Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	56922
Gene name Gene Name - the full gene name approved by the HGNC.	Methylcrotonyl-CoA carboxylase subunit 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	MCCC1
Synonyms (NCBI Gene) Gene synonyms aliases	MCC-B, MCCA, MCCCalpha
Chromosome Chromosome number	3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	3q27.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes the large subunit of 3-methylcrotonyl-CoA carboxylase. This enzyme functions as a heterodimer and catalyzes the carboxylation of 3-methylcrotonyl-CoA to form 3-methylglutaconyl-CoA. Mutations in this gene are associated with 3-Methylcrot

Show/Hide all(52)

SNP ID	Visualize variation	Clinical significance	Consequence
rs119103212	A>C	Pathogenic-likely-pathogenic, likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs119103213	T>G	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs119103214	C>G	Pathogenic	Non coding transcript variant, missense variant, intron variant, coding sequence variant
rs119103215	A>G	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs119103216	G>A	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs119103217	T>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant, genic downstream transcript variant
rs119103218	A>C	Pathogenic	Non coding transcript variant, missense variant, intron variant, coding sequence variant
rs138480247	G>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Genic downstream transcript variant, missense variant, non coding transcript variant, coding sequence variant
rs147741073	T>A,C	Pathogenic	Intron variant, stop gained, coding sequence variant, missense variant, non coding transcript variant
rs150862707	A>G,T	Pathogenic, likely-benign, benign	Stop gained, coding sequence variant, synonymous variant, non coding transcript variant
rs185741664	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs199517715	C>T	Pathogenic, uncertain-significance	Coding sequence variant, non coding transcript variant, missense variant, intron variant
rs199914879	A>T	Pathogenic	Splice donor variant
rs375996272	G>A	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs398124350	C>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs398124351	A>G	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs398124353	G>T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, intron variant, synonymous variant
rs544349961	G>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs727504001	T>-	Pathogenic	Genic downstream transcript variant, coding sequence variant, non coding transcript variant, frameshift variant
rs727504002	C>-	Pathogenic	Intron variant, coding sequence variant, non coding transcript variant, frameshift variant
rs727504005	C>T	Pathogenic	Splice acceptor variant
rs727504006	T>C	Pathogenic	Intron variant, splice acceptor variant
rs750484977	G>C	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs754460336	G>A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, intron variant, missense variant
rs760180709	T>C	Pathogenic	Intron variant, genic downstream transcript variant
rs762463137	->C	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs762463914	T>C	Likely-pathogenic	Genic upstream transcript variant, non coding transcript variant, missense variant, initiator codon variant, 5 prime UTR variant, upstream transcript variant
rs771730236	C>G	Likely-pathogenic	Splice donor variant, genic upstream transcript variant, upstream transcript variant
rs772010858	C>-	Pathogenic	Non coding transcript variant, genic downstream transcript variant, coding sequence variant, frameshift variant
rs772395858	T>C	Likely-pathogenic, pathogenic	Splice acceptor variant
rs776641008	TCATTCTACAGATGTCATGTGATTACCTTTTCA>-	Pathogenic, likely-pathogenic	Coding sequence variant, intron variant, genic downstream transcript variant, non coding transcript variant, splice donor variant
rs779412317	G>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs796051985	CA>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs796051986	G>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs886058209	CC>-	Conflicting-interpretations-of-pathogenicity, pathogenic	Splice acceptor variant, non coding transcript variant, coding sequence variant
rs905321122	C>A,G	Pathogenic	Non coding transcript variant, missense variant, stop gained, coding sequence variant, genic downstream transcript variant
rs920162850	G>A	Pathogenic	Coding sequence variant, intron variant, synonymous variant, stop gained, non coding transcript variant
rs1057520695	G>C	Pathogenic	Intron variant, missense variant, non coding transcript variant, coding sequence variant
rs1191868168	C>T	Likely-pathogenic	Splice acceptor variant
rs1212517901	T>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1307589698	G>A,T	Uncertain-significance, likely-pathogenic	Intron variant, coding sequence variant, synonymous variant, missense variant, non coding transcript variant
rs1311374961	CT>-	Pathogenic	Intron variant, non coding transcript variant, frameshift variant, coding sequence variant
rs1337201010	C>G	Likely-pathogenic	Splice acceptor variant
rs1394547323	->T	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1484347924	G>A	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs1553850609	TTCGCTTTACTAGC>-	Pathogenic	Frameshift variant, genic downstream transcript variant, non coding transcript variant, coding sequence variant
rs1553856095	AT>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1553862845	C>A	Likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1560224024	GTACTCC>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1560256569	TCTC>GCTATGCTAT	Pathogenic	Non coding transcript variant, stop gained, inframe indel, coding sequence variant
rs1577276144	->G	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1577328234	G>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant

Show/Hide all(40)

miRTarBase ID	miRNA	Experiments
MIRT1136549	hsa-miR-1253	CLIP-seq
MIRT1136550	hsa-miR-185	CLIP-seq
MIRT1136551	hsa-miR-193a-3p	CLIP-seq
MIRT1136552	hsa-miR-193b	CLIP-seq
MIRT1136553	hsa-miR-3117-5p	CLIP-seq
MIRT1136554	hsa-miR-3165	CLIP-seq
MIRT1136555	hsa-miR-3187-3p	CLIP-seq
MIRT1136556	hsa-miR-4306	CLIP-seq
MIRT1136557	hsa-miR-4529-5p	CLIP-seq
MIRT1136558	hsa-miR-4644	CLIP-seq
MIRT1136559	hsa-miR-502-5p	CLIP-seq
MIRT1136560	hsa-miR-582-3p	CLIP-seq
MIRT1136549	hsa-miR-1253	CLIP-seq
MIRT1136551	hsa-miR-193a-3p	CLIP-seq
MIRT1136552	hsa-miR-193b	CLIP-seq
MIRT1136553	hsa-miR-3117-5p	CLIP-seq
MIRT2038873	hsa-miR-3135b	CLIP-seq
MIRT1136555	hsa-miR-3187-3p	CLIP-seq
MIRT2038874	hsa-miR-320a	CLIP-seq
MIRT2038875	hsa-miR-320b	CLIP-seq
MIRT2038876	hsa-miR-320c	CLIP-seq
MIRT2038877	hsa-miR-320d	CLIP-seq
MIRT2038878	hsa-miR-320e	CLIP-seq
MIRT2038879	hsa-miR-3612	CLIP-seq
MIRT2038880	hsa-miR-4429	CLIP-seq
MIRT2038881	hsa-miR-4443	CLIP-seq
MIRT1136557	hsa-miR-4529-5p	CLIP-seq
MIRT1136560	hsa-miR-582-3p	CLIP-seq
MIRT2038882	hsa-miR-650	CLIP-seq
MIRT1136549	hsa-miR-1253	CLIP-seq
MIRT1136551	hsa-miR-193a-3p	CLIP-seq
MIRT1136552	hsa-miR-193b	CLIP-seq
MIRT1136553	hsa-miR-3117-5p	CLIP-seq
MIRT1136555	hsa-miR-3187-3p	CLIP-seq
MIRT2268858	hsa-miR-4291	CLIP-seq
MIRT2268859	hsa-miR-4310	CLIP-seq
MIRT1136557	hsa-miR-4529-5p	CLIP-seq
MIRT2268860	hsa-miR-4666-3p	CLIP-seq
MIRT1136559	hsa-miR-502-5p	CLIP-seq
MIRT1136560	hsa-miR-582-3p	CLIP-seq

Show/Hide all(29)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0004075	Function	Biotin carboxylase activity	NAS	22869039
GO:0004485	Function	Methylcrotonoyl-CoA carboxylase activity	IBA
GO:0004485	Function	Methylcrotonoyl-CoA carboxylase activity	IDA	17360195
GO:0004485	Function	Methylcrotonoyl-CoA carboxylase activity	IEA
GO:0004485	Function	Methylcrotonoyl-CoA carboxylase activity	NAS	11170888, 11181649, 11401427
GO:0005515	Function	Protein binding	IPI	17360195, 27499296, 28514442, 33961781
GO:0005524	Function	ATP binding	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	IDA	16023992, 17360195
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0005759	Component	Mitochondrial matrix	NAS	11170888
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0005829	Component	Cytosol	TAS
GO:0006552	Process	L-leucine catabolic process	IEA
GO:0006552	Process	L-leucine catabolic process	ISS	11170888
GO:0006552	Process	L-leucine catabolic process	NAS	11170888
GO:0006768	Process	Biotin metabolic process	NAS	11401427, 22869039
GO:0009083	Process	Branched-chain amino acid catabolic process	NAS	17360195
GO:0009374	Function	Biotin binding	NAS	11401427
GO:0016874	Function	Ligase activity	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:1905202	Component	Methylcrotonoyl-CoA carboxylase complex	IDA	17360195
GO:1905202	Component	Methylcrotonoyl-CoA carboxylase complex	IPI	17360195
GO:1905202	Component	Methylcrotonoyl-CoA carboxylase complex	NAS	11170888, 11181649, 11401427
GO:1905202	Component	Methylcrotonoyl-CoA carboxylase complex	TAS	22869039

MIM	HGNC	e!Ensembl
609010	6936	ENSG00000078070

Protein

UniProt ID

Q96RQ3

Protein name

Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial (MCCase subunit alpha) (EC 6.4.1.4) (3-methylcrotonyl-CoA carboxylase 1) (3-methylcrotonyl-CoA carboxylase biotin-containing subunit) (3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha)

Protein function

Biotin-attachment subunit of the 3-methylcrotonyl-CoA carboxylase, an enzyme that catalyzes the conversion of 3-methylcrotonyl-CoA to 3-methylglutaconyl-CoA, a critical step for leucine and isovaleric acid catabolism. {ECO:0000269|PubMed:1736019

PDB

2EJM , 8J4Z , 8J78 , 8J7D , 8J99 , 8JAK , 8JAW , 8JXL , 8JXM , 8JXN , 8K2V , 8XL6 , 8XL7 , 8XL8

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00289	Biotin_carb_N	48 → 157	Biotin carboxylase, N-terminal domain	Domain
PF02786	CPSase_L_D2	163 → 371	Carbamoyl-phosphate synthase L chain, ATP binding domain	Domain
PF02785	Biotin_carb_C	383 → 491	Biotin carboxylase C-terminal domain	Domain
PF00364	Biotin_lipoyl	650 → 714	Biotin-requiring enzyme	Domain

Sequence

MAAASAVSVLLVAAERNRWHRLPSLLLPPRTWVWRQRTMKYTTATGRNITKVLIANRGEI
ACRVMRTAKKLGVQTVAVYSEADRNSMHVDMADEAYSIGPAPSQQSYLSMEKIIQVAKTS
AAQAIHPGCGFLSENMEFAELCKQEGIIFIGPPPSAIRDMGIKSTSKSIMAAAGVPVVEG
YHGEDQSDQCLKEHARRIGYPVMIKAVRGGGGKGMRIVRSEQEFQEQLESARREAKKSFN
DDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLFERDCSVQRRHQKIIEEAPAPGIKSEVRK
KLGEAAVRAAKAVNYVGAGTVEFIMDSKHNFCFMEMNTRLQVEHPVTEMITGTDLVEWQL
RIAAGEKIPLSQEEITLQGHAFEARIYAEDPSNNFMPVAGPLVHLSTPRADPSTRIETGV
RQGDEVSVHYDPMIAKLVVWAADRQAALTKLRYSLRQYNIVGLHTNIDFLLNLSGHPEFE
AGNVHTDFIPQHHKQLLLSRKAAAKESLCQAALGLILKEKAMTDTFTLQAHDQFSPFSSS
SGRRLNISYTRNMTLKDGKNNVAIAVTYNHDGSYSMQIEDKTFQVLGNLYSEGDCTYLKC
SVNGVASKAKLIILENTIYLFSKEGSIEIDIPVPKYLSSVSSQETQGGPLAPMTGTIEKV
FVKAGDKVKAGDSLMVMIAMKMEHTIKSPKDGTVKKVFYREGAQANRHTPLVEFEEEESD
KRESE

Sequence length

725

Interactions

View interactions

	KEGG		Reactome
	Valine, leucine and isoleucine degradation Metabolic pathways		Biotin transport and metabolism Defective HLCS causes multiple carboxylase deficiency Branched-chain amino acid catabolism

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
3-methylcrotonyl CoA carboxylase deficiency	3-methylcrotonyl-CoA carboxylase 1 deficiency	rs1484347924, rs119103216, rs1560256569, rs544349961, rs886058209, rs150862707, rs119103217, rs920162850, rs1337201010, rs776641008, rs746267545, rs772395858, rs1553850609, rs1191868168, rs905321122 View all (39 more)	N/A
Methylcrotonyl-CoA Carboxylase Deficiency	methylcrotonyl-coa carboxylase deficiency	rs1212517901, rs544349961, rs886058209, rs119103217, rs772395858, rs142507365, rs199914879, rs119103212, rs727504001, rs376289130, rs768785753, rs764744442, rs119103213, rs727504002, rs754460336, rs185741664 View all (1 more)	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Parkinson Disease	Parkinson's disease	N/A	N/A	GWAS

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
3 methylcrotonyl CoA carboxylase 1 deficiency	Associate	11170888, 11181649, 15359379, 22642865, 40639867
Biotin deficiency	Associate	15623830
Carcinoma Renal Cell	Associate	25230976
Diabetes Mellitus Type 2	Associate	27193597
Inflammation	Associate	27629939, 40216992
Insulin Resistance	Associate	29986096
Neoplasms	Associate	24477574
Parkinson Disease	Associate	21812969, 30957308, 33436766, 40216992

MCCC1 (methylcrotonyl-CoA carboxylase subunit 1)