MCCC1

Chr 3AR

methylcrotonyl-CoA carboxylase subunit 1

Also known as: MCC-B, MCCA, MCCCalpha

This gene encodes the large subunit of 3-methylcrotonyl-CoA carboxylase, which catalyzes the carboxylation of 3-methylcrotonyl-CoA to form 3-methylglutaconyl-CoA as part of leucine catabolism. Biallelic mutations cause 3-methylcrotonyl-CoA carboxylase 1 deficiency, an autosomal recessive disorder of leucine metabolism. The pathogenic mechanism involves loss of enzyme function leading to impaired leucine breakdown.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
LOFmechanismARLOEUF 0.901 OMIM phenotype
Clinical SummaryMCCC1
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Gene-Disease Validity (ClinGen)
3-methylcrotonyl-CoA carboxylase deficiency · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📖
GeneReview available — MCCC1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
0.90LOEUF
pLI 0.000
Z-score 2.03
OE 0.64 (0.460.90)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.54Z-score
OE missense 0.92 (0.851.01)
371 obs / 401.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.64 (0.460.90)
00.351.4
Missense OE0.92 (0.851.01)
00.61.4
Synonymous OE1.05
01.21.6
LoF obs/exp: 24 / 37.4Missense obs/exp: 371 / 401.6Syn Z: -0.46
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveMCCC1-related 3-methylcrotonyl-CoA carboxylase deficiencyLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.74top 25%
GOF
0.6052th %ile
LOF
0.2874th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

MCCC1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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