BCKDHB (branched chain keto acid dehydrogenase E1 subunit beta)

Gene

• Entrez ID: 594
• Gene name: Branched chain keto acid dehydrogenase E1 subunit beta
• Gene symbol: BCKDHB
• Synonyms: BCKDE1B, BCKDH E1-beta, E1B
• Chromosome: 6
• Chromosome location: 6q14.1
• 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]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs79761867	G>A,C	Likely-pathogenic, pathogenic-likely-pathogenic, pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs121965004	C>T	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs121965005	T>G	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs148905512	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs149766077	C>G,T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs190867671	T>A,C	Likely-pathogenic	Coding sequence variant, non coding transcript variant, intron variant, synonymous variant, 3 prime UTR variant, stop gained, genic downstream transcript variant
rs371518124	G>A,C	Uncertain-significance, pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs376293687	A>C,G	Likely-benign, uncertain-significance, benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, coding sequence variant, intron variant
rs386834233	G>A	Pathogenic-likely-pathogenic, pathogenic, likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs386834234	G>T	Pathogenic, likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant, genic downstream transcript variant, 3 prime UTR variant, intron variant
rs398124560	G>A	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs398124561	C>T	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs398124562	G>A	Uncertain-significance, likely-pathogenic	Non coding transcript variant, coding sequence variant, genic downstream transcript variant, missense variant, 3 prime UTR variant, intron variant
rs398124571	G>A	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs398124572	AC>-	Uncertain-significance, pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant, intron variant
rs398124573	T>C,G	Pathogenic, likely-pathogenic	Synonymous variant, non coding transcript variant, coding sequence variant, stop gained
rs398124574	G>A	Pathogenic	Splice acceptor variant
rs398124576	T>G	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs398124577	A>T	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs398124579	C>T	Uncertain-significance, likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs398124581	C>A,G,T	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs398124582	A>T	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs398124586	CA>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs398124587	AG>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs398124589	G>A,C,T	Pathogenic, likely-pathogenic	Splice donor variant
rs398124592	G>T	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs398124593	T>A,C	Pathogenic, likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs398124594	C>G,T	Pathogenic-likely-pathogenic, pathogenic	Missense variant, non coding transcript variant, coding sequence variant, stop gained
rs398124596	T>G	Pathogenic, likely-pathogenic	Splice donor variant
rs398124598	C>T	Pathogenic-likely-pathogenic, pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs398124600	T>G	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs398124601	GGCGCGGGGCT>-,GGCGCGGGGCTGGCGCGGGGCT	Pathogenic, likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant, intron variant
rs398124602	G>A	Pathogenic	Splice acceptor variant
rs398124603	C>T	Pathogenic-likely-pathogenic, pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs398124604	T>G	Uncertain-significance, likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs749033513	G>A,T	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs751599203	C>T	Conflicting-interpretations-of-pathogenicity	Intron variant, stop gained, coding sequence variant, non coding transcript variant, 3 prime UTR variant, genic downstream transcript variant
rs751953459	G>A	Pathogenic, likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs760538465	G>A,T	Likely-pathogenic, pathogenic	Splice donor variant
rs763645251	C>G	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs774306610	T>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs774916970	G>T	Likely-pathogenic	Non coding transcript variant, intron variant, stop gained, coding sequence variant
rs776270090	C>-	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs776631396	C>T	Pathogenic-likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs796051939	T>A	Pathogenic, likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs797045411	A>-	Likely-pathogenic	3 prime UTR variant, genic downstream transcript variant, coding sequence variant, intron variant, frameshift variant, non coding transcript variant
rs867612284	T>-	Pathogenic	Frameshift variant, coding sequence variant, intron variant, non coding transcript variant
rs869312126	T>G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, non coding transcript variant
rs869312127	A>G	Pathogenic	Splice acceptor variant
rs869312128	G>A	Pathogenic	Missense variant, intron variant, initiator codon variant, non coding transcript variant
rs869312129	T>-	Pathogenic	3 prime UTR variant, genic downstream transcript variant, coding sequence variant, intron variant, frameshift variant, non coding transcript variant
rs869312130	T>A	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs869312131	A>G	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs886043103	A>T	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs940391887	T>C	Likely-pathogenic	Initiator codon variant, intron variant, missense variant, non coding transcript variant
rs962489830	G>C	Likely-pathogenic	Splice acceptor variant
rs987877790	G>C	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs994415333	G>A,T	Uncertain-significance, likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1005542482	A>G,T	Likely-pathogenic	Initiator codon variant, missense variant, non coding transcript variant, intron variant
rs1057516572	T>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1057516731	C>-	Likely-pathogenic	Intron variant, non coding transcript variant, coding sequence variant, frameshift variant
rs1057516781	GGCTGCCGGC>-	Likely-pathogenic	Intron variant, non coding transcript variant, coding sequence variant, frameshift variant
rs1057516795	CCTGGCGCGGG>-	Pathogenic-likely-pathogenic	Intron variant, non coding transcript variant, coding sequence variant, frameshift variant
rs1057516799	G>T	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs1057517124	C>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1057517414	CAGAGGCGGCA>-	Likely-pathogenic	Intron variant, non coding transcript variant, coding sequence variant, frameshift variant
rs1060499715	G>A	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant, 3 prime UTR variant, intron variant, genic downstream transcript variant
rs1064796892	C>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1085307058	C>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1131691399	G>A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1167005638	->T	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs1202365275	G>A	Likely-pathogenic	Non coding transcript variant, missense variant, 3 prime UTR variant, genic downstream transcript variant, coding sequence variant, intron variant
rs1224101411	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, missense variant
rs1380402024	TTGGTGAAGAT>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1400121541	A>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1410520713	->TGAGGGGC	Pathogenic	Non coding transcript variant, intron variant, coding sequence variant, frameshift variant
rs1554180622	GGTGCTCCGCCCTCCCCGCAGGCGGCGTGCGGCTGCATAGCCTGAGAATCCCGGTGGTGAGCGGGGATGGCGGTTGTAGCGGCGGCTGCCGGCTGGCTACTCAGGCTCAGGGCGGCAGGGGCTGAGGGGCACTGGCGTCGGCTTCCTGGCGCGGGGCTGGCGCGGGGCTTTTTGCACCCCGCCGCGACTGTCGAGGATGCGGCCCAGAGGCGGCAGGTGGCTCATTTTACTTTCCAGCCAGATCCGGAGCCCCGG	Pathogenic	Splice donor variant, upstream transcript variant, non coding transcript variant, initiator codon variant, 5 prime UTR variant, genic upstream transcript variant, intron variant
rs1554181192	C>T	Likely-pathogenic	Stop gained, coding sequence variant, non coding transcript variant, intron variant
rs1554181203	G>C,T	Likely-pathogenic	Splice donor variant, intron variant
rs1554184224	A>G	Pathogenic, likely-pathogenic	Splice acceptor variant
rs1554184237	T>G	Likely-pathogenic	Splice donor variant
rs1554189447	->A	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1554190322	G>A	Likely-pathogenic	Splice donor variant
rs1554194690	GATGTTACTCTAGT>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1554205499	A>G	Likely-pathogenic	Splice acceptor variant
rs1554205506	A>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1554205541	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, non coding transcript variant
rs1582146275	AGAATCCCGGTGGTGAGCGGGGATGG>-	Likely-pathogenic	5 prime UTR variant, frameshift variant, splice donor variant, initiator codon variant, non coding transcript variant, intron variant
rs1582146989	->TTCCTGGCAGGGGCTGAGGA	Pathogenic	Inframe indel, non coding transcript variant, coding sequence variant, intron variant, stop gained
rs1582275277	A>T	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT001381	hsa-miR-1-3p	pSILAC, Proteomics;Other	18668040

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003826	Function	Alpha-ketoacid dehydrogenase activity	IMP	2022752
GO:0003863	Function	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity	IEA
GO:0005515	Function	Protein binding	IPI	12902323, 15166214, 15576032, 28514442
GO:0005730	Component	Nucleolus	IDA
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IMP	2022752
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0005947	Component	Mitochondrial alpha-ketoglutarate dehydrogenase complex	IBA	21873635
GO:0005947	Component	Mitochondrial alpha-ketoglutarate dehydrogenase complex	IMP	2022752
GO:0007584	Process	Response to nutrient	IBA	21873635
GO:0009083	Process	Branched-chain amino acid catabolic process	IBA	21873635
GO:0009083	Process	Branched-chain amino acid catabolic process	IMP	2022752
GO:0009083	Process	Branched-chain amino acid catabolic process	TAS

Other IDs

• MIM: 248611
• HGNC: 987
• e!Ensembl: ENSG00000083123

Protein

• UniProt ID: P21953
• Protein name: 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial (EC 1.2.4.4) (Branched-chain alpha-keto acid dehydrogenase E1 component beta chain) (BCKDE1B) (BCKDH E1-beta)
• Protein function: The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3).
• PDB: 1DTW, 1OLS, 1OLU, 1OLX, 1U5B, 1V11, 1V16, 1V1M, 1V1R, 1WCI, 1X7W, 1X7X, 1X7Y, 1X7Z, 1X80, 2BEU, 2BEV, 2BEW, 2BFB, 2BFC, 2BFD, 2BFE, 2BFF, 2J9F
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02779	Transket_pyr	69 → 247	Transketolase, pyrimidine binding domain	Domain
  PF02780	Transketolase_C	261 → 382	Transketolase, C-terminal domain	Domain

• Sequence:

  MAVVAAAAGWLLRLRAAGAEGHWRRLPGAGLARGFLHPAATVEDAAQRRQVAHFTFQPDP
  EPREYGQTQKMNLFQSVTSALDNSLAKDPTAVIFGEDVAFGGVFRCTVGLRDKYGKDRVF
  NTPLCEQGIVGFGIGIAVTGATAIAEIQFADYIFPAFDQIVNEAAKYRYRSGDLFNCGSL
  TIRSPWGCVGHGALYHSQSPEAFFAHCPGIKVVIPRSPFQAKGLLLSCIEDKNPCIFFEP
  KILYRAAAEEVPIEPYNIPLSQAEVIQEGSDVTLVAWGTQVHVIREVASMAKEKLGVSCE
  VIDLRTIIPWDVDTICKSVIKTGRLLISHEAPLTGGFASEISSTVQEECFLNLEAPISRV
  CGYDTPFPHIFEPFYIPDKWKCYDALRKMINY

• Sequence length: 392