MCCC2 p.Phe377=
c.1131T>C · rs2530849467 · VCV3055932
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
MCCC2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 10.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- MCCC2
- Protein
- p.Phe377=
- Coding
- c.1131T>C
- MANE Select
- NM_022132
- dbSNP
- rs2530849467
- Type
- single nucleotide variant
- Location
- chr5:71643877 (GRCh38)
- Gene constraint
- LOEUF 0.832 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.82 · 14 PDB
- Residue 377
- the coa carboxyltransferase c-terminal domain; the 'carboxyltransferase' region
Disease context
MCCC2-related disorder
Similar variants
- MCCC2 p.Glu99Gln Pathogenic/Likely pathogenic ★★ same condition
- MCCC2 p.Val339Met Pathogenic/Likely pathogenic ★★ same condition
- MCCC2 p.Ala249Val Uncertain significance ★★ ⚠ same condition
- MCCC2 p.Arg361Gln Uncertain significance ★★ ⚠ same condition
- MCCC2 p.Ile206Thr Uncertain significance ★★ ⚠ same condition
- MCCC2 p.Phe387Val Uncertain significance ★★ ⚠ same condition
- MCCC2 p.Ile418Val Likely pathogenic ★ ⚠ same condition
- MCCC2 p.Phe377_Ser378insTer Pathogenic ★ same residue
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/mccc2-p-phe377 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown