FamilyFSP410: Italy

FamilyPresentingHPOs: HP:0002064, HP:0002464, HP:0002460, HP:0002395, HP:0007350, HP:0003487, HP:0031993, HP:0500139, HP:0003572, HP:0005961 (Spastic gait, Spastic dysarthria, Distal muscle weakness, Lower limb hyperreflexia, Hyperreflexia in upper limbs, Babinski sign, Hoffman sign, Hypoprolinemia, Low plasma citrulline, Hypoargininemia)

HPOsFreeText:

FamilyNotHPOs: HP:0001317, HP:0000973, HP:0001999 (Abnormal cerebellum morphology, Cutis laxa, Abnormal facial shape)

NotHPOsFreeText: Cutaneous findings

FamilyGenotypingMethod: Whole genome linkage analysis was performed on the family. Genotypes and exome sequencing was performed on four affected subjects (Patients 6, 8, 25, and 29). Targeted capture was performed and reads were aligned to the human genome. This identified five putatively linked loci with multipoint LOD scores (+1.64 to +1.95) and WES found two missense variants that fits the above criteria and segregates with the disease in ALDH18A1 and PDZD7. Found variants were called and annotated. Segregation in all individuals was checked through Sanger sequencing.

FamilyPreviousTesting: Amino acid levels in Table 4

FamilyAddInfo: Family displays autosomal dominant inheritance

Variant: NM_002860.4(ALDH18A1):c.359T>C (p.Val120Ala)

ClinVar: 217118 https://www.ncbi.nlm.nih.gov/clinvar/variation/217118/

gnomAD: Not in gnomAD

Affected: 9

Unaffected: 6

pLOD: 2.0

AddSegregationInfo: Whole Exome Sequencing, Figure 1 Pedigree

FamilyFSP470: France

FamilyPresentingHPOs: HP:0008969, HP:0002064, HP:0002460, HP:0003701, HP:0002395, HP:0007350, HP:0003487, HP:0031993 (Leg muscle stiffness, Spastic gait, Distal muscle weakness, Proximal muscle weakness, Lower limb hyperreflexia, Hyperreflexia in upper limbs, Babinski sign, Hoffman sign)

HPOsFreeText: N/A

FamilyNotHPOs: HP:0006938, HP:0001317, HP:0002066, HP:0002464, HP:0100543, HP:0000973 (Impaired vibration sensation at ankles, Abnoral cerebellum morphology, Gait ataxia, Spastic dysarthria, Cognitive impairment, Cutis laxa)

NotHPOsFreeText: N/A

FamilyGenotypingMethod: Exome sequencing data of 160 index patients with autosomal dominant spastic paraplegia and 275 index patients with autosomal recessive or sporadic spastic paraplegia was examined. 95 patients were screened through panel sequencing. Any determined ALDH18A1 mutations were confirmed by Sanger sequencing.

FamilyPreviousTesting: N/A

FamilyAddInfo: Family displays autosomal dominant inheritance

Variant: NM_002860.4(ALDH18A1):c.755G>A (p.Arg252Gln)

ClinVar: 217117 https://www.ncbi.nlm.nih.gov/clinvar/variation/217117/

gnomAD: Not in gnomAD

Affected: 4

Unaffected: 5

Segregations: 4

AddSegregationInfo: Whole Exome Sequencing, Figure 1 Pedigree

FamilyFSP856: Portugal

FamilyPresentingHPOs: HP:0001270, HP:0001510, HP:0002317, HP:0002273, HP:0007350, HP:0003487, HP:0003487, HP:0000020, HP:0001249, HP:0002344, HP:0000252, HP:0003700 (Motor delay, Growth delay, Spastic gait, Tetraparesis, Lower limb hyperreflexia, Hyperreflexia in upper limbs, Babinski sign, Urinary incontinence, Intellectual disability, Progressive neurologic deterioration, Microcephaly, Generalized amyotrophy)

HPOsFreeText: N/A

FamilyNotHPOs: HP:0002066, HP:0000973 (Gait ataxia, Cutis laxa)

NotHPOsFreeText: N/A

FamilyGenotypingMethod: Exome sequencing data of 160 index patients with autosomal dominant spastic paraplegia and 275 index patients with autosomal recessive or sporadic spastic paraplegia was examined. 95 patients were screened through panel sequencing. Any determined ALDH18A1 mutations were confirmed by Sanger sequencing.

FamilyPreviousTesting: N/A

FamilyAddInfo: Family displays autosomal recessive inheritance, Family is compound heterozygous for these variants

Variant1: NM_002860.4(ALDH18A1):c.1910T>C (p.Leu637Pro)

ClinVar: 217120 https://www.ncbi.nlm.nih.gov/clinvar/variation/217120/

gnomAD: Not in gnomAD

Variant2: NM_002860.4(ALDH18A1):c.383G>A (p.Arg128His)

ClinVar: 217121 https://www.ncbi.nlm.nih.gov/clinvar/variation/217121/

gnomAD: 0.00006533, https://gnomad.broadinstitute.org/variant/10-97397114-C-T

Affected: 4

Unaffected: 13

Segregations: 11

AddSegregationInfo: Whole Exome Sequencing, Figure 1 Pedigree

Case15: Male, Chinese, 6 mo (age at death)

HPOsFreeText: neonatal onset

NotHPOsFreeText: not responsive to vitamin B12

Case15 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.433G>A (p.Gly145Ser)

ClinVar: n/a

CAID: CA364404739

gnomAD: n/a

Variant2: NM_000255.3:c.1677-1G>A (p.=)

ClinVar: 550012

CAID: CA3846767

gnomAD: 0.0003511 (East Asian)

CaseAddInfo: heterozygous mutations in trans. Died at 6 mo.

Case14: Male, Chinese, 2.4 y (onset)

HPOsFreeText: 2.4 y onset

NotHPOsFreeText: not responsive to vitamin B12

Case14 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.421G>A (p.Ala141Thr)

ClinVar: 557678

CAID: CA364404763

gnomAD: n/a

Variant2: NM_000255.3:c.810_811dupGG (p.?)

ClinVar: n/a

CAID: CA3847032

gnomAD: n/a

CaseAddInfo: lost to follow up. heterozygous mutations in trans. both novel mutations

Case12: Female, Chinese, 1.5 y (end of study)

HPOsFreeText: 11 mo onset, poor neruological outcome

NotHPOsFreeText: not responsive to vitamin B12

Case 12 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.323G>A (p.Arg108His)

ClinVar: 100707

CAID: CA235522

gnomAD: 0.00006152 (African)

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

ClinVar: 218998

CAID: CA347913

gnomAD: 0.0001504 (East Asian)

CaseAddInfo: heterozygous mutations in trans

Case11: Female, Chinese, 2 y (age at death)

HPOsFreeText: 9 mo onset, responsive to vitamin B12

Case11 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3(MMUT):c.323G>A (p.Arg108His)

ClinVar: 100707

CAID: CA235522

gnomAD: 0.00006152 (African)

Variant2: NM_000255.3:c.1514T>C (p.!le505Thr)

ClinVar: n/a

CAID: CA364397174

gnomAD: n/a

CaseAddInfo: heterozygous mutations in trans, died at 2 y

Case10: Male, Chinese, 6.4 y (onset)

HPOsFreeText: 6.4 y onset

NotHPOsFreeText: not responsive to vitamin B12

Case10 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3(MMUT):c.323G>A (p.Arg108His)

ClinVar: 100707

CAID: CA235522

gnomAD: 0.00006152 (African)

Variant2: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

ClinVar: 552079

CAID: CA3847064

gnomAD: 0.0002008 (East Asian)

CaseAddInfo: lost to follow up, heterozygous mutations in trans

Case13: Female, Chinese, 7 mo (onset)

HPOsFreeText: 7 mo onset

NotHPOsFreeText: not responsive to vitamin B12

Case13 (Level 2):

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.419T>C (p.Leu140Pro)

ClinVar: n/a

CAID: CA364404765

gnomAD: n/a

Variant2: NM_000255.3:c.424A>G (p.Thr142Ala)

ClinVar: n/a

CAID: CA364404758

gnomAD: n/a

CaseAddInfo: Variant 1 is novel. Heterozygous mutations in trans. lost to follow up.

Case1: Male, Chinese, 1.8 y (end of study)

HPOsFreeText: neonatal onset, poor neurological outcome

NotHPOsFreeText: not responsive to vitamin B12

Case9 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

ClinVar: 1887

CAID: CA249732

gnomAD: 0.0008393 (Latino)

Variant2: NM_000255.3(MMUT):c.323G>A (p.Arg108His)

ClinVar: 100707

CAID: CA235522

gnomAD: 0.00006152 (African)

Variant3: NM_000255.3:c.2168G>A (p.Gly723Asp)

ClinVar: n/a

CAID: CA3846630

gnomAD: 0.00006533 (South Asian)

CaseAddInfo: Variant 1 in trans to Variants 2 and 3 (cis). Variant 3 is novel

Case8: Male, Chinese, 8 mo (onset)

HPOsFreeText 8 mo onset, responsive to vitamin B12

Case8 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.278G>A (p.Arg93His)

ClinVar: 1880

CAID: CA249728

gnomAD: 0.0004777 (European-Finnish)

Variant2: NM_000255.3:c.567T>G (p.Asn189Lys)

ClinVar: 618734

CAID: CA364404447

gnomAD: n/a

CaseAddInfo: lost to follow up, heterozygous mutations in trans

Case7: Male, Chinese, 33 d (age at death)

HPOsFreeText: Neonatal onset

NotHPOsFreeText: Not responsive to vitamin B12

Case7 (Level 2)

CasePreviousTesting: Same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.103C>T (p.Gln35Ter)

ClinVar: n/a

CAID: CA364405751

gnomAD: 0.00009950 (Ashkenazi Jewish)

Variant2: NM_000255.3:c.494A>G (p.Asp165Gly)

ClinVar: n/a

CAID: CA138799926

gnomAD: 0.00005443 (East Asian)

CaseAddInfo: died at 33d, heterozygous mutations in trans

Case6: Female, Chinese, 1 mo (onset)

HPOsFreeText: not responsive to vitamin B12

Case6 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.68C>G (p.Ser23Ter)

ClinVar: n/a

CAID: CA364405860

gnomAD: n/a

Variant2: NM_000255.3:c.323G>A (p.Arg108His)

ClinVar: 100707

CAID: CA235522

gnomAD: 0.00006152 (African)

CaseAddInfo: lost to follow up, heterozygous mutations in trans

FamilyBE1: N/A

FamilyPresentingHPOs: HP:0001396, HP:0006579, HP:0002240, HP:0002904, HP:0002151, HP:0003235, HP:0004914, HP:0001889 (Cholestasis, Prolonged neonatal jaundice, Hepatomegaly, Hyperbilirubinemia, Increased serum lactate, Hypermethioninemia, Recurrent infantile hypoglycemia, Megaloblastic anemia)

HPOsFreeText: Increased bile salts

FamilyNotHPOs: HP:0001744, HP:0000842, HP:0008163 (Splenomegaly, Hyperinsulinemia, Decreased circulating cortisol level)

NotHPOsFreeText: Abnormally coloured stools

FamilyGenotypingMethod: Whole exome sequencing of P2 revealed a homozygous mutation in ADK which led to a premature termination codon. This was retrospectively found in the deceased P1 and in the parents in the heterozygous state.

FamilyPreviousTesting: All patients received ursodeoxycholic acid (600 mg.m−2.d−1) and fat-soluble vitamin supplementation; All patients received an enriched diet with medium chain triglycerides and dextrin maltose

FamilyAddInfo: N/A

Variant: NM_006721.3:c.829C>T (p.Arg277Ter)

CAID: CA5564079, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA5564079

gnomAD: 0.000008890, https://gnomad.broadinstitute.org/variant/10-76360203-C-T

Affected: 2

Unaffected: 0

Segregations: 1

AddSegregationInfo: Not enough information, Parents are non-consanguineous

CaseST-7: Male, 1 day onset, Italy

CasePresentingHPOs: HP:0006579, HP:0001508, HP:0003215, HP:0000825, HP:0003256, HP:0006254, HP:0008947, HP:0006580, HP:0011968, HP:0002572, HP:0001251 (Prolonged neonatal jaundice, Failure to thrive, Dicarboxylic aciduria, Hyperinsulinemic hypoglycemia, Coagulopathy, Elevated alpha-fetoprotein, Infantile muscular hypotonia, Portal fibrosis, Feeding difficulties, Episodic vomiting, Ataxia)

HPOsFreeText: Small gallbladder stone

CaseNotHPOs: HP:0001250 (Seizure)

NotHPOsFreeText: N/A

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

CasePreviousTesting: See Group

CaseGenotypingMethod: See Group

Variant: NM_001123.3:c.199C>T (p.Gln67Ter)

CAID: CA5563907, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA5563907

gnomAD: 0.000008818, https://gnomad.broadinstitute.org/variant/10-76074480-C-T

CaseST-8: Female, 1 day onset, Germany

CasePresentingHPOs: HP:0006579, HP:0001643, HP:0001410, HP:0001319, HP:0006236, HP:0001786 (Prolonged neonatal jaundice, Patent ductus arteriosus, Decreased liver function, Neonatal hypotonia, Slender metacarpals, Narrow foot)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001250 (Seizure)

NotHPOsFreeText: N/A

CaseAddInfo: Family is non-consanguineous, Proband is compound heterozygous for these variants

CasePreviousTesting: See Group

CaseGenotypingMethod: See Group

Variant1: NM_001123.3:c.893C>A (p.Ala298Asp)

CAID: CA377399006, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA377399006

gnomAD: Not in gnomAD

Variant2: NM_001123.3:c.925C>T (p.Gln309Ter)

CAID: CA377398330, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA377398330

gnomAD: Not in gnomAD

CaseST-6: Male, 1 day onset, Morocco

CasePresentingHPOs: HP:0006579, HP:0001249, HP:0001270, HP:0001324, HP:0004322, HP:0000256, HP:0000316, HP:0006236, HP:0001786, HP:0008070, HP:0000708, HP:0002355, HP:0003202, HP:0002071 (Prolonged neonatal jaundice, Intellectual disability, Motor delay, Muscle weakness, Short stature, Macrocephaly, Hypertelorism, Slender metacarpals, Narrow foot, Sparse hair, Behavioral abnormality, Difficulty walking, Skeletal muscle atrophy, Abnormality of extrapyramidal motor function)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001250 (Seizure)

NotHPOsFreeText: N/A

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

CasePreviousTesting: See Group

CaseGenotypingMethod: See Group

Variant: NM_001123.3:c.685_687delinsCC (p.Thr229ProfsTer16)

CAID: CA1139768931, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA1139768931

gnomAD: Not in gnomAD

FamilyBI1: N/A

FamilyPresentingHPOs: HP:0001635, HP:0001875, HP:0001644, HP:0003756 (Congestive heart failure, Neutropenia, Dilated cardiomyopathy, Skeletal myopathy)

HPOsFreeText: N/A

FamilyNotHPOs: N/A

NotHPOsFreeText: N/A

FamilyGenotypingMethod: The family was investigated for linkage analysis via chromosomal DNA extraction from white blood cells and fibroblasts. These were tested with 28 x-chromosomal probes for heterozygosity in carriers, leading to an identified area near Xq28. The 30 genes in this region were identified and five were noted to have high heart and skeletal muscle expression. All five were sequenced and ORFs created. After PCR amplification and direct sequencing of the TAZ gene (G4.5.), each family was seen to have a unique variant that segregated with the disease.

FamilyPreviousTesting: N/A

FamilyPMIDs: 1998334, 6142097

FamilyAddInfo: N/A

Variant: NM_000116.5(TAZ):c.153C>G (p.Tyr51Ter)

ClinVar: 11101, https://www.ncbi.nlm.nih.gov/clinvar/variation/11101/

gnomAD: Not in gnomAD

Affected: 3

Unaffected: 6

Segregations: 9

pLOD: 5.24 at DXS305 multipoint LOD score

AddSegregationInfo: Pedigree in PMID: 6142097 Figure 1

FamilyBI3: N/A

FamilyPresentingHPOs: HP:0001875, HP:0001644, HP:0003756 (Neutropenia, Dilated cardiomyopathy, Skeletal myopathy)

HPOsFreeText: N/A

FamilyNotHPOs: N/A

NotHPOsFreeText: N/A

FamilyGenotypingMethod: Five genes noted to have high heart and skeletal muscle expression were sequenced and ORFs created. After PCR amplification and direct sequencing of the TAZ gene (G4.5.), each family was seen to have a unique variant that segregated with the disease.

FamilyPreviousTesting: N/A

FamilyAddInfo: N/A

Variant: NM_000116.5(TAZ):c.239-1G>A

ClinVar: 11100, https://www.ncbi.nlm.nih.gov/clinvar/variation/11100/

gnomAD: Not in gnomAD

Affected: 2

Unaffected: 3

Segregations: 4

AddSegregationInfo: Candidate gene sequencing

Case# HCU-101-3, 10yo report, Iran, Sistani

CasePresentingHPOs HP:0001249, HP:0001083, HP:0002970, HP:0001634, HP:0003235, HP:0000924

(Intellectual disability, Ectopia lentis, Genu varum, Mitral valve prolapse, Increased methionine in blood, Skeletal abnormality)

HPOsFreeText skeletal abnormality/elongated long bones, elevated, elevated plasma homocysteine, elevated urinary cysteine, elevated plasma methionine

CaseNotHPOs HP:0001010, HP:0000501

(Hypopigmentation, Glaucoma)

NotHPOsFreeText n/a

CasePreviousTesting Plasma homocysteine 330μm/l(upper normal limit 15μm/l), plasma methionine 142μm/l(normal range 6-40μm/l)

CaseMethod1 Sanger

CaseMethod2 n/a

CaseGenotypingMethod Sanger sequenced exon 3 of the CBS gene

Variant NM_000071.2(CBS):c.346G>A (p.Gly116Arg), homozygous

ClinVar 188787

gnomAD MAF=0.00002892(Latino), no homozygotes

CaseAddInfo from the province of Sistan and Baluchestan. no known consanguinity although the patient is homozygous for a founder variant

CasePMIDs n/a

CaseIV-2: Female, 4 months onset, Lebanese

CasePresentingHPOs: HP:0002463, HP:0002376, HP:0001332, HP:0002510, HP:0002522, HP:0000648, HP:0011471, HP:0011968, HP:0001508, HP:0002453, HP:0007374, HP:0002518, HP:0007042, HP:0011931, HP:0012751, HP:0200147, HP:0000252, HP:0001141, HP:0000486, HP:0002300, HP:0002421, HP:0002540, HP:0008936, HP:0002509, HP:0040288, HP:0002650, HP:0002828, HP:0002827, HP:0010465, (Language impairment, Developmental regression, Dystonia, Spastic quadriplegia, Areflexia of lower limbs, Optic atrophy, Gastrostomy tube feeding in infancy, Poor feeding, Failure to thrive, Abnormality of the globus pallidus, Atrophy/Degeneration involving the caudate nucleus, Abnormality of the periventricular white matter, Focal white matter lesion, Abnormality of the cerebellar peduncle, Abnormal basal ganglia MRI signal intensity, Neuronal loss in basal ganglia, Microcephaly, Severe visual impairment, Strabismus, Mutism, Poor head control, Inability to walk, Truncal hypotonia, Limb hypertonia, Nasogastric tube feeding, Scoliosis, Multiple joint contractures, Hip dislocation, Precocious puberty in females,

HPOsFreeText: Normal early developmental milestones, Not able to bear weight, Unable to fix or follow, Intermittent roving eye movement,

CaseNotHPOs: HP:0000240, HP:0001999, HP:0025336, (Abnormality of head circumference, Dysmorphic facies, Delayed ability to sit,

NotHPOsFreeText:

CaseAddInfo: Parents are consanguinous (first cousins),

CasePreviousTesting: Elevated hydroxy-C4-carnitine at 0.88 μM for patient 1 (control < 0.3 μM).

CaseGenotypingMethod: Whole exome sequencing was performed on the proband's sibling, with all SNVs and variants detected called, investigated, and filtered for pathogenicity. Mitochondrial DNA mutation tests were negative, as well as a southern blot for deletions in the muscle. Sanger sequencing of SURF1, SCO1, SCO2, COX10, NDUFV1, NDUFS7, and PANK2 revealed no pathogenic mutation. The WES identified a homozygous variant in HIBCH that was orthogonally validated. PCR-based Sanger sequencing was performed on the proband and the parents to confirm the presence of the mutations and recessive inheritance.

Variant: NM_014362.3:c.196C>T (p.Arg66Trp)

ClinVar: 190268 https://www.ncbi.nlm.nih.gov/clinvar/variation/190268/

gnomAD: Latino 2.892e-5, Overall 1.193e-5 https://gnomad.broadinstitute.org/variant/2-191161562-G-A

Case#: Patient 3, M, 6 days (onset), Tunisia

CasePresentingHPOs: HP:0100022, HP:0011968, HP:0000737, HP:0001250, HP:0001257, HP:0001254, HP:0001993, HP:0012088

CasePreviousTesting: Clinical diagnosis of classic MSUD due to elevated levels of plasma BCAAs and presence of L-alloisoleucine.

CaseMethod1: PCR

CaseMethod2: Direct sequencing

CaseGenotypingMethod: Entire coding regions and flanking intronic regions of BCKDHA, BCKDHB and DBT amplified from genomic DNA and sequenced.

Variant: NM_001918.3:c.1333_1336delAATG (homozygous)

CAID: CA658820833

gnomAD: Not in gnomAD

VariantEvidence: NMD unlikely. The truncated protein, however, is likely unable to self-assemble (several copies of E2 form the core of the BCKD complex).

CaseAddInfo: Consanguineous parents.

Case36 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. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 24(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 221(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 22. Patient tested negative in glutarylcarnitine blood spot test, even under carnitine supplementation.

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 V400M variant creates an NlaIII restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved. Likewise, the R227P variant creates a NlaIV site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

Variant 1. NM_000159.3(GCDH):c.1198G>A (p.Val400Met), 2. NM_000159.3(GCDH):c.680G>C (p.Arg227Pro), compound heterozygous

ClinVar 1. 2088, 2. 2089

gnomAD 1. MAF= 0.0002769(Other), no homozygotes, 2. MAF= 0.0003566(European(non-Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

each of these nucleotide positions is off by 36

so I came up with this:

NM_000159.3:c.387_388del(p.Glu129AspfsTer?)

register CAID

Mutalyzer

Case12 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 8188(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 3573(nv 2–14 mm/mol creatinine).

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 A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved. Likewise, the R402W variant destroys a MspI site. This would lead to uncleaved patient fragments and cleaved control fragments.

Variant 1. NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), 2. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), compound heterozygous

ClinVar 1. 2083, 2. 2085

gnomAD 1. MAF=0.0004013(African), no homozygotes, 2. MAF= 0.0007566(European(Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case19 sex unknown, Spain

CasePresentingHPOs HP:0001332

(Dystonia)

HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. 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 HP:0002540

(Non-ambulatory)

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 8955(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 2262(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 R372K variant destroys an MnlI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

Variant 1. NM_000159.3(GCDH):c.1115G>A (p.Arg372Lys), 2. NM_000159.3(GCDH):c.1173delG (p.Asn392Metfs), compound heterozygous

ClinVar 1. 557606, 2. 370106

gnomAD 1. not in gnomAD, 2. MAF= 0.00005646(Latino), no homozygotes

CaseAddInfo n/a

CasePMIDs see note on previous studies

Case8 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 1098(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 148(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 6.

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 A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

Variant 1. NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), 2. NM_000159.3(GCDH):c.268G>A (p.Glu90Lys), compound heterozygous

ClinVar 1. 2083, 2. 459949

gnomAD 1. MAF=0.0004013(African), no homozygotes, 2. MAF= 0.00008011(African), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case16 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 4885(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 713(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. Likewise, the R128X variant destroys a Sau961 site. This would lead to uncleaved patient DNA fragments and cleaved control fragments.

Variant 1. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), 2. NM_000159.3(GCDH):c.382C>T (p.Arg128Ter), compound heterozygous

ClinVar 1. 2085, 2. 371176

gnomAD 1. MAF=0.0007566(European(Finnish)), no homozygotes, 2. MAF= 0.00002891(Latino), no homozygotes

CaseAddInfo Sibling, case 17, had a mild phenotype: static or improving dystonia, with maintained ability to walk without assistance. GC-MS measured glutarate of 6644(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 603(nv 2–14 mm/mol creatinine).

CasePMIDs n/a

Case42 sex unknown, Spain

CasePresentingHPOs HP:0006846, HP:0000707

(Acute encephalopathy, Neurological abnormality)

HPOsFreeText Phenotypes defined as "slight," entailing minimal neurological signs and an otherwise normal life. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 35(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 268(nv 2–14 mm/mol creatinine).

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 A433V variant creates an MwpI restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved.

Variant NM_000159.3(GCDH):c.1298C>T (p.Ala433Val), homozygous

ClinVar 556228

gnomAD MAF= 0.00003266(South Asian), no homozygotes

CaseAddInfo n/a

CasePMIDs see notes on previous studies

Case1 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 3336(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 825(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 A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

Variant NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), homozygous

ClinVar 2083

gnomAD MAF= 0.0004013(African), no homozygotes

CaseAddInfo Sibling(Case 2) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 2120mmol/mol creatinine and 3-OH-glutarate was 543mmol/mol creatinine.

CasePMIDs n/a

Case24 sex unknown, Spain

CasePresentingHPOs HP:0000707

(Neurological abnormality)

HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes defined as "slight," entailing minimal neurological signs and an otherwise normal life. 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 1673(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 795(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 A304T variant destroys an AluI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved. The L309W variant creates an EcoP15 site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

Variant 1. NM_000159.3(GCDH):c.910G>A (p.Ala304Thr), 2. NM_000159.3:c.926T>G (p.Leu309Trp), compound heterozygous

ClinVar 1. 554907, 2. n/a

CAID 2. CA404319538

gnomAD 1. MAF=0.00006163(African), no homozygotes, 2. MAF= 0.000008816(European(non-Finnish)), no homozygotes CaseAddInfo n/a

CasePMIDs n/a

Case13 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 1288(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 75(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 a MspI site. This would lead to uncleaved patient DNA fragments and cleaved control fragments.

Variant NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), homozygous

ClinVar 2085

gnomAD MAF= 0.0007566(European(Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs see note on previous studies

Case27 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. Patient may have gone undetected by routine screening as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 2(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 18(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 10.

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 V400M variant creates an NlaIII site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

Variant NM_000159.3(GCDH):c.1198G>A (p.Val400Met), homozygous

ClinVar 2088

gnomAD MAF= 0.0002769(Other), no homozygotes

CaseAddInfo n/a

CasePMIDs see note on previous studies

"proband disclosed a heterozygous 18 bp deletion (c.553_570del18) in GCDH (NM_000159) predicted to result in a six amino acids deletion (p.Gly185_- Ser190del)"

I don't see any patient carrying this variant in Table 1

Case38 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. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 4(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 43(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 9. Patient tested negative in glutarylcarnitine blood spot test, even under carnitine supplementation.

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 Y155H variant creates a NcoI restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved. The R227P variant creates a NlaIV site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

Variant 1. NM_000159.3:c.463T>C(p.Tyr155His) , 2. NM_000159.3(GCDH):c.680G>C (p.Arg227Pro), compound heterozygous

ClinVar 1. n/a, 2. 2089

CAID 1. CA404317601

gnomAD 1. MAF=0.000008791(European(non-Finnish)), no homozygotes, 2. MAF= 0.0003566(European(non-Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs see notes on previous studies

Case10 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 778(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 264(nv 2–14 mm/mol creatinine).

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 A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved. Likewise, the R402W variant destroys a MspI site. This would lead to uncleaved patient fragments and cleaved control fragments.

Variant 1. NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), 2. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), compound heterozygous

ClinVar 1. 2083, 2. 2085

gnomAD 1. MAF=0.0004013(African), no homozygotes, 2. MAF= 0.0007566(European(Finnish)), no homozygotes

CaseAddInfo Sibling (Case 11) was asymptomatic. GC-MS measured glutarate of 2083(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 262(nv 2–14 mm/mol creatinine)

CasePMIDs n/a

Case#: OA-20, F, 10 months (report), Indian

CasePresentingHPOs: Classic form of MSUD.

CasePreviousTesting: Initially diagnosed with MSUD based on clinical features and biochemical tests (urine screening by DNPH and thin layer chromatography for amino acids). Confirmed diagnosis by blood amino acid quantification using HPLC.

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Genomic DNA extracted from peripheral blood leukocytes. PCR of exonic and flanking intronic regions of BCKDHA, BCKDHB, and DBT.

Variant: 1. NM_001918.3:c.827T>C (p.Phe276Cys); 2. NM_001918.3:c.190G>A (p.Val64Ile).

ClinVar: 1. 11943

CAID: CA341345584

gnomAD: 1. European (Non-Finnish) 0.0002210, Overall 0.0001154; 2. Not in gnomAD

VariantEvidence: p.Phe276Cys results in an enzyme activity of the DBT protein similar to wild type (PMID: 2914958, 1847055).

CaseAddInfo: Unsure if the variants are in trans.

Patient10: Female, 11yo, sibling to patient 11

CasePresentingHPOs:

HPOsFreeText: intermittent isovaleric acidemia, C5 (DBS) = 15.7 μmol l−1, IVA incorp (%) = 7, IVG in urine mmol permol creatinine = 4376, pH = 7.35, Protein intake (g kg−1 per day) = 0.64, treated with carnitine and glycine supplements, PDI/IQ in follow-up = 85

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

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

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: diagnosed via family evaluation at 2 days old

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

Patient6: Female, 4yo

CasePresentingHPOs:

HPOsFreeText: Asymptomatic, C5 (DBS) = 3.1 μmol l−1, IVG in urine mmol permol creatinine = 230, Ammonium (μmol l−1) = 56, pH = 7.37, Protein intake (g kg−1 per day) = 1.5, PDI/IQ in follow-up = 104

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

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

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: diagnosed with NBS at 10 days old

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_002225.3:c.158G>A listed in ClinVar as: NM_002225.4(IVD):c.149G>A (p.Arg50His)

CAID: CA7480513, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA7480513

ClinVar: 370843, https://www.ncbi.nlm.nih.gov/clinvar/variation/370843/

gnomAD: 0.00002784, http://gnomad.broadinstitute.org/variant/15-40699841-G-A

Variant2: NM_002225.3(IVD):c.941C>T (p.Ala314Val)

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

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

Patient4: Female, 3yo sibling to patient 5

CasePresentingHPOs:

HPOsFreeText: Asymptomatic, C5 (DBS) = 4.0 μmol l−1, IVA incorp (%) = 80, IVG in urine mmol permol creatinine = 242, Ammonium (μmol l−1) = 31, pH = 7.37, Protein intake (g kg−1 per day) = 1.5, treated with carnitine supplements, PDI/IQ in follow-up = 92

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

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

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: Diagnosed with NBS, diagnosed at 26 days old

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_002225.4(IVD):c.1205T>C (p.Ile402Thr)

ClinVar: 529433, https://www.ncbi.nlm.nih.gov/clinvar/variation/529433/

gnomAD: n/a

Variant2: NM_001159508.1:c.500T>C

CAID: CA391717541, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391717541

gnomAD: n/a

Patient7: Male, 2yo

CasePresentingHPOs:

HPOsFreeText: Asymptomatic, C5 (DBS) = 1.6 μmol l−1, IVG in urine mmol permol creatinine = 272, IVA incorp (%) = 72, Ammonium (μmol l−1) = 51, pH = 7.39, Protein intake (g kg−1 per day) = 1.5, PDI/IQ in follow-up = 93

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

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

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: Diagnosed with NBS at 28 days, homozygous

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_002225.3:c.706G>A

CAID: CA268780419, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA268780419

gnomAD: 0.00003187, http://gnomad.broadinstitute.org/variant/15-40705199-G-A

Case1: male, German, 4 days (onset)

CasePresentingHPOs:

HPOFreeText: Neonatal screening suggestive of MBD deficiency. Treatment since 9 months with 90 mg L-carnitine per kg body weight. Normal at 6 years old.

CaseNotHPOs:

CasePreviousTesting: Day 4: elevated C5 acylcarnitine (0.57 umol/l, ref <0.31) confirmed by 3 of 4 subsequent tests of DBS. Urinary organic acids showed normal N-isovalerylglycine but increased N-methylbutyrylglycine.

CaseGenotypingMethod: Genomic DNA extracted from DBS or peripheral blood. All exons and intron-exon boundaries of ACADSB sequenced.

Variant: NM_001609.3(ACADSB):c.38G>A (p.Arg13Lys) (homozygous)

ClinVar: 299068

gnomAD: European (Finnish): 0.4494; 1546 homozygotes

VariantEvidence: High frequency, listed as benign in ClinVar.

CaseAddInfo:

CasePMIDs:

Case5: male, Lebanon, neonatal screening 7 days

CasePresentingHPOs: HP:0045045, HP:0002155

HPOFreeText: Neonatal screening suggestive of MBD deficiency. Treatment of 150-200 mg L-carnitine/kg body weight and has shown normal development until 10 months.8 months: elevated serum triglycerides and GOT.

CaseNotHPOs:

CasePreviousTesting: Neonatal screening: elevated C5 acylcarnitine (0.51 umol/l and 0.72 umol/l; upper 99th percentile 0.29 umol/l) and C5/C2 acylcarnitine ratio (0.04 and 0.06; upper 99th percentile 0.02). 8 months: elevated serum triglycerides (673 mg/dl; ref <205) and GOT (57 U/l; ref <35).

CaseGenotypingMethod: Genomic DNA extracted from DBS or peripheral blood. All exons and intron-exon boundaries of ACADSB sequenced. Sibling and parents: only exons 1, 4, and 10 were analyzed.

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

ClinVar: 1. 9203; 2. 9202

gnomAD: 1. Latino 0.0004797, Overall 0.0002404, no homozygotes; 2. South Asian 0.002678; Overall 0.0008097, no homozygotes

VariantEvidence: 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 stability. c. 443C>T decreases ACADSB enzymatic activity to 2.8% of wild type in vitro (PMID: 20547083).

CaseAddInfo: 3 year old brother had a similar metabolite profile, but was not picked up by newborn screening (different cut-off values were used). Parents were normal. Patient also had c.38G>A polymorphism.

CasePMIDs:

Case: J.S./ BIODEF 211, female, Hispanic, 3 days

CasePresentingHPOs: HP:0008297, HP:0001252, HP:0001270

HPOText: Phe levels were 9 umol/L on day 1, 756 ummol/L on day 28. Primapterinuria was diagnosed on day 8. Following oral BH4 administration (2 mg/kg/d), neopterin normalized, and biopterin as well as primapterin increased about eight-fold; the same results were observed when dihydrobiopterin and sepiapterin were administered. At 8.5 years old, on a normal diet, the patient is developing normally with no HyperPhe.

CasePreviousTesting: n/a

CaseGenotypingMethod: Direct nucleotide-sequence determination of PCR products from blood samples was performed for the coding exons (2-4) of PCBD1.

Variant: NM_000281.3(PCBD1):c.236C>T (p.Thr79Ile)

ClinVar ID: 16797

No stars, 1 submission for OMIM.

Homozygous

gnomAD: n/a

AddCaseInfo: Family history (Family S) of HyperPhe, as the patients older brother, T.S./ BIODEF212, who is 1.5 years older, showed the same biochemical pattern and is now considered normal and normally developing.

At 8.5 years old, on a normal diet, the patient J.S. is developing normally with no HyperPhe.

VariantEvidence: The T78I/T79I variant was retained completely within the insoluble fraction of the E.Coli lysate in which the recombinant proteins were produced. When the soluble fraction was examined for PCBD1 activity, no activity was observed. The authors note that the absence of activity could be due to the absence of the protein in the soluble fraction alone, instead of being indicative of the mutation causing a loss of enzyme activity. Only if the mutant recombinant protein could be retained in the soluble fraction can the true enzyme activity be assessed.

Patient part of the BIODEF database: PMID:8830181

Case: B.E./ BIODEF 272, male, 3 weeks

CasePresentingHPOs: HP:0008297, HP:0001252, HP:0001270

HPOText: Neonatal (3 days old) plasma screen showed Phe levels at 183 umol/L, which is below the normal cutoff. Repeat screen was only performed at 3 weeks old in which the Phe level was shown to be 1600 umol/L. Peak Phe level was at 3.5 weeks and was 2589 umol/L. Child had considerable Phe tolerance ( ~100mg/kg). Initial neopterin-to-biopterin ratio of 15. A BH4-loading test (6 mg/kg) at age 6 wk showed only a slight response (Phe at 0 h, 731 μmol/liter; at 3 h, 612 μmol/liter; and at 6 h, 502 μmol/liter). A week later, at a BH4 dose of 22 mg/kg, there was a definite response (Phe at 0 h, 773 μmol/liter; at 3 h, 517 μmol/liter; and at 6 h, 155 μmol/liter). CSF neurotransmitter concentrations were normal, suggesting a peripheral deficiency. At 4 months of age, the BH4 was discontinued, no low Phe diet, and the Phe levels have remained normal. at 3.5 years, patient developing normally.

CaseNOTHPOs:

CasePreviousTesting: n/a

CaseGenotypingMethod: Direct nucleotide-sequence determination of PCR products from blood samples was performed for the coding exons (2-4) of PCBD1.

Variant: NM_000281.3(PCBD1):c.292C>T (p.Gln98Ter)

ClinVar ID: 16799

No star, one submission for OMIM

Homozygous

gnomAD: MAF (Euro-NF)= 2.2291E-4 (29/126606) hets only. No homozygotes recorded

AddCaseInfo: Family E in the article, and the proband had an older sibling that also carried the homozygous mutation in PCBD1, she was not noted as having increased Phe plasma levels, nor was ever treated with BH4 or low-Phe diet.

VariantEvidence: The mutant Q97X protein was expressed in E.Coli to determine the solubility of the mutant enzyme and the activity. The mQ97X fragment was mostly found in the insoluble fraction of the supernatant. The remaining fraction obtained in the soluble fraction did retain some activity in vitro. Interestingly, when more Q97X was obtained in the soluble fraction (by growing the E.coli at 20 degrees C), the Km (Michaelis constant) was 2-3 times higher than wildtype (text only, no figures to compare).

Patient part of the BIODEF database: PMID:8830181

Case#: Patient 13, 3 days (onset), China

CasePresentingHPOs: HP:0012758, HP:0008344

HPOsFreeText: Thiamine-responsive form of MSUD.

CasePreviousTesting: Diagnosed based on elevated blood levels of leucine, valine and the ratio of leucine to phenylalanine (tandem mass spec), as well as abnormal urine BCKAs (gas phase chromatography-mass spec). . CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Genomic DNA from peripheral blood leukocytes from patients and parents extracted. PCR amplification of exons and intron/exon boundaries for BCKDHA, BCKDHB, DBT.

Variant: 1. NM_001918.3(DBT):c.51+5G>C

ClinVar: 1. 94004

CAID: 2. CA658820834

gnomAD: 1. East Asian 6.165e-4, overall 3.229e-5 ; 2. Not in gnomAD

VariantEvidence: Predicted LOF

CaseAddInfo: Parents tested.

Case35 Male, 7.1yo report, Ethnicity: Syrian

CasePresentingHPOs HP:0003571, HP:0002789

(propionicacidemia, tachypnea)

HPOsFreeText tachypnea(6do). 55 IQ on Culture Free Test

CaseNotHPOs n/a

CasePreviousTesting Diagnosis by NBS. Patient fibroblasts had 1.5% PCC activity of control.

Variant NM_000532.4:c.1313C>T (p.Ala438Val), homozygous

ClinVar n/a

CAID CA354649295

gnomAD not in gnomAD

CaseAddInfo no parental consanguinity

CasePMIDs n/a

Case34 female, 5.5yo report, Ethnicity: German

CasePresentingHPOs HP:0003571, HP:0012523, HP:0001531, HP:0002791, HP:0001944

(propionicacidemia, oral aversion, failure to thrive in infancy, bradypnea, dehydration)

HPOsFreeText feeding refusal, failure to thrive, bradypnea, dehydration(2do). 55 IQ on Culture Free Test

CaseNotHPOs n/a

CasePreviousTesting Diagnosed on newborn screen. PCC activity in patient fibroblasts was 0.9% of control

Variant NM_000532.4:c.483dup (p.Gly162TrpfsTer?), homozygous

ClinVar n/a

CAID to register

gnomAD not in gnomAD

CaseAddInfo no parental consanguinity

CasePMIDs n/a

Case32 Male, 13.6yo report, Ethnicity: Turkish

CasePresentingHPOs HP:0003571, HP:0001531, HP:0008947, HP:0002789, HP:0001259, HP:0002045, HP:0002240

(proprionicacidemia, failure to thrive in infancy, infantile hypotonia, tachypnea, coma, hypothermia, hepatomegaly)

HPOsFreeText feeding difficulties, failure to thrive, hypotonia, tachypnea, coma, hypothermia, hepatomegaly(4do). 57 IQ on Snijders-Omen Test

CaseNotHPOs n/a

CasePreviousTesting Diagnosed by newborn screening. Patient fibroblasts had 0.7% PCC activity of controls.

Variant NM_000532.4:c.613G>T (p.Val205Phe), homozygous

ClinVar n/a

CAID CA354641901

gnomAD not in gnomAD

CaseAddInfo parental consanguinity

CasePMIDs n/a

FamilyLabel 29/30 Fam

Family29/30PresentingHPOs HP:0003571, HP:0002789

(Propionicacidemia, Tachypnea)

HPOsFreeText n/a

FamilyNotHPOs n/a

CountryOrigin n/a

Ethnicity Iraqi

Race n/a

Family29/30PreviousTesting n/a

ProbandLabel 29

Variant NM_000532.4:c.183+2T>C (p.=), homozygous

ClinVar n/a

CAID CA354738149

gnomAD not in gnomAD

FamilyAddInfo parental consanguinity

FamilyPMIDs n/a

Case23 Female, 5.2yo report, Ethnicity: Russian

CasePresentingHPOs HP:0003571, HP:0012523, HP:0001531, HP:0001944, HP:0001259, HP:0001250

(propionicacidemia, oral aversion, failure to thrive in infancy, dehydration, coma, seizures)

HPOsFreeText feeding refusal, failure to thrive, dehydration, coma, seizures(7do). 55 IQ on Culture-Free-Test.

CaseNotHPOs n/a

CasePreviousTesting Diagnosis by newborn screening. PCC activity in patient fibroblasts was 0.5% of control.

Variant NM_000532.4:c.803T>G (p.Leu268Trp), homozygous

ClinVar n/a

CAID CA354644558

gnomAD not in gnomAD

CaseAddInfo no parental consanguinity

CasePMIDs n/a

FamilyLabel 38/39 Fam

Family38/39PresentingHPOs n/a

FamilyNotHPOs n/a

CountryOrigin n/a

Ethnicity Turkish

Race n/a

Family38/39PreviousTesting Diagnosed by selective metabolic screen

ProbandLabel 38

Variant NM_000532.4(PCCB):c.1534C>T (p.Arg512Cys), homozygous

ClinVar 38879

gnomAD MAF= 0.00005440(East Asian), no homozygotes

FamilyAddInfo parental consanguinity

FamilyPMIDs n/a

Likely Variant Evidence for Variant: c.466C>T (p.Arg156Ter) ClinVar: 39743 and Variant:c.222del (p.Met74IlefsTer15) CAID: CA891862642

CaseEG1291: Female, 5 days onset

CasePresentingHPOs: HP:0200134, HP:0012469, HP:0032794, HP:0032667, HP:0002187, HP:0032792, HP:0002069, HP:0007359, HP:0010841, HP:0002188, HP:0006913, HP:0002079, HP:0001290 (Epileptic encephalopathy, Infantile spasms, Myoclonic seizure, Myoclonic status epilepticus, Profound intellectual disability, Tonic seizure, Bilateral tonic-clonic seizure, Focal-onset seizure, Multifocal epileptiform discharges, Delayed CNS myelination, Frontal cortical atrophy, Hypoplasia of the corpus callosum, Generalized hypotonia)

HPOsFreeText: N/A

CaseNotHPOs: HP:0002521 (Hypsarrhythmia)

NotHPOsFreeText: N/A

CaseAddInfo: Proband confirmed de novo heterozygous by parental sequencing; Father had two seizures as an adult, no further seizures while on LTG

CasePreviousTesting: Currently on levitiracetam and valproate; previously on pyridoxine, prednisolone, vigabatrin, zonisamide and ketogenic diet

CaseGenotypingMethod: About 10% of the original 290 genes where a single de novo variant had been identified was chosen for targeted sequencing in a new cohort. Most of these individuals had been tested for mutations of known and novel candidate genes as well as pathogenic copy-number variants. These genes were sequenced in the parents and proband to look for de novo variants.

Variant: NM_004171.4(SLC1A2):c.244G>C (p.Gly82Arg)

ClinVar: 254265, https://www.ncbi.nlm.nih.gov/clinvar/variation/254265/

gnomAD: Not in gnomAD

Case8: Female, South America

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in neonatal period

CasePreviousTesting: N/A

CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.

Variant1: NM_198271.4:c.723_733del (p.Asp242Glufs*4)

CAID: CA2488932 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.723_733del

gnomAD: Latino 2.896e-4, Overall 4.416e-5 https://gnomad.broadinstitute.org/variant/3-69168772-AAGCTCCCATCC-A

Variant2: NM_198271.4:c.976G>C (p.Gly326Arg)

CAID: CA353473660 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.976G%3EC

gnomAD: Not in gnomAD

Case9: Female, Italy

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0003798, HP:0001561, HP:0001558, HP:0000602, HP:0001622, HP:0001371 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Nemaline bodies, Polyhydramnios, Decreased fetal movements, Ophthalmoplegia, Preterm delivery, Contractures)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in 4 months

CasePreviousTesting: N/A

CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.

Variant: NM_198271.4:c.860delT (p.Phe287Serfs*3)

CAID: CA913203455 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913203455

gnomAD: Not in gnomAD

Case10: Male, Ecuador

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0001561, HP:0001558, HP:0000602, HP:0001622, HP:0001371, HP:0001623, HP:0002804 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Polyhydramnios, Decreased fetal movements, Ophthalmoplegia, Preterm delivery, Contractures, Breech presentation, Arthrogryposis)

HPOsFreeText: Bilateral femoral fractures

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in 6 weeks

CasePreviousTesting: N/A

CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.

Variant1: NM_198271.4:c.976G>C (p.Gly326Arg)

CAID: CA353473660 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.976G%3EC

gnomAD: Not in gnomAD

Variant2: NM_198271.4:c.1372C>T (p.Gln458*)

CAID: CA353470920 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.1372C%3ET

gnomAD: Not in gnomAD

Case6: Female, Japan, Asian

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0003798, HP:0001561, HP:0001558, HP:0001789, HP:0000252, HP:0001622, HP:0001371 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Nemaline bodies, Polyhydramnios, Decreased fetal movement, Hydrops fetalis, Microcephaly, Preterm delivery, Contractures)

HPOsFreeText: Atrophic myofibers

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Alive at 10 months

CasePreviousTesting: N/A

CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.

Variant: NM_198271.4:c.349C>T (p.Gln117*)

CAID: CA353477271 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.349C%3ET

gnomAD: Not in gnomAD

Case3: Female, Portugal

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0002804, HP:0001558, HP:0001561, HP:0001371 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Decreased fetal movement, Polyhydramnios, Contracture)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in neonatal period

CasePreviousTesting: N/A

CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.

Variant: NM_198271.4:c.154del (p.Met52*)

CAID: CA909810717 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.154delA

gnomAD: Not in gnomAD

Case12a: Male, Afghanistan

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0002804, HP:0001558, HP:0001622, HP:0001623, HP:0003798 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Arthrogryposis, Decreased fetal movement, Preterm delivery, Breech presentation, Nemaline bodies)

HPOsFreeText: Atrophic myofibers

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in 2 months, Has 2 siblings with same genotype/phenotype

CasePreviousTesting: N/A

CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.

Variant: NM_198271.4:c.1099_1100delAA (p.Asn367Glnfs*11)

ClinVar: 162218 https://www.ncbi.nlm.nih.gov/clinvar/variation/162218/

gnomAD: South Asian 4.575e-4, Overall 5.625e-5 https://gnomad.broadinstitute.org/variant/3-69168405-GTT-G

Case14a: Female, Australia

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0001561, HP:0001622, HP:0002804, HP:0003798, HP:0001558, HP:0000602 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Polyhydramnios, Nemaline bodies, Decreased fetal movements, Ophthalmoplegia)

HPOsFreeText: Atrophic myofibers, Percutaneous endoscopic gastrostomy performed, Nocturnal noninvasive ventilation

CaseNotHPOs: HP:0001627, HP:0002540 (Cardiac abnormality, Inability to walk)

NotHPOsFreeText: N/A

CaseAddInfo: Typical congenital nemaline myopathy, Alive at 10 yrs, Parents are not consanguineous

CasePreviousTesting: N/A

CaseGenotypingMethod: Linkage analysis combined with homozygosity mapping was used to identify candidate chromosomal loci. Whole exome sequencing in this family revealed likely pathogenic mutations in LMOD3 which agreed with the aforementioned analysis and was consistent with autosomal recessive inheritance.

Variant1: NM_198271.4:c.1103_1105del (p.Asn368del)

ClinVar: 162216 https://www.ncbi.nlm.nih.gov/clinvar/variation/162216/

gnomAD: Not in gnomAD

Variant2: NM_198271.4:c.1201C>T (p.Arg401Ter)

ClinVar: 162217 https://www.ncbi.nlm.nih.gov/clinvar/variation/162217/

gnomAD: African 4.137e-5, Overall 7.135e-6 https://gnomad.broadinstitute.org/variant/3-69168305-G-A

CaseOS-152_II-1: Female, 1 yr report, United Kingdom

CasePresentingHPOs: HP:0001992, HP:0002013, HP:0002013, HP:0040293, HP:0010628, HP:0007359 (Organic aciduria, Vomiting, Bilateral tonic-clonic seizure, Right hemiplegia, Facial palsy, Focal-onset seizure)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001263 (Global developmental delay)

NotHPOsFreeText: N/A

CaseAddInfo: Parents are non-consanguineous, Proband is confirmed compound heterozygous for these variants via parental testing, R353C variant inherited from father but R393H supposedly de novo or mosaic

CasePreviousTesting: Routine urine screening for organic acidurias by gas chromatography–mass spectrometry showed markedly increased urinary excretion of several N-acetylated amino acids; Normal cranial imaging

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

Variant1: 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

Variant2: NM_000666.3(ACY1):c.1178G>A (p.Arg393His)

ClinVar: 18114 https://www.ncbi.nlm.nih.gov/clinvar/variation/18114/

gnomAD: 0.006571 (3 homozygotes), https://gnomad.broadinstitute.org/variant/3-52023042-G-A

CaseOS-138_II-1: Female, 4 yrs report, Asian

CasePresentingHPOs: HP:0001992, HP:0002373, HP:0001263 (Organic aciduria, Febrile seizure (within the age range of 3 months to 6 years), Global developmental delay)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents are consanguineous, 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

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

Variant: NM_000666.3(ACY1):c.589C>T (p.Arg197Trp)

ClinVar: 18113, https://www.ncbi.nlm.nih.gov/clinvar/variation/18113/

gnomAD: 0.00001764, https://gnomad.broadinstitute.org/variant/3-52021009-C-T

Case 8 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

__

Variant1: NM_015506.2(MMACHC):c.394C > T (p.Arg132Ter)

ClinVar: 1423

CAID: CA251787

gnomAD: 0.0007190 (South 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 of p.R132X maternal variant

Case 9 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

__

Variant1: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

Variant2: NM_015506.2(MMACHC):c.637G>T (p.Glu213Ter)

ClinVar: n/a

CAID: CA340133779

gnomAD: n/a

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier of p.W203X maternal variant

Case 14 (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.567dupT (p.Ile190Tyrfs*13)

ClinVar: 556708

CAID: CA522810899

gnomAD: [0.0001024] (https://gnomad.broadinstitute.org/variant/1-45974604-G-GT) (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for p.K220del maternal variant

Case 2 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

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

ClinVar: 203825

CAID: CA312728

gnomAD: 0.00005560 (East Asian)

Variant2: NM_015506.2(MMACHC):c.658_660delAAG

ClinVar: 95707

CAID: CA223197

gnomAD: 0.0003071 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, not any phenotypic info given, sibling (fetus) carrier of p.R73X maternal variant

Case 15 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

__

Variant1: NM_015506.2(MMACHC):c.394C > T (p.Arg132Ter)

ClinVar: 1423

CAID: CA251787

gnomAD: 0.0007190 (South Asian)

Variant2: NM_015506.2(MMACHC):c.615C > A (p.Tyr205Ter)

ClinVar: 558292

CAID: CA340133688

gnomAD: 0.0006427 (East Asian)

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

Case1: Female, 9 days at follow up, North African ancestry

CasePresentingHPOs: HP:0002013, HP:0001944,HP:0031123, HP:0000388 (emesis, dehydration, recurrent gastroenteritis, otitis media)

HPOsFreeText: NBS C4-acylcarnitine 2.9 umol/L, plasma C4 acylcarnitine 1.35 umol/L, isoC4-acylcarnitine 0.090 umol/g protein,

CaseNotHPOs:

NotHPOsFreeText: normal urine isobutyrylglycine

CaseAddInfo: repeatedly hospitalized during first 2 years of life.

CasePMIDs:

Case (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_014384.2(ACAD8):c.988C>T (p.Arg330Trp)

ClinVar: 5357

CAID: CA117438

gnomAD: 0.00006155 (African)

CaseAddInfo: homozygous mutations

Case4: Female, 2 wks at initation of follow up, European ancestry

HPOsFreeText: NBS C4-acylcarnitine 2.0 umol/L, Plasma C4-acylcarnitine 1.52 umol/L

CaseAddInfo: no data for urine excretion, unremarkable clinical condition

Case4 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_014384.2:c.443C>T (p.Pro148Leu)

ClinVar: n/a

CAID: CA6372945

gnomAD: not in gnomAD

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

ClinVar: 5355

CAID: CA117433

gnomAD: 0.0001395 (European Non-Finnish)

CaseAddInfo: compound heterozygote, indicated alleles 1 and 2 but not specified maternal and paternal, potential splice site variant of ACAD8 at exon3 (+3A>G)

Case3a: Male, 5d at initiation of follow up, East Indian Ancestry, sibling of Case 3b (family 1)

HPOsFreeText: NBS C4-acylcarnitine 2.4 umol/L, Plasma C4-acylcarnitine 1.14 umol/L, in vitro probe isoC4-acylcarnitine 0.133 umol/ g protein,

NotHPOsFreeText: normal urine isobutyrylglycine ug/mg creatinine

CaseAddInfo: unremarkable clinical condition

Case3a (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_014384.2(ACAD8):c.867C>A (p.His289Gln)

ClinVar: 5358

CAID: CA117441

gnomAD: not in gnomAD

CaseAddInfo: homozygous mutations

Case9: Male, 2 mo at initiation of follow up, Hispanic ancestry

HPOsFreeText: NBS C4-acylcarnitine 1.8 umol/L, Plasma C4-acylcarnitine 3.28, umol/L, in vitro probe isoC4-acylcarnitine 0.074 umol/g protein, urine C4-acylcarnitine 7.86 mmol/mol creatinine, Urine C4/C3 ratio 63

NotHPOsFreeText: normal urine isobutyrylglycine

CaseAddInfo: unremarkable clinical condition

Case9 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_014384.2(ACAD8):c.233T>C (p.Met78Thr)

ClinVar: 430160

CAID: CA6372883

gnomAD: n/a

CaseAddInfo: homozygous variants, no potential splice site alterations, no data for ACADS (SCAD-deficient) gene variants

FamilyHA: White, Great Britian

FamilyPresentingHPOs: HP:0000988, HP:0002344, HP:0002359, HP:0002355, HP:0007210, HP:0000712, HP:0002066, HP:0000639, HP:0001347, HP:0008353 (Skin rash, Progressive neurologic deterioration, Frequent falls, Difficulty walking, Lower limb amyotrophy, Emotional lability, Gait ataxia, Nystagmus, Hyperreflexia, Neutral hyperaminoaciduria)

HPOsFreeText: N/A

FamilyNotHPOs: N/A

NotHPOsFreeText: N/A

FamilyGenotypingMethod: Homozygosity mapping and fine mapping in ten members of two consanguineous families (the siblings in whom Hartnup disorder was originally discovered; family A) and in siblings from the US revealed linkage of Hartnup disorder to 5p15 only in family A, with a maximum combined multipoint lod score of 2.31 at 11.24 cM. This confirmed a previous study showing linkage to the same region. Both SLC6A18 and SLC6A19 were investigated for possible pathogenicity, with SLC6A19's pattern of expression supporting it as a primary candidate. Intronic primers were used to bidirectionally sequence each exon and flanking intronic regions, locating a homozygous splice site mutation that perfectly segregated with the phenotype.

FamilyPreviousTesting: Consistent testing showed the consistent phenotypes were the hyperaminoaciduria among all family members; Linkage analysis for SLC3A2, SLC7A8, SLC1A5, SLC6A18, and SLC6A20 were all negative for amy correlation

FamilyAddInfo:

FamilyProband: Case EHAA

FamilyPMIDs: 13358233

Variant: NM_001003841.3(SLC6A19):c.1173+2T>G

ClinVar: 449553 https://www.ncbi.nlm.nih.gov/clinvar/variation/449553/

gnomAD: 0.00008019, https://gnomad.broadinstitute.org/variant/5-1217062-T-C?dataset=gnomad_r2_1

Affected: 4

Unaffected: 5

pLOD: 2.31 at 11.24 cM

AddSegregationInfo: Family is consanguineous (first cousins), Candidate gene sequencing, Pedigree in Figure 1aA

CaseKLE: Male, Japan, Asian

CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

HPOsFreeText:

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo:

CasePreviousTesting: Identified via neonatal mass screening

CaseGenotypingMethod: Both SLC6A18 and SLC6A19 were investigated for possible pathogenicity, with SLC6A19's pattern of expression supporting it as a primary candidate. Intronic primers were used to bidirectionally sequence each exon and flanking intronic regions, locating two compound heterozygous mutations that perfectly segregate with the phenotype.

Variant1: NM_001003841.3:c.340del (L114fs*114)

CAID: CA916079859 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA916079859

gnomAD: Not in gnomAD

Variant2: NM_001003841.3:c.682_683delinsTA (p.Thr228Ter)

CAID: CA916079860 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA916079860

gnomAD: Not in gnomAD

Case5 Female, 6yo diagnosis, Korean

CasePresentingHPOs HP:0001083, HP:0003235

(Ectopia lentis, Increased blood methionine)

HPOsFreeText pretreatment homocysteine was normal, increased post-treatment total homocysteine, patient treated with low-methionine diet, vitamin B6, folate, vitamin B12, and betaine after diagnosis

CaseNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText Marfan syndrome, vascular occlusion

CasePreviousTesting pretreatment/posttreatment methionine: 697/648 μM(nv 7-47), pretreatment homocysteine: 3 μM(nv 0-5), posttreatment total homocysteine 121 μM(nv 5-15)

CaseMethod1 PCR

CaseMethod2 Sanger

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

Variant 1. NM_001178008.1:c.464C>T(p.Ala155Val), 2. NM_000071.2(CBS):c.1039G>A (p.Gly347Ser), compound heterozygous

ClinVar 1. n/a, 2. 188801

CAID 1. CA410601498

gnomAD 1. not in gnomAD, 2. MAF=0.00006497(European(non-Finnish)), no homozygotes

CaseAddInfo A155V inherited from father, G347S from mother

CasePMIDs n/a

Case1 Female, 1mo diagnosis, Korean

CasePresentingHPOs HP:0003235

(Increased blood methionine)

HPOsFreeText 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 HP:0001083, HP:0001249

(Ectopia lentis, Intellectual disability)

NotHPOsFreeText Marfan syndrome, vascular occlusion

CasePreviousTesting pretreatment/posttreatment methionine: 1,239/123 μM(nv 7-47), pretreatment/posttreatment homocysteine: 28/0 μM(nv 0-5), posttreatment total homocysteine 144 μM(nv 5-15). Diagnosis upon neonatal screen

CaseMethod1 PCR

CaseMethod2 Sanger

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

Variant 1. NM_001320298.1:c.461T>A(p.Leu154Gln), 2. NM_000071.2(CBS):c.770C>T (p.Thr257Met), compound heterozygous

ClinVar 1. n/a, 2. 188927

CAID 1. CA410601512

gnomAD 1. not in gnomAD, 2. MAF=0.0001396(Other), no homozygotes

CaseAddInfo L154Q variant from father, T257M from mother. Additional R18C variant inherited from father, but protein from this SNP retains normal expression, 30-70% of enzyme activity and was found to have a 1/100 frequency in the study's control population

CasePMIDs n/a

FamilyLabel Family 15

Family15PresentingHPOs n/a

HPOsFreeText Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Affected individuals were not responsive to the treatment, plasma homocysteine levels went unchanged. Patients were given additional oral betaine(3g twice per day) with a low protein diet.

FamilyNotHPOs n/a

NotHPOsFreeText n/a

CountryOrigin n/a

Ethnicity Anglo-Celtic

Race n/a

Family15PreviousTesting 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.

FamilyMethod1 PCR

FamilyMethod2 Sanger

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

ProbandLabel Case 18

Variant NM_000071.2(CBS):c.919G>A (p.Gly307Ser), homozygous

ClinVar 117

gnomAD MAF= 0.00041539(Other), no homozygotes

FamilyAddInfo n/a

FamilyPMIDs n/a

Case29 Male, 1yo diagnosis (Family 25)

CasePresentingHPOs HP:0001256, HP:0001263

(Mild intellectual disability, Developmental delay)

HPOsFreeText Diagnosed was on the basis of developmental delay. 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 no other sequelae

CasePreviousTesting n/a

Variant 1. NM_000071.2(CBS):c.536_553del18 (p.Asp179_Leu184del), 2. NM_000071.2(CBS):c.325T>C (p.Cys109Arg), comp het

ClinVar 1. 198388, 2. 212878

gnomAD 1. MAF=0.00002683(European(non-Finnish), no homozygotes, 2. MAF= 0.0001631(Other), no homozygotes

CaseAddInfo son of patient 30

CasePMIDs n/a

FamilyLabel Family 26

Family26PresentingHPOs HP:0001083

(Lens dislocation)

HPOsFreeText Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Affected individuals were not responsive to the treatment, plasma homocysteine levels went unchanged. Patients were given additional oral betaine(3g twice per day) with a low protein diet.

FamilyNotHPOs n/a

NotHPOsFreeText n/a

CountryOrigin n/a

Ethnicity Portugese

Race n/a

Family26PreviousTesting 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.

FamilyMethod1 PCR

FamilyMethod2 Sanger

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

ProbandLabel Case 31

Variant NM_000071.2(CBS):c.374G>A (p.Arg125Gln), homozygous

ClinVar 197625

gnomAD MAF= 0.00002326(European(non-Finnish)), no homozygotes

FamilyAddInfo n/a

FamilyPMIDs n/a

Case25 9yo diagnosis, Australia, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0002342, HP:0000939, HP:0001263, HP:0001369

(Lens dislocation, Moderate intellectual disability, Osteoporosis, Developmental delay, Arthritis)

HPOsFreeText Patient had severe osteoporosis, juvenile arthritis and was diagnosed on the basis of dislocated lenses and developmental delay. 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. (PMID:9156316): Total homocysteine was 252μmol/l before and 34μmol/l after treatment of betaine, folic acid, and low-dose aspirin.

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS. (PMID: 9156316): Restriction analysis confirmed the presence of two variants. The variant c.430G>A destroys a TaqI site. Thus, TaqI digestion yielded uncleaved 155bp fragments in both the proband and his father, while the WT was cleaved into 107 and 48bp fragments. The c.1316G>A variant likewise destroys a HapII site. The proband and his father had uncleaved 120bp fragments while the WT had 87 and 33bp fragments on HapII digestion. As both variants were detected in the proband, father, and two paternal aunts, c.1316G>A and c.430G>A were proposed to be in cis.

Variant 1. NM_000071.2:c.892dup (p.Gln298ProfsTer?), 2. NM_000071.2(CBS):c.430G>A (p.Glu144Lys); 3. NM_000071.2(CBS):c.1316G>A (p.Arg439Gln), comp het, 2&3 in cis

ClinVar 1. n/a, 2. 122; 3. 189088

CAID 1. register

gnomAD 1. MAF=0.00001777(European(Non-finnish)), no homozygotes 2. MAF=0.00009799(South Asian), no homozygotes, 3. MAF=0.00005341(African), no homozygotes

CaseAddInfo n/a

CasePMIDs 9156316

Case15 3yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0001256

(Lens dislocation, Mild intellectual disability)

HPOsFreeText Diagnosis was based on dislocated lens and intellectual disability. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. This patient was not responsive to the treatment, plasma homocysteine levels went unchanged. This patient was given additional oral betaine(3g twice per day) with a low protein diet.

CaseNotHPOs n/a

NotHPOsFreeText no other sequelae

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 NM_000071.2(CBS):c.919G>A (p.Gly307Ser), homozygous

ClinVar 117

gnomAD MAF= 0.00041539(Other), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

found c.444dup in allele registry

according to Mutalyzer, for correct HGVS notation, the correct position was 2 nucleotides over. The aa consequence also looked the same as the article reported.

Case22 7yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0001256, HP:0011342

(Lens dislocation, Mild intellectual disability, Mild developmental delay)

HPOsFreeText Patient had marfanoid features and was diagnosed on the basis of dislocated lens and mild developmental delay. 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(CBS):c.919G>A (p.Gly307Ser), 2. NM_000071.2(CBS):c.536_553del18 (p.Asp179_Leu184del), comp het

ClinVar 1. 117, 2. 198388

gnomAD 1. MAF=0.00041539(Other), no homozygotes, 2. MAF= 0.00002683(European(non-Finnish)), no homozygotes

CaseAddInfo patient also carries a common 68bp insertion, 88ins68, variant that does not cause hyperhomocysteinemia.

CasePMIDs n/a

Case16 3yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0001256

(Lens dislocation, Mild intellectual disability)

HPOsFreeText Diagnosis was based on dislocated lens and marfanoid features. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. This patient was not responsive to the treatment, plasma homocysteine levels went unchanged. This 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 NM_000071.2(CBS):c.919G>A (p.Gly307Ser), homozygous

ClinVar 117

gnomAD MAF= 0.00041539(Other), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case5 14yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083

(Lens dislocation)

HPOsFreeText Diagnosis was based on dislocated lenses. Plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid.

CaseNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText no other sequelae

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(CBS):c.833T>C (p.Ile278Thr), 2. NM_000071.2(CBS):c.325T>C (p.Cys109Arg), compound heterozygous

ClinVar 1. 120, 2. 212878

gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. MAF=0.0001631(Other), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case23 5yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0001256, HP:0002751, HP:0000766

(Lens dislocation, Mild intellectual disability, Kyphoscoliosis, Abnormality of the sternum)

HPOsFreeText Patient was diagnosed on the basis of dislocated lenses. 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(CBS):c.430G>A (p.Glu144Lys), 2. IVS1+1G>A, compound heterozygous

ClinVar 1. 122, 2. n/a

CAID 2. need more info

gnomAD 1. MAF=0.00009799(South Asian), no homozygotes, 2. n/a

CaseAddInfo n/a

CasePMIDs n/a

FamilyLabel Family 1

Family1PresentingHPOs n/a

HPOsFreeText plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid.

FamilyNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText n/a

CountryOrigin n/a

Ethnicity Anglo-Celtic

Race n/a

Family1PreviousTesting 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.

FamilyMethod1 PCR

FamilyMethod2 Sanger

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

ProbandLabel Case 1

Variant NM_000071.2(CBS):c.833T>C (p.Ile278Thr), homozygous

ClinVar 120

gnomAD MAF=0.001432(European(non-Finnish)), no homozygotes

FamilyAddInfo n/a

FamilyPMIDs n/a

FamilyLabel Family 1

Family1PresentingHPOs HP:0001083, HP:0000545, HP:0000501, HP:0001249, HP:0001260, HP:0001251, HP:0007256, HP:0000577, HP:0002317, HP:0007663, HP:0030854)

(Ectopia lentis, Myopia, Glaucoma, Intellectual disability, Dysarthria, Ataxia, Pyramidal signs, Exotropia, Gait instability, Poor visual acuity, Staphyloma)

HPOsFreeText skeletal deformities, malar flush, increased serum homocysteine and methionine, corneal staphyloma, biocular lens dislocation

FamilyNotHPOs n/a

CountryOrigin China

Ethnicity n/a

Race n/a

Family1PreviousTesting Screened for variants MTHFR by PCR amplifying its coding sequence. No variants were detected in MTHFR. Also measured metabolite levels of homocysteine and methionine in plasma, both were elevated in affected individuals

FamilyMethod1 PCR

FamilyMethod2 Sanger

FamilyGenotypingMethod Coding sequences of both MTHFR and CBS were PCR amplified and Sanger sequenced detecting no variants in MTHFR. Sequence primers for CBS were designed from flanking sequences of each exon.

ProbandLabel III:3

Variant 1. NM_001178008.1:c.407T>C(p.Leu136Pro), 2. NM_001178008.1:c.473C>T(p.Ala158Val), compound heterozygous

ClinVar n/a

CAID 1. CA321097579, 2. CA410601473

gnomAD 1. MAF=0.000008809(European(non-Finnish)), no homozygotes, 2. MAF=0.00004164(South Asian), no homozygotes

FamilyAddInfo parents, grandparents and other relatives were asymptomatic for homocystinuria. A158V variant inherited from father(II:3), L136P from mother(II:4). Han Chinese

FamilyPMIDs n/a

CaseHE9: 6 month onset

CasePresentingHPOs: HP:0001250, HP:0001943, HP:0001942, HP:0012120 (Seizure, Hypoglycemia, Metabolic acidosis, Methylmalonic aciduria)

HPOsFreeText: Elevated proionyl-carnitine and methyl-citrate in urine

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is homozygous for this variant,

CasePreviousTesting: Fibroblast cell lines taken from 150 patients with mild but clear MMAuria were studied; Urinary MMA at 143–184 mmol/mol creat. (ref 0.3-1.1); Low propionate incorporation in fibroblasts both +/- OHCbl of 3.0 nmol/16 h/mg (ref 3.5–24.4 −OHCbl, 4.3–28.9 +OHCbl); Not responsive to Vitamin B12 treatment

CaseGenotypingMethod: Genomic DNA and RNA extraction was performed and the MCEE gene was sequenced to identify any likely pathogenic variants.

Variant: NM_032601.3:c.158T>G (p.Ile53Arg)

CAID: CA347189175, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA347189175

gnomAD: Not in gnomAD

Case1: Female, 1y 7m, Chinese

HPOsFreeText: (at 13 days) C4 1.31 umol/L, C4/C2 0.21, C4/C3 1.96

NotHPOsFreeText: normal urine isobutyrylglycine

Case1 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_014384.2:c.235C>G (p.Arg79Gly)

ClinVar: n/a

CAID: CA6372884

gnomAD: 0.0002718 (East Asian)

Variant2: NM_014384.2:c.1000C>T (p.Arg334Cys)

ClinVar: n/a

CAID: CA6373194

gnomAD: 0.0003007 (East Asian)

CaseAddInfo: trans heterozygous, inherited one allele from each parent

Case2: Male, 1y 7m, Chinese

HPOsFreeText: (at 11 days) 1.69 C4 umol/L, 0.19 C4/C2, 2.38 C4/C3

NotHPOsFreeText: normal urine isobutyrylglycine

Case2 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: n/a

CAID: CA6372895

gnomAD: 0.001453 (East Asian)

CaseAddInfo:

Case7: Male, 6m, Chinese

CasePresentingHPOs: HP:0002248, HP:0001290, HP:0008872, HP:0002572 (haematemesis, hypotonia, feeding difficulties in infancy, recurrent vomiting)

HPOsFreeText: (at 19 days) 1.01 C4 umol/L, 0.38 C4/C2, 1.61 C4/C3

NotHPOsFreeText: normal urine isobutyrylglycine

Case7 (Level 2):

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_014384.2:c.444G>T (p.Pro148=)

ClinVar: n/a

CAID: CA6372946

gnomAD: 0.0002772 (Other)

Variant2: NM_014384.2:c.1176G>T (p.Arg392Ser)

ClinVar: n/a

CAID: CA6373249

gnomAD: 0.0001088 (East Asian)

CaseAddInfo: trans heterozygous, inherited one allele from each parent

Case# 16392, Spanish, 4yo report

Variant NM_000709.3(BCKDHA):c.659C>T (p.Ala220Val), NM_000709.3(BCKDHA):c.853G>C (p.Ala285Pro)

ClinVar 93367(c.659), 93375(c.853)

gnomAD c.659=0.00005805(East Asian), 0.000008156(Overall), c.853=0.00007896(European (Non-Finnish)), 0.00003970(Overall)

VariantEvidence 4% of normal BCKD activity in patient fibroblasts

CaseAddInfo in trans

Case# 18804, Spanish, 3yo report

CaseHPOs asymmptomatic

Variant NM_000709.3:c.647C>T, NM_000709.3:c.889C>T

CAID CA9461230(c.647), CA9461294(889)

gnomAD c.647=0.0001332(African), 0.00002463(Overall), c.889=0.00006534(African), 0.00001624(Overall)

VariantEvidence reduced BCKD activity to 30% of normal in patient fibroblasts

CaseAddInfo in trans

Case# 20493, Spanish, 1yo reported

CasePresentingHPOs HP:0008344

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:c.757G>A, NM_000709.3:c.848G>A, NM_000709.3:c.898G>A

CAID CA9461255(757), [CA406013082(848)&CA406013351(898)]

gnomAD c.757=0.00006681(European(Non-Finnish)), 0.00003236(Overall)

VariantEvidence Patient fibroblasts had <1% of normal BCKD activity

CaseAddInfo parents genotypes confirmed (in trans)

CaseCI-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 365 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.194T>C (p.Ile65Thr)

ClinVar: 636 https://www.ncbi.nlm.nih.gov/clinvar/variation/636/

gnomAD: 0.0005574, https://gnomad.broadinstitute.org/variant/12-102894893-A-G?dataset=gnomad_r3

Variant2: NM_000277.3(PAH):c.261C>A (p.Ser87Arg)

ClinVar: 583 https://www.ncbi.nlm.nih.gov/clinvar/variation/583/

gnomAD: 0.00009294, https://gnomad.broadinstitute.org/variant/12-102894826-G-T?dataset=gnomad_r3

CaseDII-3: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 725 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.561G>A (p.Trp187Ter)

ClinVar: 102736 https://www.ncbi.nlm.nih.gov/clinvar/variation/102736/

gnomAD: 0.00001760, https://gnomad.broadinstitute.org/variant/12-103249059-C-T

Variant2: NM_000277.3(PAH):c.782G>C (p.Arg261Pro)

ClinVar: 102832 https://www.ncbi.nlm.nih.gov/clinvar/variation/102832/

gnomAD: Not in gnomAD

CaseDII-2: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 970 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.561G>A (p.Trp187Ter)

ClinVar: 102736 https://www.ncbi.nlm.nih.gov/clinvar/variation/102736/

gnomAD: 0.00001760, https://gnomad.broadinstitute.org/variant/12-103249059-C-T

Variant2: NM_000277.3(PAH):c.782G>C (p.Arg261Pro)

ClinVar: 102832 https://www.ncbi.nlm.nih.gov/clinvar/variation/102832/

gnomAD: Not in gnomAD

CaseAII-4: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 2085 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband for Family 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.143T>C (p.Leu48Ser)

ClinVar: 608 https://www.ncbi.nlm.nih.gov/clinvar/variation/608/

gnomAD: 0.001025, https://gnomad.broadinstitute.org/variant/12-102912816-A-G?dataset=gnomad_r3

CaseBI-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 375 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.1222C>T (p.Arg408Trp)

ClinVar: 577 https://www.ncbi.nlm.nih.gov/clinvar/variation/577/

gnomAD: 0.001766, https://gnomad.broadinstitute.org/variant/12-102840493-G-A?dataset=gnomad_r3

Variant2: NM_000277.3(PAH):c.688G>A (p.Val230Ile)

ClinVar: 102784 https://www.ncbi.nlm.nih.gov/clinvar/variation/102784/

gnomAD: 0.0009025, https://gnomad.broadinstitute.org/variant/12-102855154-C-T?dataset=gnomad_r3

CaseEI-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 430 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.1066-11G>A

ClinVar: 607 https://www.ncbi.nlm.nih.gov/clinvar/variation/607/

gnomAD: 0.0004116, https://gnomad.broadinstitute.org/variant/12-103237568-C-T

Variant2: NM_000277.3(PAH):c.533A>G (p.Glu178Gly)

ClinVar: 92746 https://www.ncbi.nlm.nih.gov/clinvar/variation/92746/

gnomAD: 0.0001473, https://gnomad.broadinstitute.org/variant/12-103249087-T-C

CaseAI-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 330 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.143T>C (p.Leu48Ser)

ClinVar: 608 https://www.ncbi.nlm.nih.gov/clinvar/variation/608/

gnomAD: 0.001025, https://gnomad.broadinstitute.org/variant/12-102912816-A-G?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

CaseDI-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 365 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.561G>A (p.Trp187Ter)

ClinVar: 102736 https://www.ncbi.nlm.nih.gov/clinvar/variation/102736/

gnomAD: 0.00001760, https://gnomad.broadinstitute.org/variant/12-103249059-C-T

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

Case#: GA8, England, 15 years (onset), gender unknown.

CaseHPOs: HP:0000662, HP:0012026 (night blindness, (hyperornithinemia)

CaseHPOsFreeText: Presented with visual disturbances. Vitamin B6 responsive.

CaseNotHPOs: Neonatal encephalopathy

CasePreviousTesting: No previous DNA testing noted. Plasma ornithine at diagnosis 728 umol/L (normal <100)

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Sequence analysis of the OAT gene from fibroblast or lymphocyte cDNA and genomic DNA. Variant: NM_000274.3(OAT):c.952G>A (p.Glu318Lys)

ClinVar: 56138

gnomAD: The maximum population minor allele frequency in gnomAD is 0.00002328 (European non-Finnish); no homozygotes in any population. VariantEvidence: When the variant was expressed in yeast, OAT enzymatic activity was <10% normal. This variant did not significantly affect protein levels but displayed a marked reduction of the hexamer (the active form) and an accumulation of the monomeric form.

Case#: GA5, Southern Italy, 40 years (onset), gender unknown

CaseHPOs: HP:0000662, HP:0012026 (night blindness, (hyperornithinemia)

CaseHPOsFreeText: Presented with visual disturbances at age 40 years. Plasma ornithine levels could be normalized by diet alone. Not responsive to Vitamin B6 treatment.

CaseNotHPOs: Neonatal encephalopathy

CasePreviousTesting: No previous DNA testing noted. Plasma ornithine at diagnosis 805 umol/L (normal <100)

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Sequence analysis of the OAT gene from fibroblast or lymphocyte cDNA and genomic DNA. Variant: NM_000274.3(OAT):c.1307T>A (p.Ile436Asn)

ClinVar: 56115

gnomAD: The maximum population minor allele frequency in gnomAD = 0.00002662 (European non-Finnish); no homozygotes in any population.

VariantEvidence: The variant was expressed in S. cerevisae with a deletion of CargB, the year ortholog of OAT, that cannot grow in media with ornithine as the sole nitrogen source. Whereas expression of wild type OAT allows yeast to grow in media with ornithine as the sole nitrogen source, no growth was observed when the variant was expressed. OAT enzymatic activity was measured and was <10% normal, and OAT protein was barely detectable on Western blot.

Case#: GA3, Turkey, 5 years (onset), gender unknown

CaseHPOs: HP:0012026 (hyperornithinemia)

CaseHPOsFreeText: Presented with visual disturbances at 5 years of age. No further details.

CaseNotHPOs: Neonatal encephalopathy

CasePreviousTesting: No previous DNA testing noted. Plasma ornithine at diagnosis 650umol/L (normal <100)

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Sequence analysis of the OAT gene from fibroblast or lymphocyte cDNA and genomic DNA. Variant: NM_000274.3(OAT):c.991C>T (p.Arg331Ter) (homozygous)

ClinVar: 56141

gnomAD: The maximum population minor allele frequency in gnomAD is 0.0001446 (Latino); no homozygotes in any population.

Patient1: Male, 14 yo, Thai

CasePresentingHPOs: HP:0011968, HP:0001254, HP:0001250, HP:0001876, HP:0002919, HP:0001942, HP:0001987, HP:0002187, HP:0002300, HP:0002540, HP:0006846, HP:0002901, HP:0001510 (poor feeding, lethargy, seizures, pancytopenia, ketonuria, metabolic acidosis, hyperammonemia, profound mental retardation, inability to speak, inability to walk, acute encephalopathy, hypocalcemia, growth delay)

HPOsFreeText: acute neonatal IVA, hemoglobin = 10g/dL, WBC = 3370/mm^3, platelets = 27,000/mm^3, bicarbonate = 10mmol/L, anion gap = 36mmol/L, low serum calcium, ammonia = 420µmol/L, treated with total blood exchange, treated with low-protein diet and leucine-free formula (150–250mg/kg per day of l‐glycine, and 100mg/kg per day of l‐carnitine), urine isovalerylglycine = 515

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: non-consanguineous family, symptom onset at 7 days old, diagnosed at 2wks old

CasePMIDs:

CasePreviousTesting: urine organic acid analysis with GC/MS (PMID: 27082169)

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Genomic DNA extracted from peripheral blood, IVD coding exons and flanking introns amplified with PCR (primer in table 1), PCR products purified and sequenced with Big Dye Primer Cycle Sequencing Kit and ABI 210 Genetic Analyzer

Variant1: c.457–3_2CA>GG / no ClinVar or CAID

Variant2: NM_002225.3:c.1025A>G (p.Tyr342Cys) listed in paper as (p.Tyr371Cys)

CAID: CA7480839, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_002225.3%3Ac.1025A%3EG

gnomAD: 0.000003977, https://gnomad.broadinstitute.org/variant/15-40708332-A-G

Case#: Patient 1, male, died on DOL 4, from the Faroe islands

CaseHPOs: HP:0003811 (neonatal death)

CaseHPOsFreeText: At 16 hours old, began grunting, was jittery, and had tachypnea. At 48 hours, had increased jitteriness, hypertonia, hypothermia, and alkalosis. Coma and death at 4 days. In urine, undetectable citrulline, argininosuccinate, and orotic acid. Plasma amino acids showed extremely elevated glutamine and alanine suggestive of hyperammonemia. No ammonia levels were available.

CaseNotHPOs: HP:0003218 (Orotic aciduria)

CasePreviousTesting: Analysis of urea cycle enzymes on post mortem liver tissue: CPSI activity was 30.7 U (normal >12), basal NAGS activity was 10 U (normal >34), arginine stimulated NAGS activity was 20 U (normal >144).

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Tissue or DNA from the deceased infant of family 1 was unavailable; blood genomic DNA from both parents to search for a mutation in the NAGS gene. All seven exons including intron/exon boundaries of the NAGS gene were amplified and sequenced.

Variant: NM_153006.2(NAGS):c.971G>A (p.Trp324Ter) (homozygous) (based on parental results; both parents are heterozygous)

ClinVar: 2428

gnomAD: Absent

VariantEvidence: NA

Case#: Pedigree 6 proband, Finland

CaseHPOs: HP:0012026 (hyperornithinemia)

CaseHPOsText: Patient noted to be "of historical interest" because he was the first patient in whom hyperornithinemia was recognized in gyrate atrophy (PMID 4122112). At age 8, choroidal degeneration ultimately diagnosed as gyrate atrophy, abnormal ERG; plasma ornithine concentration 10 times normal.

CaseGenotypingMethod: Variant identified by sequencing of genomic clones of OAT; sequencing of the remainder of the coding region and exon/intron boundaries was normal.

Variant: NM_000274.3(OAT):c.539G>C (p.Arg180Thr) (homozygous)

ClinVarID: 153

gnomAD: Maximum population minor allele frequency = 0.0007166 (Finnish); no homozygotes

VariantEvidence: When expressed in CHO-K1 cells, the variant results in no detectable OAT activity. Another Finnish patient (out of a group of 16) was also found to be homozygous for this variant.

CaseLE19: Male, 16 yrs report

CasePresentingHPOs: HP:0000964, HP:0002650, HP:0000501, HP:0000518, HP:0000750, HP:0010862, HP:0002572 (Eczema, Scoliosis, Glaucoma, Cataract, Delayed speech and language development, Delayed fine motor development, Episodic vomiting)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variants not confirmed in-trans due to lack of parental testing

CasePreviousTesting: Specific plasma MMA levels, urine MMA levels, urine MA levels, and MMA/MA ratio available in Table 2; Congenital unilateral persistent hyperplastic primary vitreous (PHPV), causing glaucoma and cataract

CaseGenotypingMethod: See Group

Variant1: NM_001243279.3(ACSF3):c.1075G>A (p.Glu359Lys)

ClinVar: 31136, https://www.ncbi.nlm.nih.gov/clinvar/variation/31136/

gnomAD: 0.001054, https://gnomad.broadinstitute.org/variant/16-89180844-G-A

Variant2: NM_001243279.3:c.1239+2T>G

CAID: CA397142431, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA397142431

gnomAD: Not in gnomAD

CaseLE12: Female, 23 yrs report

CasePresentingHPOs: HP:0002725 (Systemic lupus erythematosus)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variant 1 homozygous, with variant 2 in-cis with one copy confirmed via parental testing

CasePreviousTesting: Specific plasma MMA levels, urine MMA levels, urine MA levels, and MMA/MA ratio available in Table 2

CaseGenotypingMethod: See Group

Variant1: NM_001243279.3:c.1553C>A (p.Ala518Asp)

CAID: CA8238286, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA8238286

gnomAD: 0.00006153, https://gnomad.broadinstitute.org/variant/16-89212397-C-A

Variant2: NM_001243279.3:c.473C>T (p.Pro158Leu)

CAID: CA8237662, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA8237662

gnomAD: 0.0002823, https://gnomad.broadinstitute.org/variant/16-89167562-C-T

Case# Case 1, F, Chinese, 4day old Age of Onset

CasePresentingHPOs HP:0011968, HP:0001276, HP:0002373, HP:0001954, HP:0008344

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

CaseMethod1 Whole Exome

CaseMethod2 Sanger

CaseGenotypingMethod validated whole exome findings with sanger and qPCR.

Variant NM_000056.4(BCKDHB):c.508C>T (p.Arg170Cys), NM_000056.3:c.659del

ClinVar 96590 (missense)

CAID CA658820635 (c.659del)

gnomAD 0.00001791 (European(Non-Finnish)), 0.000008123 (Overall)

CasePMIDs missense mentioned in 25381949

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

CasePresentingHPOs HP:0008344, HP:0040168, HP:0008947, HP:0011968

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

CaseMethod1 Whole Exome

CaseMethod2 Sanger

CaseGenotypingMethod validated whole exome findings with sanger and qPCR.

Variant NM_000056.3:c.863C>A(p.Ala288Asp), ?

CAID CA364660141 (miss), wait for follow up (exon del)