Gene Gene information from NCBI Gene database.
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
SNPs SNP information provided by dbSNP.
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
miRNA miRNA information provided by mirtarbase database.
40
miRTarBase ID miRNA Experiments Reference
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
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
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
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
609010 6936 ENSG00000078070
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
Sequence length 725
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Valine, leucine and isoleucine degradation
Metabolic pathways
  Biotin transport and metabolism
Defective HLCS causes multiple carboxylase deficiency
Branched-chain amino acid catabolism
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
16
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
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
View all (163 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cervical cancer Likely pathogenic rs763877330 RCV005913572
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MCCC1-related disorder Likely pathogenic; Pathogenic rs776254500, rs2108479136, rs1333994006, rs119103217, rs727504005, rs185741664, rs2530057605, rs746500530, rs762463914, rs1394547323, rs1560224024, rs771730236 RCV004746362
RCV004746363
RCV003402023
RCV003390633
RCV003416001
View all (7 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
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
View all (14 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
3-METHYLCROTONYL-COA CARBOXYLASE DEFICIENCY GWAS catalog, Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Acute myeloid leukemia Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
3-methylcrotonyl CoA carboxylase 1 deficiency 3-methylcrotonyl CoA carboxylase deficiency CLINGEN_DG 11170888, 11406611, 25382614, 27601257
★☆☆☆☆
Found in Text Mining only
3-methylcrotonyl CoA carboxylase 1 deficiency 3-methylcrotonyl CoA carboxylase deficiency CLINVAR_DG 11170888, 11181649, 14680978, 15359379, 16010683, 16835865, 22264772, 22642865, 24078573, 25356967, 27601257
★☆☆☆☆
Found in Text Mining only
3-methylcrotonyl CoA carboxylase 1 deficiency 3-methylcrotonyl CoA carboxylase deficiency UNIPROT_DG 11170888, 11181649, 11406611, 16010683, 17968484, 21071250, 22150417, 22264772, 22642865, 25382614, 27601257
★☆☆☆☆
Found in Text Mining only
3-methylcrotonyl CoA carboxylase 1 deficiency 3-methylcrotonyl CoA carboxylase deficiency BEFREE 16835865, 22264772, 27417235
★☆☆☆☆
Found in Text Mining only
3-methylcrotonyl CoA carboxylase 1 deficiency 3-methylcrotonyl CoA carboxylase deficiency ORPHANET_DG 22264772, 22642865
★☆☆☆☆
Found in Text Mining only
3-methylcrotonyl CoA carboxylase 1 deficiency 3-methylcrotonyl CoA carboxylase deficiency GENOMICS_ENGLAND_DG 24816252
★☆☆☆☆
Found in Text Mining only
3-methylcrotonyl CoA carboxylase 1 deficiency 3-methylcrotonyl CoA carboxylase deficiency CTD_human_DG
★☆☆☆☆
Found in Text Mining only
3-methylcrotonyl-CoA carboxylase deficiency 3-methylcrotonyl CoA carboxylase deficiency Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Acute hepatic steatosis Hepatic steatosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Carcinoma Renal Cell Renal cell carcinoma Pubtator 25230976 Associate
★☆☆☆☆
Found in Text Mining only