Case#: KM03, F, neonatal (onset), Japanese

CasePresentingHPOs: HP:0001254, HP:0002179, HP:0001276, HP:0001263 (Lethargy, Opisthotonus, Hypertonia, Global developmental delay)

HPOsFreeText: Diagnosed at the time of newborn screening. Originally presented as classical form, but later determined to be the intermittent form.

CaseNotHPOs:

CasePreviousTesting: Lymphoblastoid cells from the patient showed reduced decarboxylation activity: 0.12 nmol/h per mg of protein (~9% of control). The authors previously showed by immunoblot analysis that the level of E2 protein was significantly reduced (PMID 3417306).

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Total RNA and genomic DNA prepared from lymphoblastoid cells or peripheral leukocytes. RT-PCR was performed with primers in exons 8 and 9 identified an insertion. Gnomic DNA was isolated and sequenced. Confirmed by restriction enzyme digestion.

Variant: NM_001918.3:c.1018-550A>G (homozygous)

ClinVar: 11946

gnomAD: Not in gnomAD

VariantEvidence: The predicted mRNA encoded a truncated protein with 282 amino acids, including 4 novel amino acids at the carboxyl terminus. 265bp fragment that included the 126 bp intronic region was subcloned into an exon trapping vector and transfected into COS-1 cells to confirm the splicing defect.

CaseAddInfo: Consanguineous, parents were heterozygous.

CasePMIDs: 3417306

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

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

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

CaseNotHPOs: HP:0001263 (Global development delay)

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

CaseMethod1: PCR

CaseMethod2: Sequencing

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

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

ClinVar: 11947

gnomAD: Not in gnomAD

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

CaseAddInfo: Consanguineous, parents and 2 siblings were heterozygous.

Case#: KM05, F, 2 years (Dx)

CasePresentingHPOs: HP:0005974 (Episodic ketoacidosis)

HPOsFreeText: At 11 years old she was eating a normal diet without restriction and plasma branched-chain amino acids were normal.

CasePreviousTesting: Lymphoblastoid cells from the patient showed reduced decarboxylation activity (~9% of control) and expression of the protein was moderately reduced (PMID 3417306).

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Total RNA was prepared from lymphoblastoid cells or peripheral leukocytes. An additional set of primers were used to distinguish each cDNA fragment from 2 different alleles. Clones were amplified and sequenced then confirmed by amplifying genomic DNA and performing restriction enzyme digestion.

Variant: 1. NM_001918.3(DBT):c.1150G>A (p.Gly384Ser); 2. NM_001918.3(DBT):c.294C>G (p.Ile98Met)

ClinVar: 1. 11949; 2. 11948

gnomAD: 1. East Asian 0.9705 (8883 homozygotes), Overall 0.9139; 2. Not in gnomAD

VariantEvidence: Variant 1 is likely benign

CaseAddInfo: Parents not available for testing.

CasePMIDs: 3417306

Case#: DBT-6

CasePresentingHPOs: Clinical information not available

Variant: NM_001918.3:c.1281+3A>G

CAID: CA658820827

gnomAD: Not in gnomAD

VariantEvidence: Non-canonical splice variant

CaseAddInfo:

CasePMIDs:

Case#: DBT-5

CasePresentingHPOs: Classic form of MSUD

Variant: NM_001918.3:c.1195T>C

CAID: CA341330334

gnomAD: Not in gnomAD

VariantEvidence: No functional evidence

CaseAddInfo:

CasePMIDs:

Case#: DBT-2

CasePresentingHPOs: Clinical information not available

Variant: NM_001918.3(DBT):c.75_76delAT (p.Cys26Trpfs) (homozygous)

ClinVar: 11950

gnomAD: Ashkenazi Jewish 0.0002959, Overall 0.00006863

VariantEvidence: Predicted LOF.

Case#: DBT-1

CasePresentingHPOs: Clinical information not available

Variant: NM_001918.3:c.61del (homozygous)

CAID: CA658820826

gnomAD: Not in gnomAD

VariantEvidence: Predicted LOF

Case#: Patient 2, Lebanon, Arab

CasePresentingHPOs: Intermediate form of MSUD

CasePreviousTesting: Previously diagnosed with MSUD by GC/MS/MS.

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Genomic DNA extracted, sequencing of BCKDHA, BCKDHB and DBT.

Variant: NM_001918.3:c.224G>A (homozygous)

CAID: CA341345382

gnomAD: Not in gnomAD

VariantEvidence: Mutation is present in lipoyl-binding domain, likely preventing binding of the lipoyl co-factor. Possibly results in a defect in the lipoyl-binding function (Alamut software analysis).

CaseAddInfo: Same variant reported in patient 1 from the same geographical location, but unrelated according to the authors.

Case#: Patient 1, Lebanon, Arab

CasePresentingHPOs: Intermediate form of MSUD

CasePreviousTesting: Previously diagnosed with MSUD by GC/MS/MS.

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Genomic DNA extracted, sequencing of BCKDHA, BCKDHB and DBT.

Variant: NM_001918.3:c.224G>A (homozygous)

CAID: CA341345382

gnomAD: Not in gnomAD

VariantEvidence: Mutation is present in lipoyl-binding domain, likely preventing binding of the lipoyl co-factor. Possibly results in a defect in the lipoyl-binding function (Alamut software analysis).

CaseAddInfo: Same variant reported in patient 2 from the same geographical location, but unrelated according to the authors.

Case#: Patient 3, Lebanon, Arab

CasePresentingHPOs: Intermediate form of MSUD

CasePreviousTesting: Previously diagnosed with MSUD by GC/MS/MS.

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Genomic DNA extracted, sequencing of BCKDHA, BCKDHB and DBT.

Variant: NM_001918.3:c.1430T>G (homozygous)

ClinVar: 93994

gnomAD: European (Non-Finnish) 8.971e-6, Overall 4.065e-6.

VariantEvidence: Mutation is present in the catalytic domain and would expect a defect in catalytic function (Alamut software analysis).

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.

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.

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.

Case#: Patient 14, N/A (onset), China

CasePresentingHPOs:

HPOsFreeText: Classic 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.713delC (homozygous)

CAID: CA658820836

gnomAD: Not in gnomAD

VariantEvidence: Predicted LOF

CaseAddInfo: Parents tested.

Case#: Patient 14, 1 month (onset), China

CasePresentingHPOs: HP:0001328, HP:0008344

HPOsFreeText: Classic 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.372_377del (homozygous)

CAID: CA658820835

gnomAD: Not in gnomAD

VariantEvidence: In frame deletion

CaseAddInfo: Parents tested.

PMID: 10915611

Gene: DBT

Disease: Maple syrup urine disease

MonDO: MONDO:0009563

InheritancePattern: AR

PMID: 26453840

Gene: DBT

Disease: Maple syrup urine disease

MonDO: MONDO:0009563

InheritancePattern: AR

Case#: 8, male, 13 days (onset), 1 y 6 m (current), Chinese

CasePresentingHPOs: HP: 0008344, HP:0012088, HP:0011968, HP:0001254, HP:0002415, HP: 0006989 (elevated A keto acids in urine, abnormal urinary odor, feeding difficulties, lethargy, leukodystrophy, dysplastic corpus callosum)

FreeTextHPOs: blood ammonia: 96 uM, hemoglobin: 98 g/L, leucin: 1047.24 uM, isoleucine: 261.09 uM, alloisoleucine: 127.05 uM

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: homozygous mutation

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_001918.3:c.1A>G (p.Met1Val)

ClinVar: not found

CAID: CA969877

gnomAD: not found

Case#: P4, F, 13 days (onset)

CasePresentingHPOs: HP:0001250, HP:0007105

CasePresentingHPOs (free text): TMS/GC-MS: Leu+Ile- 1810, Val- 275. Diagnosed with classic form of MSUD.

CasePreviousTesting: Biochemical testing (elevated BCAAs) used to make diagnosis.

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Genomic DNA extracted, coding regions (and flanking exon-intron boundaries) of BCKDHA, BCKDHB, and DBT were PCR-amplified, followed by bidirectional sequencing.

Variant: NM_001918.3(DBT):c.939G>C (p.Lys313Asn) (homozygous)

ClinVar: 94017

gnomAD: MAF (South Asian) 9.747e-5

VariantEvidence: None

Case#: P15, F, 2 months (onset)

CasePresentingHPOs: HP:0001263, HP:0200134

CasePresentingHPOs (free text): TMS/GC-MS: Leu+Ile- 517, Val- 315. Diagnosed with intermediate form of MSUD.

CasePreviousTesting: Biochemical testing (elevated BCAAs) used to make diagnosis.

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Genomic DNA extracted, coding regions (and flanking exon-intron boundaries) of BCKDHA, BCKDHB, and DBT were PCR-amplified, followed by bidirectional sequencing.

Variant: NM_001918.3(DBT):c.939G>C (p.Lys313Asn) (homozygous)

ClinVar: 94017

gnomAD: MAF (South Asian) 9.747e-5

VariantEvidence: None

Case#: Hou 2016 Proband, M, 7 days (onset), Taiwan (Amis Tribe)

CasePresentingHPOs: HP:0004396, HP:0030842, HP:0040181, HP:0002045 (continue)

HPOsFreeText:

CaseNotHPOs: .

CasePreviousTesting: Hemoglobin 1.36 mM (normal 1.4-2.17 mM); 613x10^9 platelets/L (normal 150-400x10^9); glucose 2.16 mM (normal 3.3-5.5 mM). Valine 1026 uM (normal 84.07-354 uM); leucine/isoleucine 829.41 uM (normal 56.82-287 uM).

CaseGenotypingMethod: Direct sequencing and duplex PCR of DBT.

Variant: 1. NM_001918.3(DBT):c.1282-4142_*(434_435)del; . NM_001918.3:c.650dup

ClinVar: 1. 11951

CAID: 2. CA658820832

gnomAD: 1. Not in gnomAD; Not in gnomAD

VariantEvidence: The deletion includes the 3' half of intron 10, the entire coding region of the terminal exon 11, and the 5' part of the 3' UTR of DBT.

CaseAddInfo: The 4.7 kb deletion had been previously reported in Paiwan tribe in Taiwan.