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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	56922
Gene name	Methylcrotonyl-CoA carboxylase subunit 1
Gene symbol	MCCC1
Synonyms (NCBI Gene)	MCC-BMCCAMCCCalpha
Chromosome	3
Chromosome location	3q27.1
Summary	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

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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

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

906

Show/Hide Causal Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
3-methylcrotonyl-CoA carboxylase 1 deficiency	Likely pathogenic; Pathogenic	rs398124350, rs768630906, rs776254500, rs2108474093, rs2108479136, rs2108505736, rs2108526541, rs1163620394, rs2108569910, rs1000891879, rs2108441527, rs2108478897, rs2108528645, rs2108437770, rs1486240538 View all (149 more)	RCV000803322 RCV001378210 RCV001377562 RCV001385129 RCV001387388 RCV001383341 RCV001390502 RCV001380802 RCV001382304 RCV005023194 RCV005860240 RCV001783634 RCV001782419 RCV001782420 RCV001884741 RCV001959352 RCV002045717 RCV001937351 RCV002010633 RCV001953706 RCV001949253 RCV001934714 RCV001877254 RCV001999544 RCV001989030 RCV001918827 RCV001949048 RCV002037961 RCV001972462 RCV001956381 RCV001956382 RCV001972774 RCV001972566 RCV002033638 RCV001918239 RCV001967531 RCV001975056 RCV002027189 RCV000002006 RCV000002007 RCV000002008 RCV000002009 RCV000002010 RCV000002011 RCV000002012 RCV001231585 RCV000174585 RCV001850096 RCV001850097 RCV002466916 RCV003600440 RCV003077725 RCV000174145 RCV002610439 RCV002624602 RCV002664326 RCV003112801 RCV002574854 RCV002576507 RCV000179961 RCV002605181 RCV002642488 RCV005025305 RCV000808142 RCV000687710 RCV000281372 RCV002750386 RCV002819597 RCV002846799 RCV002870730 RCV002863059 RCV002982252 RCV003025197 RCV003057937 RCV000705149 RCV003229528 RCV003470055 RCV003470056 RCV003461829 RCV003461830 RCV003470057 RCV003470058 RCV003470059 RCV003461831 RCV003461832 RCV003470060 RCV003461833 RCV003470061 RCV003461834 RCV003470062 RCV003470063 RCV003461835 RCV003470064 RCV003470065 RCV003461836 RCV003461837 RCV003461838 RCV003470066 RCV003461839 RCV003461840 RCV003470067 RCV003470068 RCV003470069 RCV003498846 RCV003498208 RCV003499095 RCV003498877 RCV003498432 RCV003499429 RCV003499393 RCV000288396 RCV003599896 RCV003600049 RCV003600050 RCV003600227 RCV003601938 RCV003813716 RCV003854993 RCV003879924 RCV003989404 RCV004574824 RCV004574825 RCV004574826 RCV004574827 RCV000543528 RCV000532293 RCV000524927 RCV000549808 RCV000541919 RCV000527269 RCV000531058 RCV000653486 RCV000763509 RCV000591068 RCV000653488 RCV001386926 RCV000653495 RCV000653492 RCV000653497 RCV000653493 RCV000695486 RCV000704278 RCV000690996 RCV000817601 RCV000804238 RCV000822030 RCV000808799 RCV000796753 RCV000810043 RCV000810504 RCV000807500 RCV000794932 RCV000804750 RCV001043256 RCV001034783 RCV001063409 RCV001064711 RCV004570320 RCV001095700 RCV001223878 RCV001220421 RCV001214771 RCV001210556 RCV001226502 RCV001245155 RCV001239953 RCV001246334 RCV001310013
Cervical cancer	Likely pathogenic	rs763877330	RCV005913572
MCCC1-related disorder	Likely pathogenic; Pathogenic	rs776254500, rs2108479136, rs1333994006, rs119103217, rs727504005, rs185741664, rs2530057605, rs746500530, rs762463914, rs1394547323, rs1560224024, rs771730236	RCV004746362 RCV004746363 RCV003402023 RCV003390633 RCV003416001 RCV003390913 RCV003400255 RCV004745481 RCV003403504 RCV003424257 RCV003403612 RCV003413611
Methylcrotonyl-CoA carboxylase deficiency	Likely pathogenic; Pathogenic	rs1000891879, rs119103212, rs119103213, rs119103217, rs727504001, rs727504002, rs1012193526, rs544349961, rs772395858, rs768785753, rs185741664, rs886058209, rs199914879, rs764744442, rs746500530 View all (4 more)	RCV004587179 RCV000614611 RCV001275509 RCV001273490 RCV002509256 RCV001273492 RCV002470112 RCV001275510 RCV001275516 RCV001275506 RCV001275513 RCV001275515 RCV001275517 RCV001275508 RCV001275512 RCV003226348 RCV001275507 RCV003987713 RCV001275518
Nonpapillary renal cell carcinoma	Likely pathogenic	rs2530461749	RCV005932023
Ovarian serous cystadenocarcinoma	Likely pathogenic	rs2108446715	RCV005928622

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Uncertain significance	rs186406584	RCV005897635
Cholangiocarcinoma	Benign	rs13088830	RCV005906889
Colon adenocarcinoma	Likely benign	rs777026304	RCV005932546
Malignant tumor of urinary bladder	Uncertain significance	rs2108486818	RCV005924234
Sarcoma	Conflicting classifications of pathogenicity	rs144182725	RCV005907011
Uterine corpus endometrial carcinoma	Likely benign; Conflicting classifications of pathogenicity	rs777026304, rs138937107	RCV005932547 RCV005913599

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)