BCKDHA (branched chain keto acid dehydrogenase E1 subunit alpha)

Gene

• Entrez ID: 593
• Gene name: Branched chain keto acid dehydrogenase E1 subunit alpha
• Gene symbol: BCKDHA
• Synonyms: BCKDE1A, MSU, MSUD1, OVD1A
• Chromosome: 19
• Chromosome location: 19q13.2
• Summary: The branched-chain alpha-keto acid (BCAA) dehydrogenase (BCKD) complex is an innter mitochondrial enzyme complex that catalyzes the second major step in the catabolism of the branched-chain amino acids leucine, isoleucine, and valine. The BCKD complex consists of three catalytic components: a heterotetrameric (alpha2-beta2) branched-chain alpha-keto acid decarboxylase (E1), a dihydrolipoyl transacylase (E2), and a dihydrolipoamide dehydrogenase (E3). This gene encodes the alpha subunit of the decarboxylase (E1) component. Mutations in this gene result in maple syrup urine disease, type IA. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs137852870	T>A	Pathogenic-likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs137852871	G>A,C	Pathogenic-likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs137852872	T>G	Pathogenic	Coding sequence variant, missense variant
rs137852873	C>T	Conflicting-interpretations-of-pathogenicity, pathogenic	Coding sequence variant, missense variant
rs137852874	G>A	Pathogenic	Coding sequence variant, missense variant
rs137852875	C>G	Pathogenic	Coding sequence variant, missense variant
rs137852876	C>G	Pathogenic	Coding sequence variant, missense variant
rs146932786	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs147021347	C>G,T	Likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs151227241	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs182923857	C>T	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs199599175	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs201168715	G>A,T	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant, stop gained
rs367823977	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs373336888	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs373390136	C>A,G,T	Likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs373713279	C>A	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs374625613	C>T	Likely-pathogenic	Coding sequence variant, stop gained
rs375785084	C>T	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs376456598	C>A	Likely-pathogenic	Coding sequence variant, stop gained
rs398123486	G>A	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant
rs398123489	C>-,CC,CCC	Pathogenic	Coding sequence variant, frameshift variant
rs398123490	G>A	Pathogenic-likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs398123491	C>A,T	Likely-benign, pathogenic	Stop gained, coding sequence variant, synonymous variant
rs398123492	AC>-	Pathogenic	Coding sequence variant, frameshift variant
rs398123493	C>A	Pathogenic	Stop gained, coding sequence variant
rs398123496	G>A	Pathogenic-likely-pathogenic, pathogenic	Splice donor variant
rs398123497	C>T	Conflicting-interpretations-of-pathogenicity, pathogenic	Intron variant
rs398123499	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs398123503	C>T	Pathogenic-likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs398123504	->T	Pathogenic	Coding sequence variant, frameshift variant
rs398123505	TCT>-	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Inframe deletion, coding sequence variant
rs398123508	G>C	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs398123509	A>C	Pathogenic	Coding sequence variant, missense variant
rs398123510	GT>-	Pathogenic	Coding sequence variant, frameshift variant
rs398123512	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs398123513	C>T	Pathogenic	Stop gained, coding sequence variant
rs398123514	C>G,T	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, missense variant, synonymous variant
rs398123515	G>A	Pathogenic-likely-pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs753216964	G>C	Likely-pathogenic, pathogenic	Splice acceptor variant
rs753698250	C>A,T	Pathogenic	Synonymous variant, stop gained, coding sequence variant
rs760494152	A>G	Pathogenic	Splice acceptor variant, intron variant
rs762084007	C>-	Pathogenic-likely-pathogenic	Coding sequence variant, frameshift variant
rs762199542	C>T	Pathogenic	Coding sequence variant, stop gained
rs764247545	C>G,T	Pathogenic	Missense variant, coding sequence variant, stop gained
rs765543886	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs773048903	G>A	Pathogenic	Missense variant, coding sequence variant
rs794727847	AGGCCCCG>-	Pathogenic	Frameshift variant, coding sequence variant
rs796051938	TACG>-	Likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant
rs863225262	A>T	Pathogenic-likely-pathogenic	Coding sequence variant, stop gained
rs869312124	G>C	Pathogenic	Missense variant, coding sequence variant
rs869312125	A>C	Pathogenic	Missense variant, coding sequence variant
rs1057519059	C>AA	Pathogenic	Coding sequence variant, frameshift variant
rs1330793674	CAGCACCA>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1555765593	T>-	Pathogenic	Frameshift variant, coding sequence variant
rs1555766066	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1555766993	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1555767028	G>T	Likely-pathogenic	Splice donor variant
rs1555767090	->A	Likely-pathogenic	Coding sequence variant, stop gained
rs1555767169	G>-	Likely-pathogenic	Coding sequence variant, splice donor variant
rs1555767285	A>G	Likely-pathogenic	Splice acceptor variant
rs1568503938	T>C	Pathogenic	Coding sequence variant, missense variant
rs1568506608	T>-	Pathogenic	Frameshift variant, coding sequence variant
rs1599962569	CCAAGGCTGG>-	Likely-pathogenic	Frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT041443	hsa-miR-193b-3p	CLASH	23622248
MIRT044243	hsa-miR-29c-3p	CLASH	23622248

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003826	Function	Alpha-ketoacid dehydrogenase activity	IBA	21873635
GO:0003826	Function	Alpha-ketoacid dehydrogenase activity	IDA	7883996
GO:0003863	Function	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity	IEA
GO:0005515	Function	Protein binding	IPI	12902323, 15166214, 15576032, 28514442
GO:0005739	Component	Mitochondrion	HDA	20833797
GO:0005739	Component	Mitochondrion	TAS	11839747
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0005947	Component	Mitochondrial alpha-ketoglutarate dehydrogenase complex	IBA	21873635
GO:0005947	Component	Mitochondrial alpha-ketoglutarate dehydrogenase complex	IDA	7883996
GO:0009083	Process	Branched-chain amino acid catabolic process	IBA	21873635
GO:0009083	Process	Branched-chain amino acid catabolic process	IDA	7883996
GO:0009083	Process	Branched-chain amino acid catabolic process	TAS
GO:0016831	Function	Carboxy-lyase activity	TAS	11839747
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 608348
• HGNC: 986
• e!Ensembl: ENSG00000248098

Protein

• UniProt ID: P12694
• Protein name: 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial (EC 1.2.4.4) (Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain) (BCKDE1A) (BCKDH E1-alpha)
• 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
  PF00676	E1_dh	106 → 406	Dehydrogenase E1 component	Family

• Sequence:

  MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAE
  FIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILY
  ESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYG
  NISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGA
  ASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG
  NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHP
  ISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQL
  RKQQESLARHLQTYGEHYPLDHFDK

• Sequence length: 445