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BCKDHB branched chain keto acid dehydrogenase E1 subunit beta [ Homo sapiens (human) ]

Gene ID: 594, updated on 11-Apr-2024

Summary

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Official Symbol
BCKDHBprovided by HGNC
Official Full Name
branched chain keto acid dehydrogenase E1 subunit betaprovided by HGNC
Primary source
HGNC:HGNC:987
See related
Ensembl:ENSG00000083123 MIM:248611; AllianceGenome:HGNC:987
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
E1B; OVD1B; MSUD1B; BCKDE1B; BCKDH E1-beta
Summary
This gene encodes the E1 beta subunit of branched-chain keto acid dehydrogenase, which is a multienzyme complex associated with the inner membrane of mitochondria. This enzyme complex functions in the catabolism of branched-chain amino acids. Mutations in this gene have been associated with maple syrup urine disease (MSUD), type 1B, a disease characterized by a maple syrup odor to the urine in addition to mental and physical retardation and feeding problems. Alternative splicing at this locus results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Expression
Ubiquitous expression in liver (RPKM 2.7), fat (RPKM 2.3) and 25 other tissues See more
Orthologs
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Genomic context

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See BCKDHB in Genome Data Viewer
Location:
6q14.1
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (80106610..80466676)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (81315017..81677450)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (80816327..81055987)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Rho GTPase activating protein 21 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:80816184-80816684 Neighboring gene adenylate kinase 4 pseudogene 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:80921809-80922003 Neighboring gene ribosomal protein L17 pseudogene 25 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:81148056-81149255 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:81193272-81193889 Neighboring gene uncharacterized LOC112267962 Neighboring gene ribosomal protein SA pseudogene 72 Neighboring gene NANOG hESC enhancer GRCh37_chr6:81225104-81225623 Neighboring gene Sharpr-MPRA regulatory region 6183 Neighboring gene uncharacterized LOC105377869 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:81245601-81246800 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:81257567-81258766

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Neonatal maple syrup urine disease in China: two novel mutations in the BCKDHB gene and literature review. Jiang HH, et al. J Pediatr Endocrinol Metab, 2021 Sep 27. PMID 34187135
  2. Identification of novel mutations in BCKDHB and DBT genes in Vietnamese patients with maple sirup urine disease. Nguyen TTN, et al. Mol Genet Genomic Med, 2020 Aug. PMID 32515140, Free PMC Article
  3. [Mutation analysis and prenatal diagnosis for a pedigree affected with maple syrup urine disease]. Mei S, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2018 Oct 10. PMID 30298494
  4. Two novel compound heterozygous mutations in the BCKDHB gene that cause the intermittent form of maple syrup urine disease. Guo Y, et al. Metab Brain Dis, 2015 Dec. PMID 26239723
  5. Two novel mutations in the BCKDHB gene (R170H, Q346R) cause the classic form of maple syrup urine disease (MSUD). Wang YP, et al. Gene, 2012 Apr 25. PMID 22326532

See all (72) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Three novel mutations of the BCKDHA, BCKDHB and DBT genes in Chinese children with maple syrup urine disease.
    Title: Three novel mutations of the BCKDHA, BCKDHB and DBT genes in Chinese children with maple syrup urine disease.
  2. Neonatal maple syrup urine disease in China: two novel mutations in the BCKDHB gene and literature review.
    Title: Neonatal maple syrup urine disease in China: two novel mutations in the BCKDHB gene and literature review.
  3. Association of BCAT2 and BCKDH polymorphisms with clinical, anthropometric and biochemical parameters in young adults.
    Title: Association of BCAT2 and BCKDH polymorphisms with clinical, anthropometric and biochemical parameters in young adults.
  4. Identification of novel mutations in BCKDHB and DBT genes in Vietnamese patients with maple sirup urine disease.
    Title: Identification of novel mutations in BCKDHB and DBT genes in Vietnamese patients with maple sirup urine disease.
  5. Two heterozygous mutations c.284G>C (p.Gly95Ala) and c.853C>T (p.Arg285*) of the BCKDHB gene were associated with a pedigree affected with maple syrup urine disease.
    Title: [Mutation analysis and prenatal diagnosis for a pedigree affected with maple syrup urine disease].
  6. Six different novel genetic variants were validated in BCKDHB gene and BCKDHA gene, including c.523 T > C, c.659delA, c.550delT, c.863G > A and two gross deletions
    Title: Clinical characteristics and mutation analysis of five Chinese patients with maple syrup urine disease.
  7. Data suggest that the following genetic modifications are involved in patients with maple syrup urine disease in Iran: (1) mutation in BCKDHA (branched chain keto acid dehydrogenase E1 alpha); (2) mutation in BCKDHB (branched chain keto acid dehydrogenase E1 subunit beta); (3) mutation in DBT (dihydrolipoamide branched chain transacylase E2; one patient).
    Title: Four novel mutations of the BCKDHA, BCKDHB and DBT genes in Iranian patients with maple syrup urine disease.
  8. we identified seven novel genetic variants: p.Leu549Pro, p.Glu564*, p.Leu641Pro in MUT, p.Tyr206Cys in PCCB, p.His194Arg, p.Val298Met in BCKDHA and p.Glu286_Met290del in BCKDHB gene. In silico and/or eukaryotic expression studies confirmed pathogenic effect of all novel genetic variants
    Title: Molecular and phenotypic characteristics of seven novel mutations causing branched-chain organic acidurias.
  9. Five novel mutations in BCKDHB were identified in MSUD patients.
    Title: Eleven novel mutations of the BCKDHA, BCKDHB and DBT genes associated with maple syrup urine disease in the Chinese population: Report on eight cases.
  10. we describe the presenting symptoms and clinical course of a Chinese boy with intermittent Intermittent maple syrup urine disease from BCKDHB gene mutation
    Title: Two novel compound heterozygous mutations in the BCKDHB gene that cause the intermittent form of maple syrup urine disease.
Submit: New GeneRIF Correction See all GeneRIFs (24)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
EBI GWAS Catalog
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ17880, FLJ44134, DKFZp686A09102

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity IDA
Inferred from Direct Assay
more info
 PubMed 
contributes_to 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
contributes_to branched-chain alpha-keto acid dehydrogenase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in branched-chain amino acid catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in branched-chain amino acid catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in branched-chain amino acid catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in lipid metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in response to cAMP IEA
Inferred from Electronic Annotation
more info
  
involved_in response to glucocorticoid IEA
Inferred from Electronic Annotation
more info
  
involved_in response to nutrient IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of branched-chain alpha-ketoacid dehydrogenase complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial matrix NAS
Non-traceable Author Statement
more info
 PubMed 
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
located_in mitochondrion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
part_of oxoglutarate dehydrogenase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of oxoglutarate dehydrogenase complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of oxoglutarate dehydrogenase complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
2-oxoisovalerate dehydrogenase subunit beta, mitochondrial
Names
E1b-beta subunit of the branched-chain complex
branched chain alpha-ketoacid dehydrogenase E1-beta subunit
branched chain keto acid dehydrogenase E1 beta
branched chain keto acid dehydrogenase E1, beta polypeptide
branched-chain alpha-keto acid dehydrogenase E1 component beta chain
testis secretory sperm-binding protein Li 240mP
NP_000047.1
NP_001305904.1
NP_001410964.1
NP_001410965.1
NP_001410966.1
NP_001410967.1
NP_001410968.1
NP_001410969.1
NP_001410970.1
NP_001410971.1
NP_001410972.1
NP_001410973.1
NP_001410974.1
NP_898871.1
XP_005248813.1
XP_047275163.1
XP_047275166.1
XP_047275167.1
XP_047275168.1
XP_047275169.1
XP_047275170.1
XP_054212115.1
XP_054212118.1
XP_054212120.1
XP_054212122.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009775.3 RefSeqGene

    Range
    5063..244662
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000056.5 → NP_000047.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 1 precursor

    See identical proteins and their annotated locations for NP_000047.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate segment in the 3' UTR compared to transcript variant 1. Both variants 1 and 2 encode the same protein (isoform 1).
    Source sequence(s)
    CA447889, U50708
    Consensus CDS
    CCDS4994.1
    UniProtKB/Swiss-Prot
    P21953, Q5T2J3, Q9BQL0
    UniProtKB/TrEMBL
    A0A0K2GN21, A0A140VKB3
    Related
    ENSP00000348880.5, ENST00000356489.9
    Conserved Domains (1) summary
    PTZ00182
    Location:66 → 390
    PTZ00182; 3-methyl-2-oxobutanate dehydrogenase; Provisional

  2. NM_001318975.1 → NP_001305904.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' region and initiates translation at a downstream start codon compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Variants 3 and 13 both encode the same isoform (2).
    Source sequence(s)
    AK304353, AL049696, CA447889, DC422376, M55575
    UniProtKB/TrEMBL
    B4E2N3, B7ZB80
    Conserved Domains (1) summary
    PTZ00182
    Location:1 → 320
    PTZ00182; 3-methyl-2-oxobutanate dehydrogenase; Provisional

  3. NM_001424035.1 → NP_001410964.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) encodes the longest isoform (3).
    Source sequence(s)
    AL049696, AL359715, AL391595

  4. NM_001424036.1 → NP_001410965.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AL049696, AL359715, AL391595
    UniProtKB/Swiss-Prot
    P21953, Q5T2J3, Q9BQL0
    UniProtKB/TrEMBL
    A0A140VKB3

  5. NM_001424037.1 → NP_001410966.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AL049696, AL359715, AL391595

  6. NM_001424038.1 → NP_001410967.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 5 precursor

    Status: REVIEWED

    Source sequence(s)
    AL049696, AL391595

  7. NM_001424039.1 → NP_001410968.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 6 precursor

    Status: REVIEWED

    Source sequence(s)
    AL049696, AL391595

  8. NM_001424040.1 → NP_001410969.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 7 precursor

    Status: REVIEWED

    Source sequence(s)
    AL049696, AL391595

  9. NM_001424041.1 → NP_001410970.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 8 precursor

    Status: REVIEWED

    Source sequence(s)
    AL049696, AL391595

  10. NM_001424042.1 → NP_001410971.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 9 precursor

    Status: REVIEWED

    Source sequence(s)
    AL049696, AL391595

  11. NM_001424043.1 → NP_001410972.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL049696, AL391595
    UniProtKB/TrEMBL
    B7ZB80

  12. NM_001424044.1 → NP_001410973.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 10 precursor

    Status: REVIEWED

    Source sequence(s)
    AL391595

  13. NM_001424045.1 → NP_001410974.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 11 precursor

    Status: REVIEWED

    Source sequence(s)
    AL391595
    Related
    ENSP00000358775.4, ENST00000369760.8

  14. NM_183050.4 → NP_898871.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform 1 precursor

    See identical proteins and their annotated locations for NP_898871.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1. Both variants 1 and 2 encode the same protein (isoform 1).
    Source sequence(s)
    AL049696, CA447889, DC372349, M55575
    Consensus CDS
    CCDS4994.1
    UniProtKB/Swiss-Prot
    P21953, Q5T2J3, Q9BQL0
    UniProtKB/TrEMBL
    A0A0K2GN21, A0A140VKB3
    Related
    ENSP00000318351.5, ENST00000320393.9
    Conserved Domains (1) summary
    PTZ00182
    Location:66 → 390
    PTZ00182; 3-methyl-2-oxobutanate dehydrogenase; Provisional

RNA

  1. NR_134945.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL049696, BC034481, CA447889

  2. NR_187561.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL049696, AL391595

  3. NR_187562.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL049696, AL391595

  4. NR_187563.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL049696, AL391595

  5. NR_187564.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL049696, AL391595

  6. NR_187565.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL049696, AL391595

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    80106610..80466676
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047419211.1 → XP_047275167.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform X9

  2. XM_047419212.1 → XP_047275168.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform X9

  3. XM_047419210.1 → XP_047275166.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform X8

  4. XM_047419207.1 → XP_047275163.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    P21953, Q5T2J3, Q9BQL0
    UniProtKB/TrEMBL
    A0A140VKB3

  5. XM_005248756.6 → XP_005248813.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform X3

    UniProtKB/TrEMBL
    A0A0K2GN21
    Conserved Domains (2) summary
    cd07036
    Location:75 → 241
    TPP_PYR_E1-PDHc-beta_like; Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins
    pfam02780
    Location:262 → 346
    Transketolase_C; Transketolase, C-terminal domain

  6. XM_047419213.1 → XP_047275169.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform X5

  7. XM_047419214.1 → XP_047275170.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform X7

    UniProtKB/TrEMBL
    B7ZB80

RNA

  1. XR_001743546.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    81315017..81677450
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356140.1 → XP_054212115.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    P21953, Q5T2J3, Q9BQL0
    UniProtKB/TrEMBL
    A0A140VKB3

  2. XM_054356143.1 → XP_054212118.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform X3

  3. XM_054356145.1 → XP_054212120.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform X5

  4. XM_054356147.1 → XP_054212122.1  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial isoform X7

    UniProtKB/TrEMBL
    B7ZB80

RNA

  1. XR_008487369.1 RNA Sequence

  2. XR_008487371.1 RNA Sequence

  3. XR_008487372.1 RNA Sequence

  4. XR_008487373.1 RNA Sequence

  5. XR_008487370.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P21953.2 GenPept UniProtKB/Swiss-Prot:P21953

Gene LinkOut

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