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

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

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

CaseMethod1 Whole Exome

CaseMethod2 Sanger

CaseGenotypingMethod validated whole exome findings with sanger and qPCR.

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

ClinVar 189101 (dup)

CAID CA658820648 (del)

gnomAD low quality site (dup)

Case# Case 3, M, Chinese, 3day onset

CasePresentingHPOs HP:0008344, HP:0001954, HP:0005972, HP:0011968, HP:0008947

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.659del(p.D229fs)

CAID CA658820635

CaseAddInfo Mother was not tested but WES was used in the patient and father

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)

Case# Case 2, M, Chinese, 1day old Age of Onset

CasePresentingHPOs HP:0001276, HP:0000737, 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_000056.3:c.523T>C

CAID CA364657780, exon1-7 del waiting on follow up

VariantEvidence in trans with massive deletion

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

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

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

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: detected by newborn screening, unsure cis or trans

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: not found, 96590

CAID: CA364657700, CA224301

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

Case#: 6, male, 18 m (onset), 2 y 6 m (current), Chinese

CasePresentingHPOs: HP: 0008344, HP; 0012088, HP: 0011342, HP: 0001332, HP:0002543, HP: 0012751, HP:0012747 (elevated A keto acids in urine, abnormal urinary odor, mild global developmental delay, dystonia, abnormal globus pallidus, abnormal basal ganglia, abnormal brainstem MRI signal intensity)

HPOsFreeText: damage to cerebellar dentate nucleus, damage to corpora quadrigemina, damage to frontal lobe, damage to insular cortex, Isoleucine: 167.13 uM, Alloisoleucine: 44.88 uM

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: unsure cis or trans

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_183050.3:c.767A>G (p.Tyr256Cys), NM_183050.3:c.768C>G (p.Tyr256Ter)

ClinVar: neither found

CAID: CA364659935, CA142287564

gnomAD: 0.000008820 (European, non-Finnish), not found

Case#: Guo 2015 Proband, M, 18 months (onset), Chinese

CasePresentingHPOs: HP:0002329, HP:0011968, HP:0002317, HP:0012088, HP:0001946

Onset of symptoms upon episode of fever. Slightly reduced muscle tension. Second episode 2 months later and plasma amino acid analysis was performed: 431.67 umol/L leucine (normal 4.2-367), 167.13 umol/L isoleucine (normal 26.9-146), 47.81 umol/L valine (normal 117.6-495.7), 44.88 umol/L alloisoleucine (normal 0-7.7).

CaseNotHPOs: HP:0002373, HP:0002013, HP:0002361

CaseGenotyping Method: BCKDHA, BCKDHB, DBT, and DLD were screened for mutations using second generation sequencing. Direct sequencing was performed on the parents to confirm variants.

Variant: 1. NM_000056.3:c.767A>G (p.Y256C); 2. NM_000056.3:c.768C>G (p.Y256X)

CAID: 1. CA364659935; 2. CA142287564

gnomAD: 1. 4.069e-6 overall

Case# PB1, Saudi Arabia

CasePresentingHPOs HP:0000707, HP:0003011, HP:0025031, HP:0001939, HP:0002715

CasePreviousTesting Blood spot newborn screen/presented symptoms in Hospital

CaseMethod1 PCR

CaseGenotypingMethod PCR of coding exons of BCKDHA (9 exons), BCKDHB (11 exons) DBT (11 exons) and DLD (14 exons).

Variant NM_000056.3:c.1A>T

CAID CA364657845

gnomAD 0.00003656 (European (Non-Finnish)), 0.00001346 (Overall)

VariantEvidence none

CaseAddInfo consanguineous family

Case# PB5, Saudi Arabia

CasePresentingHPOs HP:0000707, HP:0003011, HP:0025031, HP:0001939, HP:0002715

CasePreviousTesting Blood spot newborn screen/presented symptoms in Hospital

CaseMethod1 PCR

CaseGenotypingMethod PCR of coding exons of BCKDHA (9 exons), BCKDHB (11 exons) DBT (11 exons) and DLD (14 exons).

Variant NM_000056.4(BCKDHB):c.574G>A (p.Gly192Arg)

ClinVar 96596

VariantEvidence none

CaseAddInfo consanguineous family

Case# PB6, Saudi Arabia

CasePresentingHPOs HP:0000707, HP:0003011, HP:0025031, HP:0001939, HP:0002715

CasePreviousTesting Blood spot newborn screen/presented symptoms in Hospital

CaseMethod1 PCR

CaseGenotypingMethod PCR of coding exons of BCKDHA (9 exons), BCKDHB (11 exons) DBT (11 exons) and DLD (14 exons).

Variant NM_000056.4(BCKDHB):c.817A>C (p.Thr273Pro)

ClinVar 96610

VariantEvidence none

CaseAddInfo consanguineous family

Case# PB4, Saudi Arabia

CasePresentingHPOs HP:0000707, HP:0003011, HP:0025031, HP:0001939, HP:0002715

CasePreviousTesting Blood spot newborn screen/presented symptoms in Hospital

CaseMethod1 PCR

CaseGenotypingMethod PCR of coding exons of BCKDHA (9 exons), BCKDHB (11 exons) DBT (11 exons) and DLD (14 exons).

Variant NM_000056.4(BCKDHB):c.502C>T (p.Arg168Cys)

ClinVar 96586

VariantEvidence none

CaseAddInfo consanguineous family

CasePMIDs previously studied in 17922217

Case# PB3, Saudi Arabia

CasePresentingHPOs HP:0000707, HP:0003011, HP:0025031, HP:0001939, HP:0002715

CasePreviousTesting Blood spot newborn screen/presented symptoms in Hospital

CaseMethod1 PCR

CaseGenotypingMethod PCR of coding exons of BCKDHA (9 exons), BCKDHB (11 exons) DBT (11 exons) and DLD (14 exons).

Variant NM_000056.3:c.286del

CAID CA658820633

VariantEvidence null

CaseAddInfo consanguineous family

Case# PB2, Saudi Arabia

CasePresentingHPOs HP:0000707, HP:0003011, HP:0025031, HP:0001939, HP:0002715

CasePreviousTesting Blood spot newborn screen/presented symptoms in Hospital

CaseMethod1 PCR

CaseGenotypingMethod PCR of coding exons of BCKDHA (9 exons), BCKDHB (11 exons) DBT (11 exons) and DLD (14 exons).

Variant NM_000056.3:c.197G>C

CAID CA364658947

VariantEvidence none

CaseAddInfo consanguineous family

PMID: 14742428

Gene: BCKDHB

Disease: MSUD, type 1a

MonDO: MONDO:0023691

InheritancePattern: AR