_014384.2(ACAD8):c.289G>A (p.Gly97Arg)

ClinVar: 281037

CAID: CA6372897

gnomAD: 0.0002175 (East Asian)

Variant2: NM_014384.2(ACAD8):c.455T>C (p.Met152Thr)

ClinVar: 5355

CAID: CA117433

gnomAD: 0.0001395 (European Non-Finnish)

CaseAddInfo: compound heterozygous, potential splice-site alteration on ACAD8 at Exon 3 (+3A>G), homozygous for two common ACADS (SCAD-deficient) gene variants (625G>A/625G>A) which has 22% frequency in general population and correlates with increased accumulation of butyrylcarnitine

Patient14: Male, 24yo

CasePresentingHPOs: HP:0011968, HP:0002013, HP:0001944, HP:0001254, HP:0001259, HP:0001987, HP:0001941

(poor feeding, vomiting, dehydration, lethargy, coma, hyperammonemia, acidosis)

HPOsFreeText: intermittent isovaleric acidemia, C5 (DBS) = 4.3 μmol l−1, IVA incorp (%) = 12, IVG in urine mmol permol creatinine = 16594, Ammonium (μmol l−1) = 126, pH = 7.17, Protein intake (g kg−1 per day) = 0.7, treated with carnitine and glycine supplements, PDI/IQ in follow-up = 88

CaseNotHPOs:

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: diagnosed via clinical findings at 1yo, hospitalized outside of detection period

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: c.1-?_c.295+? (Delexons 1–3) no ClinVar or CAID

Variant2: NM_002225.4(IVD):c.1184G>A (p.Arg395Gln) listed in paper as (p.Arg395His)

CAID: CA268781747, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA268781747

ClinVar: 529434, https://www.ncbi.nlm.nih.gov/clinvar/variation/529434/

gnomAD: 0.00001415, http://gnomad.broadinstitute.org/variant/15-40710365-G-A

Patient11: Female, 19yo, sibling to patient 10

CasePresentingHPOs: HP:0011968, HP:0002013, HP:0001944, HP:0001254, HP:0001259

(poor feeding, vomiting, dehydration, lethargy, coma)

HPOsFreeText: intermittent isovaleric acidemia, IVA incorp (%) = 13, IVG in urine mmol permol creatinine = 3488, Ammonium (μmol l−1) = 47 pH = 7.33, Protein intake (g kg−1 per day) = 1.0, treated with carnitine and glycine supplements, PDI/IQ in follow-up = 85, sweaty feet odor

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: Diagnosed via clinical findings at 2yo

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_002225.3(IVD):c.884T>C (p.Leu295Pro)

ClinVar: 555464, https://www.ncbi.nlm.nih.gov/clinvar/variation/555464/

gnomAD: n/a

Variant2: NM_002225.3:c.1211A>G

CAID: CA391724518, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391724518

gnomAD: n/a

Patient13 Male, 9yo

CasePresentingHPOs: HP:0011968, HP:0001254, HP:0001259, HP:0001987

(poor feeding, lethargy, coma, hyperammonemia)

HPOsFreeText: acute isovaleric acidemia, C5 (DBS) = 16.3 μmol l−1, IVA incorp (%) = 5.5, IVG in urine mmol permol creatinine = 3352, Ammonium (μmol l−1) = 606, pH = 7.26, Protein intake (g kg−1 per day) = 0.8, treated with carnitine and glycine supplements, PDI/IQ in follow-up = 87, sweaty feet odor

CaseNotHPOs: HP:0002013, HP:0001944 (vomiting, dehydration)

NotHPOsFreeText:

CaseAddInfo: diagnosed via clinical findings at 20 days old, homozygous

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_002225.3:c.158G>C listed in clinvar as NM_002225.4(IVD):c.149G>C (p.Arg50Pro)

CAID: CA274129, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA274129

ClinVar: 188922, https://www.ncbi.nlm.nih.gov/clinvar/variation/188922/

gnomAD: 0.00001591, http://gnomad.broadinstitute.org/variant/15-40699841-G-C

CaseF1: Male, 6 yrs report, Italy

CasePresentingHPOs: HP:0004923 (Hyperphenylalaninemia)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents were confirmed heterozygous, Splicing variant is predicted to lead to a null protein

CasePreviousTesting: Pre-treatment phenylalanine levels determined soon after birth were above 20 mg / 100 ml, Proband has been under treatment since birth and currently tolerates less than 20 mg Phe/kg bodyweight per day

CaseGenotypingMethod: DNA as isolated from leukocytes and haplotype analysis performed. Enzymatic digestion of PCR-amplified DNA fragments was performed and DGGE analysis of all 13 exons and flanking introns were carried out. The resulting samples containing abberant bands were sequenced and cleaved by MaeI and MaeIII for analysis.

Variant1: NM_000277.2(PAH):c.611A>G (p.Tyr204Cys)

ClinVar: 590 https://www.ncbi.nlm.nih.gov/clinvar/variation/590

gnomAD: 0.0001632, https://gnomad.broadinstitute.org/variant/12-103249009-T-C

Variant2: NM_000277.2(PAH):c.442-2A>C

ClinVar: 120276 https://www.ncbi.nlm.nih.gov/clinvar/variation/120276

gnomAD: Not in gnomAD

CaseKDC23: Male, 38 yrs onset, Korea, Asian

CasePresentingHPOs: HP:0002131, HP:0002321, HP:0001260, HP:0000640, HP:0011477, HP:0100543 (Episodic ataxia, Vertigo, Dysarthria, Gaze-evoked nystagmus, Upbeat nystagmus, Cognitive impairment)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband has no family history of disease

CasePreviousTesting: Negtive response to acetazolamide

CaseGenotypingMethod: Next-generation sequencing was perfomed on all probands with 40 candidate genes and five known EA genes.

Variant: NM_004172.5:c.952A>G (p.Thr318Ala)

CAID: CA3235581, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3235581

gnomAD: 0.002656, https://gnomad.broadinstitute.org/variant/5-36679820-A-G NOTE EXTREMELY HIGH gnomAD FREQUENCY

CaseP1 Male, 4.5yr report, Austrian

CasePresentingHPOs HP:0010818, HP:0010851, HP:0001290, HP:0011343, HP:0007359, HP:0001942, HP:0002376, HP:0001290

(Generalized tonic seizures, EEG with burst suppression, Hypotonia, moderate GDD, focal seizures, Metabolic acidosis, Developmental regression, Hypotonia)

HPOsFreeText born 40wk gestation. (neonatal, pre-treatment) apgar scores at 1min:8, 5min:9, 10min: 10, generalized tonic fits at <1d old and burst suppression EEG. (3d:) introduced pyridoxine therapy, 100mg I/v trial dose/route, complete cessation of seizures, apnoea(3d), hypotonia, sleepiness, initial maintenance daily dose of 10 mg/kg. (infancy/childhood:) hypotonia, moderate IQ delay. (4d:) withdrew from pyridoxine trial then focal seizures recurrenced 3 weeks after(definite PDE). (PMID: 0894227) gestational toxicosis, birth weight 3,260g, myoclonic jerks of both arms with hours of birth.Paroxysms of polyspike-wave-activity on EEG, normal cranial imaging,CSF analysis

CaseNotHPOs n/a

CasePreviousTesting Administration of pyridoxine relieved patient's seizures. CSF pipecolic acid: 3.4(nv<0.15μM), urine AASA: 168 before treatment(nv<1 mmol/mol creatinine). Blood lactate: 4.0mM and CSF lactate: 4.2mM (nv <2.5mM). (PMID:17068770:)post treatment testing: Pipecolic acid in plasma 4.7(nv 0.7-2.6mmol/liter), AASA in plasma 2.6(nv<0.2mmol/liter), urine AASA 17(nv<1mmol/molcreatinine). (PMID: 0894227) CSF analysis, organic acids in urine, amino acids in serum, and VLCFAs were normal. Plasma PA at 1st week 49µmol/L(before treatment)(nv 1-3.2), at 1-6mo 14.3µmol/L, 6-12mo 10.1µmol/L, CSF PA at 0-1yr 3.38µmol/L.

Variant NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), homozygous

ClinVar 17994

gnomAD MAF= 0.0006123(European(Non-Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs 10894227 (Patient 2), 17068770 (Patient 11)

Patient1: Male, 6yo

CasePresentingHPOs:

HPOsFreeText: Blood C5-carnitine (μM) = 18.96, under a protein restricted diet with carnitine and glycine supplementation, normal development

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: 10days old 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_002225.3:c.386A>G (p.Tyr99Cys) listed in paper as (p.His100Arg)

CAID: CA391716511, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391716511

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

Patient5-1: Female, 2.5yo, sibling to patient 5-2

CasePresentingHPOs:

HPOsFreeText: under a protein restricted diet with carnitine and glycine supplementation, normal development

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: 2mo 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

CaseSA2P: Female, 3 months onset, European

CasePresentingHPOs: HP:0001988, HP:0000825, HP:0001987 (Recurrent hypoglycemia, Hyperinsulinemic hypoglycemia, Hyperammonemia)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is confirmed de novo via parental teting and confirmed paternity

CasePreviousTesting: Leucine load test showed leucine sensitivity in some patients; Protein/leucine restriction was effective at reducing symptoms

CaseGenotypingMethod: Genomic DNA was prepared from all patients via peripheral blood leukocytes. The GLUD1 gene exons 1-13 and the flanking intronic regions were PCR-amplified and directly sequenced. All variants were confirmed via restriction enzyme analysis. Additionally, paternity testing was performed by HLA typing and by southern blot analysis of DNA fragments as well as PCR analysis of STRs.

Variant: NM_005271.5(GLUD1):c.965G>A (p.Arg322His)

ClinVar: 16129, https://www.ncbi.nlm.nih.gov/clinvar/variation/16129/

gnomAD: Not in gnomAD

Patient8: Group 2

CasePresentingHPOs: same as group 2

CasePreviousTesting: same as group 2

CaseGenotypingMethod: same as group 2

Variant1: NM_002225.3(IVD):c.941C>T (p.Ala314Val) listed in paper as c.932C>T (p.Ala282Val)

ClinVar: 100060, https://www.ncbi.nlm.nih.gov/clinvar/variation/100060/

gnomAD: 0.0006507, http://gnomad.broadinstitute.org/variant/15-40707653-C-T

Variant2: NM_002225.3:c.262G>T

CAID: CA391745812, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391745812

gnomAD: n/a

Case# 5888, Spanish, 10mo death

Variant NM_000709.3(BCKDHA):c.940C>T (p.Arg314Ter), NM_000709.3(BCKDHA):c.1037G>A (p.Arg346His)

ClinVar 224072(c.940), 93336(c.1037)

gnomAD c.940=0.000008958(European (Non-Finnish)), 0.000004064(Overall)

CaseAddInfo not confirmed in trans

Case# 16243, Spanish, 5yo reported

CasePresentingHPOs HP:0008344, HP:0001315

CasePreviousTesting categorized into classical and variant phenotypes based on BCKD deficiency assessed by measuring the L-[1-14C] leucine decarboxylation rate by intact cells in absence of BCKD kinase inhibitors (Duran, et al., 1978), plasma amino acid levels, and mode of clinical presentation

CaseMethod1 Direct Sequencing

CaseMethod2 PCR

CaseGenotypingMethod direct sequencing of PCR fragments obtained after amplification of the entire coding sequence of BCKDHA, BCKDHB or DBT genes. sequenced both strands (forward and reverse) of corresponding exons and their intronic flanking sequence for confirmation.

Variant NM_000709.3(BCKDHA):c.117delC (p.Arg40Glyfs), NM_000709.3(BCKDHA):c.117dupC (p.Arg40Glnfs)

ClinVar 93342(del), 166741(dup)

gnomAD del=0.0007494(African), 0.0001696(Overall)

CaseAddInfo in trans

CasePMIDs duplication variant in 8037208

Case# P7, 5day onset, Bangladesh

CasePresentingHPOs HP:0002151, HP:0001946, HP:0001942, HP:0001987

CasePreviousTesting Of the negative samples, we include here only those negative for NAGS and CPS1 genes. NAGS testing was done by single-exon amplification and DNA sequencing.24 CPS1 testing was done by RNA sequencing, in most cases using stimulated lymphocytes

CaseGenotypingMethod sequence analysis of coding exons, including flanking intronic regions of CA5A and CA5B, was performed.

Variant NM_001739.1(CA5A):c.721G>A (p.Glu241Lys)

ClinVar 388645

gnomAD 0.002694 (South Asian), 0.0003177 (Overall)

VariantEvidence CA5A variant in Sf9 insect cells exhibited 26.1% of WT enzyme activity (Fig 2d).

CaseAddInfo consanguineous

Case# Patient 6, Female, 8mo diagnosis

Variant NM_000320.2:c.148G>A (p.G23D)

CAID CA2868208

gnomAD 0.001332 (African)

CaseGM01454: Male, 7 years report, Asian, China

CasePresentingHPOs: HP:0003153 (Cystathioninuria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is a homozygote for this variant.

CasePreviousTesting: N/A

CaseGenotypingMethod: Primers were developed and the CTH exons 1-12 and exon-intron boundaries were PCR amplified and sequenced. All sequence variations were verified by restriction enzyme analysis and/or repeat sequencing.

Variant: CTH, 2-BP DEL, 940CT AKA: NM_001902.5:c.784_785del (p.Leu262Thrfs*21)

ClinVar: 2937 https://www.ncbi.nlm.nih.gov/clinvar/variation/2937/

gnomAD: East Asian 1.088e-4, Overall 7.960e-6 https://gnomad.broadinstitute.org/variant/1-70897822-ACT-A

Case14 age/gender unknown, Caucasian, Bosnia

CasePresentingHPOs HP:0001250

(Seizures)

HPOsFreeText seizure onset in neonatal period from minutes after birth until 3 weeks of age. Definite PDE: formal pyridoxine withdrawal had resulted in reoccurrence of seizures that again responded to pyridoxine.

CaseNotHPOs n/a

CasePreviousTesting post treatment testing: Pipecolic acid in plasma 2.8(nv 0.7-2.6µmol/liter), AASA in plasma 0.5(nv<0.2µmol/liter), urine AASA 1.6(nv<1mmol/molcreatinine). Normal urine PA after pyridoxine treatment.

Variant 1. NM_001182.4:c.605G>T (p.Gly202Val ), 2. NM_001182.4:c.1184T>G (p.Val395Gly), compound heterozygous

ClinVar n/a

CAID 1. CA360731073, 2. CA360723766

gnomAD neither in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

Case13 age/gender unknown, Caucasian, Germany

CasePresentingHPOs HP:0001250

(Seizures)

HPOsFreeText seizure onset in neonatal period from minutes after birth until 3 weeks of age. Possible PDE: no trial of pyridoxine withdrawal performed and no antecedent affected.

CaseNotHPOs n/a

CasePreviousTesting pre-treatment testing: Pipecolic acid in plasma 53(nv 1-3.2µmol/liter), PA in urine 410µmol/mmol creati-nine(nv 0.55–24.1), AASA in plasma 14(nv<0.2µmol/liter), urine AASA 342(nv<1mmol/molcreatinine).

Variant NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), homozygous

ClinVar 17994

gnomAD not in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

Case1 age/gender unknown, Caucasian, German

CasePresentingHPOs HP:0001250

(Seizures)

HPOsFreeText seizure onset in neonatal period from minutes after birth until 3 weeks of age. Possible PDE: no trial of pyridoxine withdrawal performed and no antecedent affected

CaseNotHPOs n/a

CasePreviousTesting post treatment testing: Pipecolic acid in plasma 16(nv 0.4-4.9µmol/liter), AASA in plasma 3.9(nv<0.2µmol/liter), urine AASA 62(nv<1mmol/molcreatinine). Normal urine PA after pyridoxine treatment.

Variant 1. NM_001182.4(ALDH7A1):c.902A>T (p.Asn301Ile), 2. NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), compound heterozygous

ClinVar 1. 18001, 2. 17994

gnomAD neither in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

Case12 age/gender unknown, Caucasian, Italy

CasePresentingHPOs HP:0001250

(Seizures)

HPOsFreeText seizure onset in neonatal period from minutes after birth until 3 weeks of age. Definite PDE: formal pyridoxine withdrawal had resulted in reoccurrence of seizures that again responded to pyridoxine.

CaseNotHPOs n/a

CasePreviousTesting post treatment testing: Pipecolic acid in plasma 5.4(nv 0.7-2.6µmol/liter), AASA in plasma 9.6(nv<0.2µmol/liter), urine AASA 24(nv<1mmol/molcreatinine). Normal urine PA after pyridoxine treatment.

Variant NM_001182.4:c.1003C>T (p.Arg335Ter), homozygous

ClinVar n/a

CAID CA126889823

gnomAD MAF= 0.0001307(South Asian), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

CaseAII-5: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 440 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.165del (p.Phe55fs)

ClinVar: 611 https://www.ncbi.nlm.nih.gov/clinvar/variation/611/

gnomAD: 0.00002639, https://gnomad.broadinstitute.org/variant/12-103306571-CA-C?dataset=gnomad_r3

Variant2: NM_000277.3(PAH):c.898G>T (p.Ala300Ser)

ClinVar: 92751 https://www.ncbi.nlm.nih.gov/clinvar/variation/92751/

gnomAD: 0.006318, https://gnomad.broadinstitute.org/variant/12-102851701-C-A?dataset=gnomad_r3

CaseAII-3: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 370 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.165del (p.Phe55fs)

ClinVar: 611 https://www.ncbi.nlm.nih.gov/clinvar/variation/611/

gnomAD: 0.00002639, https://gnomad.broadinstitute.org/variant/12-103306571-CA-C?dataset=gnomad_r3

Variant2: NM_000277.3(PAH):c.898G>T (p.Ala300Ser)

ClinVar: 92751 https://www.ncbi.nlm.nih.gov/clinvar/variation/92751/

gnomAD: 0.006318, https://gnomad.broadinstitute.org/variant/12-102851701-C-A?dataset=gnomad_r3

Patient4: Male, 2.5yo

CasePresentingHPOs: HP:0002033, HP:0001254, HP:0001987, HP:0001873, HP:0002013 (poor sucking, lethargy, hyperammonaemia, thrombocytopenia, vomiting)

HPOsFreeText: acute neonatal IVA, treated with IVA special formula along with sodium benzoate and glycine (benzoate and glycine discontinued after 1yr), elevated isovalerylglycine, C5-carnitine = 17.4 µmol/l, birth weight = 3kg, able to sit at 6mo, walked at 13mo, began to babble at 17mo, did not have bladder/bowel control until 2.5yo, current weight = 14kg, current height = 86.5cm

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: symptom onset at 5do, diagnosis at 30do via clinical presentation, consanguineous family

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_002225.4(IVD):c.863C>T (p.Ala288Val) listed in paper as c.872C>T (p.Ala291Val)

ClinVar: 281076, https://www.ncbi.nlm.nih.gov/clinvar/variation/281076/

gnomAD: n/a

Variant2: NC_000015.9:g.40699940T>C (NM_002225.4(IVD):c.234+14C=)

CAID: CA147572, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NC_000015.9%3Ag.40699940T%3EC

ClinVar: 94053, https://www.ncbi.nlm.nih.gov/clinvar/variation/94053/

gnomAD: 0.6830, https://gnomad.broadinstitute.org/variant/15-40699940-T-C

Patient1: Male, 4yo, Twin A, Family A (fig. 2)

CasePresentingHPOs:

HPOsFreeText: acute neonatal IVA, treated with IVA special formula, elevated isovalerylglycine in urine organic acids, C5-carnitine = 6.15 µmol/l, at 2yo stopped formula and switched to vegetarian diet with L-carnitine supplements, admitted every 3-4mo due to metabolic crisis, at 4yo began formula again along with vegetarian diet and L-carnitine supplements, sat alone at 6mo, walked alone at 1yo, spoke first word at 1yo, unremarkable systemic examination at 4yo

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: diagnosed at 3 days old via NBS (positive family history and 3 sibling deaths), consanguineous family

CasePMIDs: PMID: 24516753

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_002225.4(IVD):c.1184G>A (p.Arg395Gln) listed in paper as c.1193G>A (p.R398Q)

ClinVar: 529434, https://www.ncbi.nlm.nih.gov/clinvar/variation/529434/

gnomAD: n/a

Variant2: NC_000015.9:g.40699940T>C (NM_002225.4(IVD):c.234+14C=)

CAID: CA147572, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NC_000015.9%3Ag.40699940T%3EC

ClinVar: 94053, https://www.ncbi.nlm.nih.gov/clinvar/variation/94053/

gnomAD: 0.6830, https://gnomad.broadinstitute.org/variant/15-40699940-T-C

CaseTS: Male, Poland

CasePresentingHPOs: HP:0000256, HP:0001263, HP:0000729, HP:0001992 (Macrocephaly, Global developmental delay, Autistic behavior, Organic aciduria)

HPOsFreeText: Apgar score of 9

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents are non-consanguineous though grandfathers were from neighboring villages, Older brother is healthy, Proband is confirmed homozygous via parental testing

CasePreviousTesting: Biochemical tests included urinary organic acid analysis, amino acid analysis, transaminases, transferrin isoforms, phosphoribosylaminoimidazole-succinocarboxamide (SAICAr), and D-arabinitol; Urinary organic acids analysis by GC-MS was performed repeatedly and revealed N-acetylated derivatives of methionine, glutamic acid, alanine, and glycine in large amounts, as well as leucine, valine, and isoleucine in smaller amounts with brother and parent analysis being unremarkable

CaseGenotypingMethod: PCR amplification and bidirectional sequencing of all exons and exon-intron boundaries was performed on genomic DNA.

Variant: NM_000666.3(ACY1):c.1057C>T (p.Arg353Cys)

ClinVar: 18110 https://www.ncbi.nlm.nih.gov/clinvar/variation/18110/

gnomAD: 0.004135 (4 homozygotes), https://gnomad.broadinstitute.org/variant/3-52022837-C-T

CaseOS-120_II-1: Female, Birth onset, German/Italian

CasePresentingHPOs: HP:0001992, HP:0011343 (Organic aciduria, Moderate global developmental delay)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Younger brother is unaffected; Proband is confirmed compound heterozygous as mother is heterozygous for R353C but father is unavailable

CasePreviousTesting: GS-MS analysis identified urinary organic acids dominated by N-aceylated AAs, supported by NMR spectroscopy of urine samples with serum samples being negative; Values of excreted AAs are in Table 1; Neuropediatric evaluation performed

CaseGenotypingMethod: Genomic DNA was extracted from blood samples or after EBV transformation of peripheral blood lymphocytes. Exons and exon-intron boundaries were amplified and bidirectionally sequenced.

Variant1: NM_000666.3(ACY1):c.699A>C (p.Glu233Asp)

ClinVar: 18111, https://www.ncbi.nlm.nih.gov/clinvar/variation/18111/

gnomAD: 0.0001846, https://gnomad.broadinstitute.org/variant/3-52021204-A-C

Variant2: NM_000666.3(ACY1):c.1057C>T (p.Arg353Cys)

ClinVar: 18110, https://www.ncbi.nlm.nih.gov/clinvar/variation/18110/

gnomAD: 0.004135 (4 homozygotes), https://gnomad.broadinstitute.org/variant/3-52022837-C-T

Case# F1-2:1, Female, European, 3wk

CasePresentingHPOs HP:0001254, HP:0002789, HP:0001943, HP:0001987, HP:0001950

CasePreviousTesting sequencing and deletion/duplication analysis of known urea cycle defects and primary causes of hyperlactatemia. metabolic analysis of blood (Table 1).

CaseMethod1 Sanger

CaseMethod2 WES

CaseGenotypingMethod Sanger of CA5A

Variant NM_001739.1(CA5A):c.697T>C (p.Ser233Pro)

ClinVar 127087

VariantEvidence COS-7 cells with the p.Ser233Pro substitution showed 20% of the activity of the WT and quickly denatured at body temperature (Figure 1)

CaseAddInfo nonconsanguineous family, WES performed on heterzygous parents and affected siblings.

CaseF-2 male, 14mo onset, Ethnicity: North Indian, Hindu

CasePresentingHPOs HP:0001263, HP:0003571

(Developmental delay, Propionicacidemia)

HPOsFreeText normal plasma amino acids, acylcarnitines 13.9(normal <3.6nmol/mL), normal development by 6.5 years

CaseNotHPOs HP:0001942, HP:0001987

(Metabolic acidosis, Hyperammonemia)

CasePreviousTesting Also screened for variants in PCCA

Variant NM_000532.4(PCCB):c.1210G>A (p.Glu404Lys)

ClinVar 217891

gnomAD MAF= 0.00003266(South Asian), no homozygotes

CaseAddInfo nonconsanguineous, no abnormality in family history noted

CasePMIDs n/a

CaseOS-146_II-1: Male, 5 yrs report, Romani

CasePresentingHPOs: HP:0001992, HP:0000954, HP:0000431, HP:0000316, HP:0040194, HP:0004322, HP:0001250, HP:0010819, HP:0032792, HP:0002121, HP:0000752, HP:0002342 (Organic aciduria, Single transverse palmar crease, Wide nasal bridge, Hypertelorism, Increased head circumference, Short stature, Seizure, Atonic seizure, Tonic seizure, Generalized non-motor (absence) seizure, Hyperactivity, Moderate Intellectual disability)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents are healthy consanguineous cousins, Two cousins and a niece of the mother have epilepsy, Proband is homozygous for this variant

CasePreviousTesting: Routine urine screening for organic acidurias by gas chromatography–mass spectrometry showed markedly increased urinary excretion of several N-acetylated amino acids; Cerebral MRI was normal at the ages of 17 months and 2.5 years

CaseGenotypingMethod: PCR-amplification and bidirectional sequencing of all exons and exon-intron boundaries was performed on genomic DNA.

Variant: NM_000666.3(ACY1):c.1057C>T (p.Arg353Cys)

ClinVar: 18110 https://www.ncbi.nlm.nih.gov/clinvar/variation/18110/

gnomAD: 0.004135 (4 homozygotes), https://gnomad.broadinstitute.org/variant/3-52022837-C-T

Case1: Newborn

CasePresentingHPOs:

HPOFreeText: Identified by NBS and is healthy with normal development.

CaseNotHPOs:

CasePreviousTesting: DBS C5 carnitine 1.2, 2.5, 1.1 umol/L (ref <0.46); plasma alloisoleucine 2.6 umol/L (ref <2.1); urine C5 carnitine 84.4, 58.1, 64.8 umol/mmol creatine (ref <3.0); urine 2-EHA 36, 31, 22 U (ref <5); urine 2-MBG 36.3, 29.3, 35.2 (ref <2.3); urine 2-methylbutyric acid conjugates as R-isomer 45%, 40% (ref 43-56%).

CaseGenotypingMethod: PCR amplification and sequencing of genomic DNA (entire coding region) from patient and available family members.

Variant: 1. NM_001609.3:c.1165A>G (p.Met389Val), 2. NM_001609.3:c.848A>G (p.Tyr283Cys)

CAID: 1. CA5730948; 2. CA5730830

gnomAD: 1. East Asian 0.0005513; 2. East Asian 0.0007068

VariantEvidence:

CaseAddInfo: In trans

CasePMIDs:

Case21 sex unknown, Spain

CasePresentingHPOs HP:0006846, HP:0002540, HP:0001344, HP:0001332

(Acute encephalopathy, Non-ambulatory, Nonverbal, Dystonia)

HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 204(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 143(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 2.

CaseMethod1 SSCP

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A195T variant destroys a BanI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

Variant 1. NM_000159.3:c.583G>A (p.Ala195Thr), 2. NM_000159.3(GCDH):c.356C>T (p.Ser119Leu), compound heterozygous

ClinVar 1. n/a, 2. 288248

CAID 1. CA404318183

gnomAD 1. not in gnomAD, 2. MAF=0.0001984(Ashkenazi Jewish), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case18 sex unknown, Spain

CasePresentingHPOs HP:0002540, HP:0001344, HP:0001332

(Non-ambulatory, Nonverbal, Dystonia)

HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 4097(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 212(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was <0.5.

CaseMethod1 SSCP

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The R402W variant destroys an MspI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

Variant 1. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), 2. NM_000159.3(GCDH):c.1173delG (p.Asn392Metfs), compound heterozygous

ClinVar 1. 2085, 2. 370106

gnomAD 1. MAF=0.0007566(European(Finnish)), no homozygotes, 2. MAF= 0.00005646(Latino), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case1: Female, Mixed, Birth onset

CasePresentingHPOs: HP:0001508, HP:0000252, HP:0002076, HP:0002018, HP:0002013, HP:0011342, HP:0000750, HP:0001270, HP:0007018 (Failure to thrive, Microcephaly, Migraine, Nausea, Emesis, Mild global developmental delay, Delayed speech and language development, Motor delay, Attention deficit hyperactivity disorder)

HPOsFreeText: Seizure-like episodes, Persistent head tilting, Symptoms impreoved over time

CaseNotHPOs: HP:0001252 (Muscular hypotonia)

NotHPOsFreeText: No brain MRI abnormalities

CaseAddInfo: Parents are non-consanguineous

CasePreviousTesting: Born at full term after a pregnancy complicated by maternal hypertension with no postnatal complications; Elevated levels of plasma 2-aminoadipate (37 μmol/L, nl < 4) with elevated 2-ketoadipate (434 mmol/mol creatinine, nl < 2) and 2-hydroxyadipate (28 mmol/mol creatinine, nl < 2) in urine; Electroencephalogram, magnetic resonance imaging, and magnetic resonance angiogram of the brain were unremarkable

CaseGenotypingMethod: 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.

Variant1: NM_018706.6:c.2143C>T (p.Arg715Cys)

ClinVar: 242503 https://www.ncbi.nlm.nih.gov/clinvar/variation/242503/

gnomAD: 0.0002007, https://gnomad.broadinstitute.org/variant/10-12150003-C-T

Variant2: NM_018706.6(DHTKD1):c.2185G>A (p.Gly729Arg)

ClinVar: 39564 https://www.ncbi.nlm.nih.gov/clinvar/variation/39564/

gnomAD: 0.002748, https://gnomad.broadinstitute.org/variant/10-12154929-G-A

Case4 Female, 7yo diagnosis, Korean

CasePresentingHPOs HP:0001083, HP:0001249, HP:0003235

(Ectopia lentis, Intellectual disability, Increased blood methionine)

HPOsFreeText Marfan syndrome, vascular occlusion, increased pre-treatment blood homocysteine and post-treatment total homocysteine, patient treated with low-methionine diet, vitamin B6, folate, vitamin B12, and betaine after diagnosis

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting pretreatment/posttreatment methionine: 24/575 μM(nv 7-47), pretreatment/posttreatment: 34/0 μM(nv 0-5), posttreatment total homocysteine 194 μM(nv 5-15)

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified all 16 coding exons of CBS gene, then direct sequenced

Variant 1. NM_000071.2(CBS):c.1006C>T (p.Arg336Cys), 2. NM_000071.2(CBS):c.1058C>T (p.Thr353Met), compound heterozygous

ClinVar 1. 92423, 2. 131

gnomAD 1. MAF=0.00004417(European(non-Finnish)), no homozygotes, 2. MAF=0.0002916(African), no homozygotes

CaseAddInfo R336C variant was paternally inherited, T353M variant was maternally inherited

CasePMIDs n/a

Case27 6yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0001256, HP:0002616, HP:0006280, HP:0002583

(Lens dislocation, Mild intellectual disability, Aortic root dilation, Chronic pancreatitis, Colitis)

HPOsFreeText Patient diagnosed on the basis of presenting marfanoid features. Patient had chronic pancreatitis requiring TPN and colitis requiring colostomy. Final CT scan of patient looking like multi-infarct dementia. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Patient was not responsive to the treatment, plasma homocysteine levels went unchanged. Patient was given additional oral betaine(3g twice per day) with a low protein diet

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

Variant 1. NM_000071.2:c.684C>A (p.Asn228Lys), 2. IVS11+1G>A, comp het

ClinVar 1. n/a, 2 n/a

CAID 1. CA410600617, 2. not enough info

gnomAD 1. MAF=0.00001759(European(non-Finnish)), no homozygotes, 2. n/a

CaseAddInfo n/a

CasePMIDs n/a

CasePA008 10mo report, Taiwan

CasePresentingHPOs HP:0001987, HP:0001943, HP:0011342, HP:0003571

(Hyperammonemia, Hypoglycemia, mild global developmental delay, propionicacidemia)

HPOsFreeText hyperammonemia and hypoglycemia for a few days after birth. Showed mild developmental delay at 10 months old

CaseNotHPOs n/a

CasePreviousTesting coding regions and flanking areas of PCCA also analyzed with PCR and Sanger

Variant 1. NM_000532.4(PCCB):c.1301C>T (p.Ala434Val), 2. NM_000532.4:c.-4156_183+3713del

ClinVar 1. 554490, 2. n/a

CAID 2. n/a

gnomAD 1. MAF=0.0003510(East Asian), no homozygotes, 2. n/a

CaseAddInfo n/a

CasePMIDs n/a

Case2: European

CasePresentingHPOs:

HPOFreeText: Identified by NBS with elevated C5-carnitine levels. Asymptomatic up to 3 year follow up. Levels of C5-carnitine decreased with time.

CaseNotHPOs:

CasePreviousTesting: Followup C5 carnitine 1.89 nM/ml (ref <0.63). Additional testing was performed on patients identified by NBS: all either had elevation of 2-methylbutyrlglycine in urine (with no intermediates consistent with isovaleric acidemia), or increase in 2-methylbutyrylcarnitine in culture from fibroblasts.

CaseGenotypingMethod: Bidirectional sequence analysis of genomic DNA.

Variant: 1. NM_001609.3(ACADSB):c.443C>T (p.Thr148Ile) 2. NM_001609.3(ACADSB):c.1159G>A (p.Glu387Lys)

ClinVar: 1. 9202 2. 9203

gnomAD: 1. South Asian 0.002678 2. Latino 0.0004797

VariantEvidence: 1. Decreases ACADSB enzymatic activity to 2.8% of wild type in vitro 2. In vitro expression of c.1159G>A in E. coli shows no protein on Western blot, reduced enzymatic activity to 2% and defects in protein folding and stabilit

CaseAddInfo: No info on cis or trans. Also heterozygous for p.R13K polymorphism.

CasePMIDs:

Case4:

CasePresentingHPOs:

HPOFreeText: Identified by NBS with elevated C5-carnitine levels. Asymptomatic up to 3 year follow up. Levels of C5-carnitine decreased with time.

CaseNotHPOs:

CasePreviousTesting: Followup C5 carnitine 2.58 nM/ml (ref <0.63). Additional testing was performed on patients identified by NBS: all either had elevation of 2-methylbutyrlglycine in urine (with no intermediates consistent with isovaleric acidemia), or increase in 2-methylbutyrylcarnitine in culture from fibroblasts.

CaseGenotypingMethod: Bidirectional sequence analysis of genomic DNA.

Variant: NM_001609.3(ACADSB):c.303+1G>A (homozygous)

ClinVar: 203367

gnomAD: Other 0.0005549

VariantEvidence: Canonical splice site variant. Discrupts canonical splicing signal of intron 3.

CaseAddInfo:

CasePMIDs:

CaseII-2: Female, Japanese, 4 years death

CasePresentingHPOs: HP:0001290, HP:0001263, HP:0002453, HP:0004372, HP:0001942, HP:0045011, HP:0002339, HP:0002138, HP:0002795, HP:0007695, HP:0008000, HP:0001635, HP:0001942 (Generalized hypotonia, Developmental delay, Abnormality of the globus pallidus, Lowered consciousness, Metabolic acidosis, Decreased urine bicarbonate concentration, Abnormality of the caudate nucleus, Subarachnoid hemorrhage, Abnormal respiration, Abnormal pupillary light reflex, Decreased corneal reflex, Heart failure, Metabolic acidosis)

HPOsFreeText: Her birth weight was 2714 g, She measured 44 cm (− 2.6 SD) in length, Had an occipitofrontal circumference of 32.5 cm (− 0.5 SD), Could hold her head up at 5 months and roll over at 10 months, Febrile illness at 15 months, Required ventilator support, Absence of brain activity, Auditory brainstem response audiometry showed no response

CaseNotHPOs: HP:0009782, HP:0001250, HP:0001332 (Aplasia/Hypoplasia of the biceps, Seizures, Dystonia)

NotHPOsFreeText:

CaseAddInfo: Parents are nonconsanguineous, Older sister of patient II-2 who is also homozygous for the mutation and has the disorder, Parents are confirmed heterozygous for the mutation

CasePreviousTesting: Lactate and pyruvate levels in arterial blood (16.5 mg/dL and 1.48 mg/dL, respectively; normal range: 5–20 mg/dL and 0.3–0.9 mg/dL, respectively) and cerebrospinal liquor (13.5 mg/dL and 1.12 mg/dL, respectively; normal range: 9.1–18.8 mg/dL and 0.26–1.32 mg/dL, respectively) were almost normal, Arterial blood ketone bodies, pH, pCO2, and base excess were (8700 μmol/L; normal range: < 130 μmol/L), 7.051, 6.7 mm Hg, and − 26.9 mEq/L, respectively, CSF lactate at 1.5 (< 2.0 mmol/L reference)

CaseGenotypingMethod: Whole exome analysis was performed on the parents and the proband. Afterwards, genomic DNA was extracted from peripheral blood leukocytes and targeted sequences were amplified and sequenced. All SNVs and Indels were evaluated and filtered to confirm the mutations. Afterwards, after identifying the exon 4 mutation, a DNA segment was amplified via PCR and sequenced to confirm these findings.

Variant: NM_014362.3:c.287C>A (p.Ala96Asp)

CAID: CA349896230 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_014362.3%3Ac.287C%3EA

gnomAD: Not in gnomAD

Case1: Male, 3 months onset, Pakistan,

CasePresentingHPOs: HP:0002376, HP:0008947, HP:0001336, HP:0002197, HP:0002490, HP:0012240, HP:0002572, HP:0000737, HP:0002360, HP:0002453, HP:0002352, HP:0002283, HP:0001332, HP:0002871, HP:0000648, HP:0000365, HP:0000252 (Developmental regression, Infantile hypotonia, Myoclonic jerks, Generalized seizures, Increased CSF lactate, Increased muscle lipid droplets, Episodic vomiting, Irritability, Sleep disturbance, Abnormality of the globus pallidus, Leukoencephalopathy, Global brain atrophy, Dystonia, Central apnea, Optic atrophy, Hearing loss, Microcephaly)

HPOsFreeText: Born at term weighing 3.2 kg, Loss of smile

CaseNotHPOs: HP:0002151, HP:0003200, HP:0003688, HP:0010663, HP:0006846 (Increased serum lactate, Ragged-red fibres, Cytochrome C oxidase-negative muscle fibers, Abnormality of thalamus morphology, Acute encephalopathy)

NotHPOsFreeText: N/A

CaseAddInfo: Parents were distantly related, Died at 3 years, Has a younger brother with the same variant, Has a family history of neurological/neuromuscular disorders, Variant was confirmed by parental testing

CasePreviousTesting: At 8 months Nissen fundoplication was performed because of persistent vomiting, Mildly elevated CSF lactate at 2.2 mmol/l (reference range <2 mmol/l) at 8 months, with a normal venous blood lactate of 1.7 mmol/l (reference range < 1.8 mmol/l), Complex I at 0.068 (Reference; 0.104-0.268 ratio to citrate synthase activity), Complexes II + III at 0.010 (0.040-0.204 ratio to citrate synthase activity), Complex IV (COX) at 0.010 (0.014-0.034 ratio to citrate synthase activity)

CaseGenotypingMethod: Genomic DNA was extracted from skin fibroblasts. Exons and flanking intronic sequences of HIBCH was sequenced after PCR amplification. Sequence data was compared to the reference sequence and filtered for variants.

Variant: NM_014362.3:c.950G>A (p.Gly317Glu)

ClinVar: 187864 https://www.ncbi.nlm.nih.gov/clinvar/variation/187864/

gnomAD: Not in gnomAD

Case#: KM24, M, 7 months (Dx), Japanese

CasePresentingHPOs: HP:0001945, HP:0001250, HP:0002013, HP:0002014, HP:0001254 (Fever, Seizures,Vomiting, Diarrhea, Lethargy)

HPOsFreeText: Newborn screening for MSUD was negative. Diagnosis of intermittent MSUD was established by blood and urine analysis after an illness.

CaseNotHPOs: HP:0001263 (Global development delay)

CasePreviousTesting: Lymphoblastoid cells from the patient showed reduced decarboxylation activity (~20% of control).

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: cDNAs from the patient were amplified, subcloned and sequenced. Confirmed by restriction enzyme digestion.

Variant: NM_001918.3(DBT):c.1448G>T (p.Ter483Leu) (homozygous)

ClinVar: 11947

gnomAD: Not in gnomAD

VariantEvidence: The variant adds 7 amino acids at the carboxyl terminus of the protein. No functional evidence.

CaseAddInfo: Consanguineous, parents and 2 siblings were heterozygous.

Case: Cecconi_Patient#905, male, 30 yrs old at onset of HCM

CasePresentingHPOs:

CasePresentingHPOsFreeText: In adults, a maximal LV wall thickness (LVWT) ≥15 mm (not provided for this proband); 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. LVEF is not provided. Family history of HCM.

CaseNOTHPOs:

CaseNOTHPOSFreeText: no family history of SCD

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.1655G>A p.(Gly552Asp)

ClinVarID: or CAID: CA401714383

gnomAD: This proband has a missense variant, Gly552Asp. Not present in gnomAD. Proband has a variant in another HCM gene-MYH7.

AddCaseInfo: history of heart transplant, automatic implantable cardioverter defibrillator

PreviouslyPublished: no

VariantEvidence: none

Case: Cecconi_Patient#907, male, 37 yrs old at onset of HCM

CasePresentingHPOs:

CasePresentingHPOsFreeText: In adults, a maximal LV wall thickness (LVWT) ≥15 mm (<15mm for this proband-diagnosis of borderline HCM); 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. LVEF of 60%

CaseNOTHPOs:

CaseNOTHPOSFreeText: family history of HCM

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.432-1G>T

ClinVarID: or CAID: CA401717111

gnomAD: This proband has a splice site variant, c.432-1G>T. MAF=0.00001597 in European (non-Finnish) (2/125212 alleles), total allele frequency=0.000007246. No homozygotes. gnomAD v2.1.1.

AddCaseInfo: history of ECG abnormalities

PreviouslyPublished: no

VariantEvidence: none

genotype phenotype information for probands

Case#: Consequence 13 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.1358G>A (p.Arg453His)

ClinVar: 42838 https://www.ncbi.nlm.nih.gov/clinvar/variation/42838/

CAID: n/a

gnomAD: 0.0000 African https://gnomad.broadinstitute.org/variant/3-49167319-C-T

Case#: Consequence 22 Table 1 in Data Supplement (6 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.2722C>G (p.Leu908Val)

ClinVar: 14097 https://www.ncbi.nlm.nih.gov/clinvar/variation/14097/

CAID: n/a

gnomAD: 0.00006482 European (non-Finnish) https://gnomad.broadinstitute.org/variant/14-23893316-G-C

Case#: Consequence 32 Table 1 in Data Supplement (1 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.788T>C (p.Ile263Thr)

ClinVar: 43106 https://www.ncbi.nlm.nih.gov/clinvar/variation/43106/

CAID: n/a

gnomAD: 0.000008792 European (non-Finnish) https://gnomad.broadinstitute.org/variant/14-23900635-A-G

Case#: Consequence 27 Table 1 in Data Supplement (1 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.2609G>A (p.Arg870His)

ClinVar: 14120 https://www.ncbi.nlm.nih.gov/clinvar/variation/14120/

CAID: n/a

gnomAD: 0.00001549 European (non-Finnish) https://gnomad.broadinstitute.org/variant/14-23894048-C-T

Case#: Consequence 19 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.1491G>T (p.Glu497Asp)

ClinVar: 14124 https://www.ncbi.nlm.nih.gov/clinvar/variation/14124/

CAID: n/a

gnomAD: 0.0001984 Ashkenazi Jewish https://gnomad.broadinstitute.org/variant/14-23897796-C-A

Case#: Consequence 15 Table 1 in Data Supplement (1 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.2167C>T (p.Arg723Cys)

ClinVar: 14095 https://www.ncbi.nlm.nih.gov/clinvar/variation/14095/

CAID: n/a

gnomAD: 0.00003266 South Asian https://gnomad.broadinstitute.org/variant/14-23895023-G-A

Case#: Consequence 10 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.1816G>A (p.Val606Met)

ClinVar: 14091 https://www.ncbi.nlm.nih.gov/clinvar/variation/14091/

CAID: n/a

gnomAD: 0.00001548 European (non-Finnish) https://gnomad.broadinstitute.org/variant/14-23896866-C-T

CaseA009-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: 2.1mL, sperm concentration: 34.5million/mL, progressive motility: 0.2%, motility: 7.7%, normal spermatozoa: 6.5%, absent flagella: 30.0%, short flagella: 41.5%, coiled flagella: 18.5%, angulation: 2.5%, irregular caliber: 1.0%. 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 NM_144668.5:c.799C>T(p.Arg267Ter)

ClinVar n/a

CAID CA6840411

gnomAD Maximum population minor allele frequency in gnomAD = 0.00005903 (East Asian); no homozygotes

CaseAddInfo parents unavailable for testing

CasePMIDs n/a

Case# B12, Male, UK

CasePresentingHPOs HP:0010872

CasePreviousTesting re-sequenicing of genome

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

Variant NM_024334.2(TMEM43):c.934C>T (p.Arg312Trp)

ClinVar 36873

gnomAD 0.03553 link

Case# 39

CasePresentingHPOs HP:0000508, HP:0000601, HP0001290, HP:0000717, HP:0001249 (Ptosis, Hypertelorism, Hypotonia, Autism, Intellectual disability)

HPOFreeText: axonal neuropathy

CaseNotHPOs n/a

NotHPOFreeText: n/a

CasePreviousTesting Screened for Inherited peripheral neuropathy variants, results negative.

CaseMethod1 WES

CaseMethod2 n/a

CaseGenotypingMethod n/a

Variant NM_001163435.2:c.1652T>C (p.L551P)

ClinVar n/a

CAID CA357822100

gnomAD n/a

VariantEvidence n/a

CaseAddInfo positive family history, MAF >1% in reported ExAC findings

CasePMIDs n/a

CaseF10:III-1: Italy

CasePresentingHPOs: N/A

CaseAddInfo: Proband for F10

CaseF5:II-2: Male, Italy

CasePresentingHPOs: HP:0001631, HP:0001634 (Atrial septal defect, Mitral valve prolapse)

CaseAddInfo: Proband for F5, 2 other family members share MVP and 5 share ASD

additional phenotype info for this proband scored in PMID: 19336477

Proband KH6 was 6yo at report, has the Hurler/Scheie phenotype, and has this variant but a second variant does not appear to have been detected.

Proband KH3 was 13yo at report, has the Hurler phenotype, and has this variant in compound heterozygosity with second missense variant on exon 3, but that variant is not provided.

Case# Subject 4, female, 17yo report, European

CasePresentingHPOs HP:0001252, HP:0001263, HP:0010864, HP:0007033, HP:0000750 (Hypotonia, Global developmental delay, Severe intellectual disability, Cerebellar dysplasia, Speech delay

HPOFreeText: hemispheric cerebellar dysplasia with abnormal lobule and fissure orientation in the inferior hemispheres(5 years); severe intellectual disability/speech delay(13 years)

CaseNotHPOs HP:0011968, HP:0012372, HP:0000453, HP:0001627, HP:0000077, HP:0002650 (Poor feeding, Abnormal eye morphology, Choanal atresia, Congenital heart defects, Renal anomaly, Scoliosis)

CasePreviousTesting n/a

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES confirmed with sanger in patient and parents

Variant NM_012102.3:c.4303C>T(p.His1435Tyr), de novo

ClinVar n/a

CAID CA338168785

gnomAD n/a

VariantEvidence n/a

CaseAddInfo n/a

CasePMIDs n/a

Case# Subject 3, male, 21yo report, European

CasePresentingHPOs HP:0030842, HP:0001631, HP:0001263, HP:0001249, HP:0001252, HP:0001251, HP:0000722, HP:0002474, HP:0001488, HP:0000565, HP:0010535, HP:0002650, HP:0002079, HP:0002363, HP:0000961, HP:0000733, HP:0002058, HP:0000490, HP:0000218, HP:0001222, HP:0001795 (Choking episodes, Atrial septal defect, Developmental delay, Intellectual disability, Hypotonia, Ataxia, OCD, Expressive language deficit, Bilateral ptosis, Esotropia, Sleep apnea, Scoliosis, Thin corpus callosum, Cyanosis, Stereotypy, Myopathic facies, Deep set eyes, High-arched palate, Spatulate thumbs, Hyperconvex nails

HPOFreeText: Choking episodes and atrial septal defect in infancy; recurrent cyanosis, mild hypotonia, ataxia, scoliosis, bilateral ptosis, esotropia, developmental delay and OCD (7 years); sleep apnea, throbbing headaches, thin corpus callosum, flattening of braistem, thin rim of sella, chronic right temporal membrane perforation and mild left sensorineural hearing loss(8 years); repetitive hand movements, limited speech, elongated/myopathic face/midfacial retraction, bilateral ptosis, deep-set eyes, high arched palate, spatulate thumbs and finger/toenail hyperconvexity(19 years).

CaseNotHPOs HP:0012372, HP:0000453, , HP:0000077 (Abnormal eye morphology, Choanal atresia, Renal anomaly)

CasePreviousTesting Reduced succinate cytochrome c reductaseactivity (19%), NADH and NADH cytochrome c activity were 40% of control.

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES confirmed with sanger in patient and parents

Variant NM_012102.3:c.4300T>C(p.Ser1434Pro), de novo

ClinVar n/a

CAID CA338168793

gnomAD n/a

VariantEvidence n/a

CaseAddInfo n/a

CasePMIDs n/a

Case: Bolino Proband 2 (Case 25 in PMID:10677858), female, reported at 5yo, symptom onset at 2yo

CasePresentingHPOs: HP:0001270, HP:0030319, HP:0008959, HP:0008994, HP:0009053, HP:0002522, HP:0003474, HP:0000218, HP:0001761, HP:0003447, HP:0012447 (motor delay, facial weakeness, distal upper limb muscle weakness, proximal lower limb muscle weakness, distal lower limb muscle weakness, lower limb areflexia, sensory impairment, high palate, pes cavus, axonal loss, abnormal myelination)

HPOsFreeText: walked at 17mo, tendon reflexes absent in lower limbs but present in upper limbs, sensory action potential absent in all nerves tested , CMAPs had small amplitude and temporal dispersion in upper limbs and were not detectable in lower limbs, EMG of tibialis anterior showed neurogenic features, presence of myelin loops and excessive outfolding, thick and irregular myelin sheaths

NotHPOs: HP:0003383 (onion bulb formation)

CountryOrigin: Saudi Arabia

PreviouslyPublished: 10677858

FamilyInfo: consanguineous family

GenotypingMethod: RT-PCR of RNA from patient lymphoblastoid cell line, available family members analyzed and segregation of variant with disease confirmed in pedigree

Variant 1: NM_003912.1:c.1480_1593del

ClinVar: 637472, https://www.ncbi.nlm.nih.gov/clinvar/variation/637472/

gnomAD: absent

Variant 2: NM_016156.5(MTMR2):c.826G>T (p.Glu276Ter)

ClinVar: 6233, https://www.ncbi.nlm.nih.gov/clinvar/variation/6233/

gnomAD: absent

ScoringNotes: both variants stated to be homozygous on same allele, assume variants in trans

Case: Bolino Proband 1 (proband 1945), male, reported at 4yo, symptom onset at 42mo

CasePresentingHPOs: HP:0001349, HP:0003701, HP:0001284, HP:0001288, HP:0003474, HP:0003693, HP:0003722, HP:0003391, HP:0001761, HP:0003383, HP:0012447 (bilateral facial weakness, proximal muscle weakness, areflexia, abnormal gait, sensory impairment, distal limb muscle atrophy, neck flexor weakness, Gower's sign, pes cavus, onion bulb formation, abnormal myelination)

HPOsFreeText: walked at 14mo, eyes reported to be normal, gait - bilateral steppage, pes equinovarus deformity of both feet, frequent falling, had normal early motor milestones, bilateral pes cavus with retraction of Achille's tendon, intellectually normal. Laboratory testing normal: full blood count, fasting blood glucose, serum electrolytes, creatine kinase, lactic acid, urinary organic acids, serum and urine carnitine, EEG, ECG, and liver echography, segmental demyelination in 92% of fibers, redundant loops of myelin sheath irregularly arrayed near axon, muscle biopsy of rectus femoris showed atrophic and angulated fibers in clusters and large type grouping, lipid accumulation

Median nerve conduction studies: compound motor action potential = 4.6uV, distal motor latency = 7.8msec, sensory action potential = 3.3uV, motor nerve conduction velocity = 17msec, sensory nerve conduction velocity = 18msec

Peroneal nerve conduction studies: compound motor action potential = 0.21uV, distal motor latency = 7.8msec, motor nerve conduction velocity = 14

Sural nerve conduction studies: sensory action potential = no response, sensory nerve conduction velocity = no response

CountryOrigin: Italy

FamilyInfo: consanguineous family, parents reported to be normal at clinical and electrophysiological exams

PreviouslyPublished: PMID:10673338, PMID:8817346, PMID: 8628474, PMID: 8017168

GenotypingMethod: RT-PCR of RNA from patient lymphoblastoid cell line, available family members analyzed and segregation of variant with disease confirmed in pedigree - PMID:8817346 - homozygosity mapping and haplotype sharing through microsatellite and linkage analysis

Variant: NM_016156.5(MTMR2):c.1276C>T (p.Gln426Ter) homozygous

ClinVar: 6231, https://www.ncbi.nlm.nih.gov/clinvar/variation/6231/

gnomAD: 0.000007085, https://gnomad.broadinstitute.org/variant/11-95578227-G-A

Case#: Patients 2 (male), 4 (male), and 5 (female). Kuwait. Onset between 1wk-3mo.

DiseaseAssertion: MPS I Hurler

FamilyInfo: Patients are from the same extended pedigree (family in Kuwait)

CasePresentingHPOs: α-L-iduronidase activity= 3.73 umol/g/hr (normal range 10–50) after commencing ERT. ERT for 9 wks. Congestive cardiac failure. LV fractional shortening=10%. LV ejection fraction=29%. HSCT at 17mo. α-L-iduronidase activity= 11.24 umol/g/hr (normal range 10–50) at follow up. GAG= 31.3 after transplant. Enzyme replacement therapy results in a significant reduction in urine GAGs (either total or heparan sulfate)

CaseHPOFreeText:

CaseNotHPOs:

CaseNotHPOFreeText:

GenotypingMethod:

PreviouslyPublished: n/a

Variant: Arg628Ter homozygous. Proband was homozygous for this variant. 0 points (maximum for homozygous cases has already been reached)

ClinVar: 550421

CAID: CA2802462

SupplementalData: n/a

Case# A13, male, 7

CasePresentingHPOs HP:0003124 Hypercholesterolemia

CasePreviousTesting The APOB domains, including amino acids 2955–3092 and amino acids 3303–3492, were analysed in the 600 molecularly undefined ADH cases by direct Sanger sequencing

CaseMethod1 as mentioned

CaseMethod2 as mentioned

CaseGenotypingMethod Exome sequencing

Variant NM_000384.2(APOB):c.9175C>T (p.Arg3059Cys)

ClinVar 69508

gnomAD 0.00003249 link

VariantEvidence Deficient LDL uptake (fig. 2)

Case#: KMP 8, female, 60 yrs, East Slovakia

DiseaseAssertion: HCM

FamilyInfo: n/a

CasePresentingHPOs: n/a

CaseHPOFreeText: symptomatic, LVOTO yes; LVEF 55-60%; 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

MultipleGeneVariants:

(1) SCN5A Variant:

Variant: NM_198056.2(SCN5A):c.3784G>A (p.Gly1262Ser)

ClinVar: 9399 https://www.ncbi.nlm.nih.gov/clinvar/variation/9399/

CAID: n/a

gnomAD: 0.0001307 South Asian https://gnomad.broadinstitute.org/variant/3-38607956-C-T

Case#: KMP 4, female, 69 yrs, East Slovakia

DiseaseAssertion: HCM

FamilyInfo: n/a

CasePresentingHPOs: n/a

CaseHPOFreeText: symptomatic; LVEF 60%; NYHA II.-III.; ECG; echocardiography;

CaseNotHPOs: n/a

CaseNotHPOFreeText: no LVOTO; 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#: KMP 22, male, 21 yrs, East Slovakia

DiseaseAssertion: HCM

FamilyInfo: n/a

CasePresentingHPOs: n/a

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

CaseNotHPOs: n/a

CaseNotHPOFreeText: no LVOTO

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#: KMP 18, female, 71 yrs, East Slovakia

DiseaseAssertion: HCM

FamilyInfo: n/a

CasePresentingHPOs: n/a

CaseHPOFreeText: symptomatic; LVEF 60%; NYHA I.-II.; ECG; echocardiography;

CaseNotHPOs: n/a

CaseNotHPOFreeText: no LVOTO; 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# Subject 8, male, 10yo, European

CasePresentingHPOs HP:0011968, HP:0002033, HP:0002360, HP:0002020, HP:0011848, HP:0000483, HP:0000349, HP:0000494, HP:0011230, HP:0000347, HP:0000691, HP:0003186, HP:0200055, HP:0004209, HP:0010862, HP:0000750, HP:0000729, HP:0007018, (Poor feeding, Poor suck, Difficulty sleeping, Gastroesophageal reflux, Abnormal colic, Astigmatism, Widow's peak, Downslanted palpebral fissures, Laterally extended eyebrow, Micrognathia, Microdontia, Small hands, 5th finger clinodactyly, Fine motor delay, Speech delay, Autisim spectrum disorder, ADHD

HPOFreeText: Poor latch and suck, narrow dental arches, small lower arch teeth and other phenotypes reported postnatally. Fine motor delay, speech delay, autistic spectrum, and ADHD reported at 11 months. Brain MRI normal.

CaseNotHPOs HP:0001250, HP:0001252, HP:0000708, HP:0001285, HP:0001273, HP:0006808, HP:0002334, HP:0002119, HP:0007361, HP:0025100, HP:0030301, HP:0012448, HP:0000589, HP:0000648, HP:0000568, HP:0000659, HP:0000525, HP:0000581, HP:0000407, HP:0000453, HP:0410030, HP:0001629, HP:0001655, HP:0001643, HP:0010772, HP:0002247, HP:0001734, HP:0002021, HP:0000076, HP:0000107, HP:0000047, HP:0000028, HP:0001159, HP:0001385, HP:0002650, HP:0002938, HP:0001511, HP:0000098, HP:0004322, HP:0000256, HP:0000252, HP:0011328, HP:0002007, HP:0000325, HP:0000601, HP:0000316, HP:0000582, HP:0045025, HP:0000286, HP:0000490, HP:0000598, HP:0004467, HP:0000414, HP:0000463, HP:0000319, HP:0012471, HP:0000160, HP:0000221, HP:0000187, HP:0000218, HP:0002557, HP:0011297, HP:0001792, HP:0010490, HP:0004532, HP:0000957, (Seizures, Hypotonia, Behavioral problems, Spastic quadriparesis, Abnormal Corpus Callosum, Cerebral hypomyelination, Abnormality of cerebellar vermis, Ventriculomegaly, Abnormality of the pons, Abnormal morphology of the hippocampus, Abnormality of the anterior commissure, Delayed myelination, Coloboma, Optic atrophy, Microphthalmia, Peter's anomaly, Iris anomalies, Blepharophimosis, Sensorineural hearing loss, Choanal atresia, Cleft lip, Ventricular septal defect, Patent foramen ovale, Patent ductus arteriosus, Anomalous pulmonary venous return, Duodenal atresia, Annular pancreas, Pyloric stenosis, Vesicoureteral reflux, Cystic kidney, Hypospadias, Cryptorchidism, Syndactyly, Hip dysplasia, Scoliosis, Lumbar lordosis, Intrauterine growth retardation, Tall stature, Short stature, Macrocephaly, Microcephaly, Fontanel abnormality, Frontal bossing, Triangular face, Hypotelorism, Hypertelorism, Upslanting palpebral fissures, Small palpebral fissures, Epicanthal folds, Deeply set eyes, Abnormal ears, Preauricular pits, Bulbous nose, Anteverted nares, Flat philtrum, Full lips, Small mouth, Furrowed tongue, Broad alveolar ridges, High-arched palate, Small nipples, Digital Anomalies, Nail hypoplasia, Abnormal palmar creases, Sacral hypertrichosis, Café Au Lait spots)

CasePreviousTesting n/a

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES confirmed with sanger

Variant NM_012102.3(RERE):c.1104delA, (p.Leu369Cysfs∗16)

CAID CA658820843

gnomAD n/a

VariantEvidence n/a

CaseAddInfo No paternal DNA to prove de novo status, variant suspected to trigger NMD

CasePMIDs n/a

Case# Subject 7, male, 11yo, Dutch

CasePresentingHPOs HP:0410030, HP:0001263, HP:0001252, HP:0000494, HP:0000954, HP:0007018, HP:0001256, HP:0001273, HP:0030301, HP:0006808, HP:0011968, HP:0004322, HP:0000252 (Cleft lip, Developmental delay, Hypotonia, Down-slanting palpebral fissures, Single palmar crease, ADHD, Mild intellectual disability, Abnormal Corpus Callosum, Abnormality of the anterior commissure, Cerebral hypomyelination, Poor feeding, Short Stature, Microcephaly)

HPOFreeText: Phenotypes recorded postnatally. Brain MRI at 7 years showed phenotypes including small anterior commissure and blunting of rostrum.

CaseNotHPOs HP:0001250, HP:0000708, HP:0001285, HP:0002334, HP:0002119, HP:0007361, HP:0025100, HP:0012448, HP:0000589, HP:0000648, HP:0000568, HP:0000659, HP:0000525, HP:0000581, HP:0000407, HP:0000453, HP:0001629, HP:0001655, HP:0001643, HP:0010772, HP:0002020, HP:0002247, HP:0001734, HP:0002021, HP:0000076, HP:0000107, HP:0000047, HP:0000028, HP:0001159, HP:0001385, HP:0002650, HP:0002938, HP:0001511, HP:0000098, HP:0000256, HP:0011328, HP:0002007, HP:0000325, HP:0000534, HP:0000601, HP:0000316, HP:0000582, HP:0045025, HP:0000286, HP:0000490, HP:0000598, HP:0004467, HP:0000414, HP:0000463, HP:0000319, HP:0012471, HP:0000160, HP:0000221, HP:0000164, HP:0000187, HP:0000218, HP:0000347, HP:0002557, HP:0003186, HP:0200055, HP:0004209, HP:0011297, HP:0001792, HP:0000349, HP:0004532, HP:0000957 (Seizures, Behavioral problems, Spastic quadriparesis, Abnormality of cerebellar vermis, Ventriculomegaly, Abnormality of the pons, Abnormal morphology of the hippocampus, Delayed myelination, Coloboma, Optic atrophy, Microphthalmia, Peter's anomaly, Iris anomalies, Blepharophimosis, Sensorineural hearing loss, Choanal atresia, Ventricular septal defect, Patent foramen ovale, Patent ductus arteriosus, Anomalous pulmonary venous return, Gastroesophageal reflux, Duodenal atresia, Annular pancreas, Pyloric stenosis, Vesicoureteral reflux, Cystic kidney, Hypospadias, Cryptorchidism, Syndactyly, Hip dysplasia, Scoliosis, Lumbar lordosis, Intrauterine growth retardation, Tall stature, Macrocephaly, Fontanel abnormality, Frontal bossing, Triangular face, Abnormal eyebrows, Hypotelorism, Hypertelorism, Upslanting palpebral fissures, Small palpebral fissures, Epicanthal folds, Deeply set eyes, Abnormal ears, Preauricular pits, Bulbous nose, Anteverted nares, Flat philtrum, Full lips, Small mouth, Furrowed tongue, Abnormal teeth, Broad alveolar ridges, High-arched palate, Micrognathia, Small nipples, Inverted nipples, Small hands, 5th finger clinodactyly, Digital Anomalies, Nail hypoplasia, Widow's peak, Sacral hypertrichosis, Café Au Lait spots)

CasePreviousTesting Tested negative for presence of de novo c.3382_3383delGA variant in ANKRD11 that twin sister had.

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES results confirmed with sanger sequencing in patient and parents

Variant NM_012102.3:c.1411G>A(p.Val471Ile), de novo

ClinVar n/a

CAID CA571729

gnomAD 0.0001824(other), 0.00002032(total)

VariantEvidence n/a

CaseAddInfo Compound heterozygous for a frameshift and missense variant in FSIP2, encodes a sperm flagellum protein and is not currently associated with a human disease. Healthy older sister, but twin sister has KBG syndrome brought on by de novo deletion variant in ANKRD11 gene.

CasePMIDs n/a

Case# Subject 6, female, 6yo, Northern European/Hispanic

CasePresentingHPOs HP:0001263, HP:0001252, HP:0002938, HP:0000256, HP:0000325, HP:0000316, HP:0045075, HP:0011229, HP:0000368, HP:0000463, HP:0000319, HP:0012170, HP:0012168, HP:0001270, HP:0000750, HP:0000708, HP:0002311, HP:0000316, HP:0200055, HP:0011297 (Global developmental delay, Hypotonia, Lumbar lordosis, Macrocephaly, Triangular face, Sparse eyebrows, Broad eyebrows, Low-set-posteriorly rotated ears, Anteverted nares, Flat philtrum, Nail biting, Head bainging, Motor delay, Speech delay, Behavioral problems, Diifficulties in Coordination, Hypertelorism, Small hands, Digital anomalies)

HPOFreeText: Speech and motor delay noted at 2 years. Mildly flattened philtrum and remaining phenotypes presented postnatally.

CaseNotHPOs HP:0001250, HP:0001285, HP:0007018, HP:0011968, HP:0000589, HP:0000648, HP:0000568, HP:0000659, HP:0000525, HP:0000581, HP:0000407, HP:0000453, HP:0410030, HP:0001629, HP:0001655, HP:0001643, HP:0010772, HP:0002020, HP:0002247, HP:0001734, HP:0002021, HP:0000076, HP:0000107, HP:0001159, HP:0001385, HP:0002650, HP:0001511, HP:0000098, HP:0004322, HP:0000252, HP:0011328, HP:0002007, HP:0000601, HP:0000582, HP:0000494, HP:0045025, HP:0000286, HP:0000490, HP:0004467, HP:0000414, HP:0012471, HP:0000160, HP:0000221, HP:0000164, HP:0000187, HP:0000218, HP:0000347, HP:0002557, HP:0003186, HP:0200055, HP:0004209, HP:0011297, HP:0001792, HP:0000349, HP:0004532, HP:0000957 (Seizures, Spastic quadriparesis, ADHD, Poor feeding, Coloboma, Optic Atrophy, Microphthalmia, Peter's anomaly, Iris abnormality, Blepharophimosis, Senseorineural hearing loss, Choanal atresia, Cleft lip, Ventricular septal defect, Patent foramen ovale, Patent ductus arteriosus, Anomalous pulmonary venous return, Gastroesophageal reflux, Duodenal atresia, Annular pancreas, Pyloric stenosis, Vesicoureteral reflux, Cystic kidneys, Syndactyly, Hip dysplasia, Scoliosis, Intrauterine growth retardation, Tall stature, Short stature, Microcephaly, Fontanel abnormality, Frontal bossing, Hypotelorism, Upslanted palpebral fissures, Downslanted palpebral fissures, small palpebral fissures, Epicanthus, Deep set eyes, Preauricular pits, Bulbous nose, Full lips, Small mouth, Furrowed tongue, Abnormal teeth, Broad alveolar ridges, High-arched palate, Micrognathia, Small nipple, Inverted nipples, Small hands, Clinodactyly of the 5th finger, Digital anomalies, Nail hypoplasia, Widow's peak, Sacral hypertrichosis, Cafe-au-lait spots)

CasePreviousTesting n/a

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES results confirmer with sanger

Variant NM_012102.3:c.3122delC(p.Pro1041Lysfs∗40)

ClinVar n/a

CAID CA658820831

gnomAD n/a

VariantEvidence n/a

CaseAddInfo unknown if de novo like the rest, no parent testing. Family history of intellectual disability and mental illness also suggests it may not be de novo. Speculated that due to deletion being in exon 17 or 21 that NMD will occur.

CasePMIDs n/a

Case# Subject 4, female, 9yo, Northern European

CasePresentingHPOs HP:0001252, HP:0002342, HP:0001250, HP:0001999, HP:0002020, HP:0001385, HP:0000076, HP:0002079, HP:0001320, HP:0006808, HP:0001943, HP:0005968, HP:0000490, HP:0000286, HP:0000356, HP:0000221, HP:0010490, HP:0011304, HP:0001156, HP:0000708, (Hypotonia, Moderate intellectual disability, Seizures, Dysmorphic facies, Gastroesophageal reflux, Hip dysplasia, Vesicoureteral reflux, Thin corpus callosum, Cerebellar vermis hypoplasia, Cerebral hypomyelination, Hypoglycemia, Temperature instability, Deep set eyes, Epicanthus, Auricle abnormality, Furrowed tongue, Abnormal palmar creases, broad thumbs, Brachydactyly, Behavioral problems)

HPOFreeText: Fleshy auricles, deep furrow in posterior third of tongue, bilateral single palmar creases, mild brachydactyly, developmental hip dysplasia, severe vesicoureteral reflux, severe behavioral issues and other phenotypes are postnatal. Brain MRI results including diminished cerebellar vermis with deep fissures at 1 year of age.

CaseNotHPOs HP:0001285, HP:0007018, HP:0011968, HP:0002119, HP:0007361, HP:0025100, HP:0030301, HP:0012448, HP:0000589, HP:0000648, HP:0000568, HP:0000659, HP:0000525, HP:0000581, HP:0000407, HP:0000453, HP:0410030, HP:0001629, HP:0001655, HP:0001643, HP:0010772, HP:0002247, HP:0001734, HP:0002021, HP:0000107, HP:0001159, HP:0002650, HP:0002938, HP:0001511, HP:0000098, HP:0004322, HP:0000256, HP:0000252, HP:0011328, HP:0002007, HP:0000325, HP:0000534, HP:0000601, HP:0000316, HP:0000582, HP:0000494, HP:0045025, HP:0004467, HP:0000414, HP:0000463, HP:0000319, HP:0012471, HP:0000160, HP:0000164, HP:0000187, HP:0000218, HP:0000347, HP:0002557, HP:0003186, HP:0200055, HP:0004209, HP:0001792, HP:0000349, HP:0004532, HP:0000957 (Spastic quadriparesis, ADHD, Poor feeding, Ventriculomegaly, Abnormality of the pons, Abnormal morphology of the hippocampus, Abnormality of the anterior commissure, Delayed myelination, Coloboma, Optic atrophy, Microphthalmia, Peter's anomaly, Iris anomalies,Blepharophimosis, Sensorineural hearing loss, Choanal atresia, Cleft lip, Ventricular septal defect, Patent foramen ovale, Patent ductus arteriosus, Anomalous pulmonary venous return, Duodenal atresia, Annular pancreas, Pyloric stenosis, Cystic kidney, Syndactyly, Scoliosis, Lumbar lordosis, Intrauterine growth retardation, Tall stature, Short stature, Macrocephaly, Microcephaly, Fontanel abnormality, Frontal bossing, Triangular face, Abnormal eyebrows, Hypotelorism, Hypertelorism, Upslanting palpebral fissures, Down-slanting palpebral fissures, Small palpebral fissures, Preauricular pits, Bulbous nose, Anteverted nares, Flat philtrum, Full lips, Small mouth, Abnormal teeth, Broad alveolar ridges, High-arched palate, Micrognathia, Small nipples, Inverted nipples, Small hands, 5th finger clinodactyly, Nail hypoplasia, Widow's peak, Sacral hypertrichosis, Café Au Lait spots)

CasePreviousTesting n/a

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES results confirmed with Sanger in pateint and parents

Variant NM_012102.3:c.4293C>G(p.His1431Gln), de novo

ClinVar n/a

CAID CA338168808

gnomAD n/a

VariantEvidence n/a

CaseAddInfo mosaic, de novo SCN2A missense variant. SCN2A associated with 613721 and 607745

CasePMIDs n/a

Case3: Female, Italy, 7 yrs report

CasePresentingHPOs: HP:0003798, HP:0003325, HP:0001270, HP:0002093, HP:0002650, HP:0002355, HP:0003324, HP:0001283, HP:0003306 (Nemaline bodies, Limb-girdle muscle weakness, Motor delay, Respiratory impairment, Scoliosis, Difficulty walking, Generalized muscle weakness, Bulbar palsy, Spinal rigidity)

HPOsFreeText: Semi-solid diet

CaseNotHPOs: HP:0003560, HP:0003715, HP:0001627, HP:0000602, HP:0001557, HP:0001290 (Muscular dystrophy, Myofibrillar myopathy, Cardiac abnormality, Ophthalmoplegia, Prenatal movement abnormality, Hypotonia)

NotHPOsFreeText: Congenital myasthenic syndromes

CaseAddInfo: Intermediate NM presentation, Parental segregation was confirmed, Variant 2 creates a new splicing donor site and activates an upstream acceptor site which partially expresses intron 125 and causes a premature termination codon

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_001271208.2:c.24559C>T (p.Arg8187Ter)

ClinVar: 496135 https://www.ncbi.nlm.nih.gov/clinvar/variation/496135/

gnomAD: Not in gnomAD

Variant2: NM_001271208.1:c.19429-381_19429-379delinsA (p.=)

CAID: CA913203565 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913203565

gnomAD: Not in gnomAD

Case2: Male, Italy, Birth onset

CasePresentingHPOs: HP:0003798, HP:0002033, HP:0003325, HP:0001558, HP:0001270, HP:0002093, HP:0000194, HP:0006830, HP:0003701, HP:0002650, HP:0003458 (Nemaline bodies, Poor suck, Limb-girdle muscle weakness, Decreased fetal movement, Motor delay, Respiratory impairment, Open mouth, Congenital hypotonia, Proximal muscle weakness, Scoliosis, EMG: myopathic abnormalities)

HPOsFreeText: Wheelchair dependent

CaseNotHPOs: HP:0003560, HP:0003715, HP:0001627, HP:0000602, HP:0001283, HP:0003306 (Muscular dystrophy, Myofibrillar myopathy, Cardiac abnormality, Ophthalmoplegia, Bulbar palsy, Spinal rigidity)

NotHPOsFreeText: Congenital myasthenic syndromes

CaseAddInfo: Intermediate 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.17737-2A>T (p.=)

CAID: CA348804839 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_001271208.2%3Ac.17737-2A%3ET

gnomAD: Not in gnomAD

Variant2: NM_001271208.1:c.21423del (p.Lys7141Asnfs*23)

CAID: CA913203564 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913203564

gnomAD: Not in gnomAD

Case: Family B Proband BII-3, male, Arabic, Israeli, 19yo at report

CasePresentingHPOs: HP:0000953, HP:0030053, HP:0000998, HP:0002619, HP:0002240, HP:0001629, HP:0000365, HP:0007380

CasePresentingHPOsFreeText: Dilated scleral vessels, MRI of the lower limbs demonstrated severe, symmetric, diffuse infiltration of the subcutaneous fat of the lower limbs, showing low signal in T1 and high signal intensity in T2 and fat suppressed–weighted images.

CaseNOTHPOs: HP:0008064, HP:0000054, HP:0000520, HP:0012385

CaseNOTHPOSFreeText: scrotal masses

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

Variant: G427S homozygous

ClinVarID: or CAID: 563/CA114349

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.

AddCaseInfo: parents were consanguineous, heterozygous. brother (BII-4) is also genotype/phenotype +

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).

Case: Family F Proband FII-6, female, Arabic, Israeli, 27yo at report

CasePresentingHPOs: HP:0000953, HP:0030053, HP:0000998, HP:0002619, HP:0000520, HP:0007380, HP:0100324, HP:0100727

CasePresentingHPOsFreeText: dilated scleral vessels

CaseNOTHPOs: HP:0008064, HP:0001433, HP:0011025, HP:0000365, HP:0012385

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: 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. brother (FII-5) is het and unaffected.

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# A3054-21, Macedonian, Male, 5yr age of onset

CasePresentingHPOs HP:0001919, HP:0000121, HP:0000074

CasePreviousTesting 30 genes previously linked to nephrolithiasis were screened by exon sequencing in these individuals, but no causative mutations were detected

CaseMethod1 NGS

CaseGenotypingMethod list of 18 hypothetical candidate genes and performed exon amplification with consecutive next-generation sequencing in a multicenter cohort of 348 individuals with nephrolithiasis or isolated nephrocalcinosis

Variant NM_134425.2(SLC26A1):c.554C>T (p.Thr185Met), NM_022042.3(SLC26A1):c.1073C>T (p.Ser358Leu)

ClinVar 242374, 242375

gnomAD 0.0004342, 0.0005655

VariantEvidence Immunofluorescence of SLC26A1 protein, when overexpressed in HEK293 cells, showed that p.Thr185Met causes protein to fail to reach plasma membrane (Figure 2). Monitoring of intracellular pH showed that p.Thr185Met has severely reduced activity (Figure 4). PCR of slc26a1 transcript in H293K cells showed no change in amount of transcript suggesting that the low p.Ser363Leu band levels in the immunoblot (Figure 3) were due to low portein stability.

Case# B641-12, "European," Male

CasePresentingHPOs HP:0000787

CaseNotHPOs HP:0003159

CasePreviousTesting 30 genes previously linked to nephrolithiasis were screened by exon sequencing in these individuals, but no causative mutations were detected

CaseMethod1 NGS

CaseGenotypingMethod list of 18 hypothetical candidate genes and performed exon amplification with consecutive next-generation sequencing in a multicenter cohort of 348 individuals with nephrolithiasis or isolated nephrocalcinosis

Variant NM_134425.2(SLC26A1):c.166G>A (p.Ala56Thr)

ClinVar 242376

gnomAD 0.0005655

VariantEvidence Monitoring of intracellular pH in transfected HEK293 demonstrated that p.Ala56Thr had reduced anion exchange activity. (Figure 4)

CaseAddInfo homozygous, consanguineous parents

Case1: Male, Birth onset

CasePresentingHPOs: HP:0008936, HP:0002058, HP:0200096, HP:0000218, HP:0000774, HP:0005957, HP:0001290, HP:0001284, HP:0002938, HP:0003324, HP:0009046, HP:0008994, HP:0009027, HP:0003722, HP:0002650, HP:0000278, HP:0001724, HP:0002792, HP:0002877, HP:0003557, HP:0100299, HP:0003803 (Muscular hypotonia of the trunk, Myopathic facies, Triangular-shaped open mouth, High-arched palate, Narrow chest, Abnormal breathing, Generalized hypotonia, Areflexia, Exaggerated lumbar lordosis, Generalized muscle weakness, Difficulty running, Proximal muscle weakness in lower limbs, Foot dorsiflexor weakness, Neck flexor weakness, Scoliosis, Retrognathia, Aortic dilatation, Reduced vital capacity, Nocturnal hypoventilation, Increased variation in fiber size, Muscle fiber inclusion bodies, Type 1 muscle fiber predominance)

HPOsFreeText: Crawled at age 10 months and walked independently at age 15 months, Inability to jump, PVC was 37% of predicted, BiPAP commenced at age 20, Cap-like structures

CaseNotHPOs: HP:0003115, HP:0003798 (Abnormal ECG, Nemaline bodies)

NotHPOsFreeText: N/A

CaseAddInfo: No family history of muscle weakness, Variant is de novo and confirmed absent in the parents

CasePreviousTesting: Tested caps appeared pale on all myosin ATPase stains and dark on Gomori Trichrome and NADH stains and were strongly reactive for troponin T, α-actinin-2, myotilin, tropomyosin, actin and desmin by immunoperoxidase, No positive staining for neonatal or embryonic myosin isoforms, Large regions of disorganised thin filament structures containing Z band remnants were present in subsarcolemmal positions

CaseGenotypingMethod: Bidirectional sequencing on TPM2 and TPM3 for all exons and exon-intron boundaries was performed using genomic DNA.

Variant: NM_152263.4(TPM3):c.502C>T (p.Arg168Cys)

ClinVar: 12454 https://www.ncbi.nlm.nih.gov/clinvar/variation/12454/

gnomAD: Not in gnomAD

Case# F2:II-4, 18mo diagnosis, M, Finnish

CasePresentingHPOs HP:0001873, HP:0011950, HP:0001875, HP:0000639, HP:0002141, HP:0001387, HP:0002395, HP:0002863, HP:0002721, HP:0007018, HP:0001310, HP:0002172

HPO free text: "Thrombocytopenia at 2 mo followed by trilineage cytopenia at 14 mo of age. Bronchiolitis at 6 wk and varicella infection at 4 mo of age, both requiring hospitalization; recurrent otitis and laryngitis before the HSCT. MDS −7 at 18 mo of age; normal bone marrow cellularity and dysplastic megakaryocytes and clear myelodysplasia in the megakaryopoiesis." Hb[82-128(28/90) vs 117-122], MCV[73-90(82-98) vs 82-98], Platlets[37-444(32/90) vs 150-360], WBC[2.5-12.3(61-90) vs 3.4-8.2]

CasePreviousTesting Absolute lymphocyte counts and assays of cytotoxic lymphocyte phenotype and function. Hemoglobin(82-128[28/90 abnormal readings/total readings] vs 117-122 normal), Platelets(37-444[32/90] vs 150-360), WBC(2.5-12.3[61/90] vs 3.4-8.2), MCV(73-90[15/90] vs 117-122).

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES then confirmed variant with Sanger

Variant NM_152703.4(SAMD9L):c.2672T>C (p.Ile891Thr)

ClinVar 446529

VariantEvidence (Figure 5) 293FT cells transfected with p.Ile891Thr showed more limited cell proliferation than WT SAMD9L

CaseAddInfo Uniparental Disomy of WT allele in patient

CasePMIDs 28852709

CaseIV-3: Female, 5 years, Turkey

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

HPOsFreeText: -3.33 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 de novo and confirmed with parental testing, Variant is a splice donor-site mutation that skips exon 14

CasePreviousTesting: Calcium levels (9.4 mg/dL), Decreased serum phosphate levels (2.0 mg/dL; reference 3.7-5.6), Elevated serum ALP (559 IU/L; reference 90-325), 25OHD3 levels (28.3 ng/ml), 1,25(OH)2D3 levels (N/A pg/mL), PTH levels (138 ng/L), TPR levels (79.6), Decreased TmP/GFR levels (1.59; 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.1586+2T>G

CAID: CA412575011 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000444.5%3Ac.1586%2B2T%3EG

gnomAD: Not in gnomAD

CaseXIV-3: Female, 2.7 years, Turkey

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

HPOsFreeText: -2.01 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: Proband's mother shares the mutation and disease, Variant is at a splice donor site in intron 12

CasePreviousTesting: Calcium levels (9.4 mg/dL), Decreased serum phosphate levels (2.2 mg/dL; reference 3.8-6.5), Elevated serum ALP (364 IU/L; reference 90-325), 25OHD3 levels (27 ng/ml), PTH levels (49 ng/L), TPR levels (75), Decreased TmP/GFR levels (1.65; 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.1404+1del

CAID: CA913187413 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913187413

gnomAD: Not in gnomAD

CaseIX-3: Male, 2.1 years, Turkey

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

HPOsFreeText: -0.75 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: Proband is hemizyogus for this mutation, Variant is a splice donor site at intron 4

CasePreviousTesting: Calcium levels (10.1 mg/dL), Decreased serum phosphate levels (2.6 mg/dL; reference 3.8-6.5), Elevated serum ALP (827 IU/L; reference 90-325), 25OHD3 levels (32.3 ng/ml), PTH levels (107.1 ng/L), TPR levels (74), Decreased TmP/GFR levels (1.92; 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.436+1G>T

CAID: CA412571215 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000444.5%3Ac.436%2B1G%3ET

gnomAD: Not in gnomAD

CaseXV-3: Female, 3.3 years, Turkey

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

HPOsFreeText: -3.04 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 de novo and is confirmed by parental testing

CasePreviousTesting: Calcium levels (9.4 mg/dL), Decreased serum phosphate levels (2.9 mg/dL; reference 3.8-6.5), Elevated serum ALP (677 IU/L; reference 90-325), 25OHD3 levels (107 ng/ml), 1,25(OH)2D3 levels (54.2 pg/mL), PTH levels (79.3 ng/L), TPR levels (83.4), Decreased TmP/GFR levels (2.8; 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.1206del (p.Gln402Hisfs*6)

CAID: CA913187414 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913187414

gnomAD: Not in gnomAD

Case11 Female, Finland

CasePresentingHPOs HP:0000202, HP:0000347, HP:0001161, HP:0001627, HP:0000157, HP:0002101, HP:0000238, HP:0001341, HP:0007370, HP:0010664, HP:0002126, HP:0007260, HP:0030449

(Oral cleft, Micrognathia, Hand polydactyly, Congenital heart defect, Tongue abnormality, Defective lung lobation, Hydrocephalus, Olfactory lobe agenesis, Callosal agenesis, Fused thalami, Polymicrogyria, Type II lissencephaly, Therapeutic abortion)

HPOsFreeText Crown-heel body length 25cm, body weight 360g, brain weight 40g, abnormal larynx/trachea, hydrocephalus/open-book, occipitotemporal hypoplasia, infratentorial hypoplasia, occipitoschisis/keyhole, leptomeningeal heterotopia, absent developed and identifiable mamillary bodies, absent anterior commissure, difficult to identify nucleus dentatus

CaseNotHPOs HP:0007165

(Periventricular neuronal heterotopia)

NotHPOsFreeText Uterus duplex, hydranencephaly/anencephaly, neuroepithelial rosettes, 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 induced abortion at 20+5wk gestational age

CasePMIDs n/a

Case4 Female, Finland

CasePresentingHPOs HP:0000202, HP:0000347, HP:0001161, HP:0001829, HP:0002101, HP:0000238, HP:0001341, HP:0007370, HP:0010664, HP:0002126, HP:0030449

(Oral cleft, Micrognathia, Hand polydactyly, Foot polydactyly, Defective lung lobation, Hydrocephalus, Olfactory lobe agenesis, Callosal agenesis, Fused thalami, Polymicrogyria, Therapeutic abortion)

HPOsFreeText Crown-heel body length 19cm, Body weight 160g, Brain weight 16g, abnormal larynx/trachea, Hydrocephalus/open-book, occipitotemporal hypoplasia, infratentorial hypoplasia, occititoschisis/keyhole, hypothalamic plate protrusion-hamartoma, steep rhombencephalic flexure with hypoplasia of posterior fossa contents, absent developed and identifiable mamillary bodies, absent anterior commissure, difficult to identify nucleus dentatus

CaseNotHPOs HP:0001627, HP:0000157, HP:0007260, HP:0007165

(Congenital heart defect, Tongue abnormality, Type II lissencephaly, Periventricular neuronal heterotopia)

NotHPOsFreeText Uterus duplex, Hydranencephaly/anencephaly, leptomeningeal heterotopia, neuroepithelial rosettes, 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 induced abortion at 18+0wk gestational age

CasePMIDs n/a

Case15 Male, Finland

CasePresentingHPOs HP:0003826, HP:0000202, HP:0001161, HP:0001829, HP:0001627, HP:0002101, HP:0000238, HP:0001341, HP:0007370, HP:0010664, HP:0002126, HP:0007260, HP:0007165

(Stillbirth, Oral cleft, Micrognathia, Hand polydactyly, Foot polydactyly, Congenital heart defect, Defective lung lobation, Hydrocephalus, Olfactory lobe agenesis, Callosal agenesis, Fused thalami, Polymicrogyria, Type II lissencephaly, Periventricular neuronal heterotopia)

HPOsFreeText Crown-heel body length 45cm, body weight 2520g, brain weight 146g, polydactyly of toes with multiple extra toes, 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

CaseNotHPOs HP:0000157

(Tongue abnormality)

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 stillborn at 34+0wk gestational age

CasePMIDs n/a

Case10 Male, Finland

CasePresentingHPOs HP:0000347, HP:0001829, HP:0010066, HP:0002101, HP:0000238, HP:0001341, HP:0007370, HP:0010664, HP:0002126, HP:0007260, HP:0030449

(Micrognathia, Foot polydactyly, Duplicated hallux, Defective lung lobation, Hydrocephalus, Olfactory lobe agenesis, Callosal agenesis, Fused thalami, Polymicrogyria,Type II lissencephaly, Therapeutic abortion)

HPOsFreeText Crown-heel body length 25cm, body weight 250g, Brain weight 35g, abnormal larynx/trachea, hydrocephalus/open-book, occipitotemporal hypoplasia, infratentorial hypoplasia, occipitoschisis/keyhole, leptomeningeal heterotopia, neuroepithelia rosettes, absent developed and identifiable mamillary bodies, absent anterior commissure, difficult to identify nucleus dentatus

CaseNotHPOs HP:0000202, HP:0001161, HP:0001627, HP:0000157, HP:0002444, HP:0007165

(Oral cleft, Hand polydactyly, Congenital heart defect, Tongue abnormality, Hypothalamic hamartoma, Periventricular neuronal heterotopia)

NotHPOsFreeText Uterus duplex, hydranencephaly/anencephaly, hypothalamic hamartoma/bulging, true alobar or semilobar holoprosencephaly, widely separated hemispheres without midline structures; only meningeal remnants cross the midline showing classical open-book appearance of HLS

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 induced abortion at 19+5wk gestational age

CasePMIDs n/a

Case1 female, Finland

CasePresentingHPOs HP:0000202, HP:0000347, HP:0001341, HP:0000238, HP:0002126, HP:0007165, HP:0030449

(Oral Cleft, Micrognathia, Olfactory lobe agenesis, Hydrocephalus, Polymicrogyria, Periventricular neuronal heterotopia, Therapeutic abortion)

HPOsFreeText crown-heel length: 8cm, weight: 9g, hydrocephalus/open-book, occipitotemporal hypoplasia, infratentorial hypoplasia, occipitoschisis/keyhole, neuroepithelial rosettes, absent developed and identifiable mamillary bodies, absent anterior commissure, difficult to identify nucleus dentatus

CaseNotHPOs HP:0001161, HP:0001829, HP:0001627, HP:0000157, HP:0002101, HP:0007370, HP:0010664, HP:0002444, HP:0007260

(Hand polydactyly, Foot polydactyly, Congenital heart defect, Tongue abnormality, Defective lung lobation, Callosal agenesis, Fused thalami, Hypothalamic hamartoma, Type II lissencephaly)

NotHPOsFreeText abnormal larynx/trachea, uterus duplex, hydranencephaly/anencephaly, hypothalamic bulging, leptomeningeal heterotopia, 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 induced abortion at 12+1wk gestational age

CasePMIDs n/a

Patient: P13

Variant: c.550G > T (p.Gly184Trp)

CAID: CA380695715

Functional effect: N/A

Patient: ID396

Variant: c.305_317delCCACCCAACCAACnew p.Pro102Tyrfs*41

ClinVarID/CAID: 1460243

Functional effect: Monoallelic expression of full-length allele (wt only)

Patient: ID26

Variant: c.1225_1249 + 19del (p.Met409Asnfs*14)

CAID: CA2580612035

Functional effect: Normal exon inclusion (band B) *, exon 7 skipping (band C), use of cryptic splice site: c.1249 + 64; use of cryptic splice site: c.1249 + 67; use of cryptic splice site: c.1249 + 137 (band A). Observed in blood.

Patient: ID266

Variant: c.685delG

CAID: CA2580612031

Functional effect: Normal exon inclusion (band A) *, exon 4 skipping (band B), exon 4 + 5 skipping. Observed in blood.

Case# Barletta 3:1, female, 17yo

CasePresentingHPOs HP:0004758

CasePreviousTesting no

CaseMethod1 PCR

CaseGenotypingMethod amplified 11 exons of CASQ2

Variant NM_001232.3(CASQ2):c.500T>A (p.Leu167His), NM_001232.3(CASQ2):c.339_354del16 (p.Ser113Argfs)

ClinVar 17612, 17611

VariantEvidence (fig5.) L167H variant had reduced Ca2+ sparks in infected myoctes comparable to levels in G112+5X and both significantly less than WT.

CaseAddInfo Authors admit that the functional evaluation of L167H is not as convincing as with G112+5X, the latter showing complete functional impairment and the former preserving major biochemical and biophysical properties of CASQ2.

Case# Barletta 3:2, male, 6yo

CasePresentingHPOs HP:0004758

CasePreviousTesting no

CaseMethod1 PCR

CaseGenotypingMethod amplified 11 exons of CASQ2

Variant NM_001232.3(CASQ2):c.339_354del16 (p.Ser113Argfs)

ClinVar 17611

VariantEvidence G112+5X variant decrease in Ca2+ transients and decrease in SR ability to store Ca2+ (fig.4&5)