COX7A2 p.Val49Ile
c.145G>A · rs2533736457 · VCV2331700
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.013 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -8.3 | GERP -4.4 |
| Regional constraint | o/e 1.05 | unconstrained · MANE · 5,801 bp · p 0.61 · regional, not allelic |
| Overall | ||
| CADD | 0.002 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,178,438 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000137%
2/1,458,064 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- COX7A2
- Protein
- p.Val49Ile
- Coding
- c.145G>A
- MANE Select
- NM_001366293
- dbSNP
- rs2533736457
- Type
- single nucleotide variant
- Location
- chr6:75240349 (GRCh38)
- Gene constraint
- LOEUF 1.864 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 87.99 · 3 PDB
Similar variants
- COX7A2 c.-14C>T Uncertain significance ★ same type
- COX7A2 c.-26G>A Uncertain significance ★ same type
- COX7A2 c.-41T>G Uncertain significance ★ same type
- COX7A2 c.-50T>A Uncertain significance ★ same type
- COX7A2 c.-77A>G Uncertain significance ★ same type
- COX7A2 c.-89C>T Uncertain significance ★ same type
- COX7A2 c.-90A>T Uncertain significance ★ same type
- COX7A2 c.-91T>G Uncertain significance ★ same type
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/cox7a2-p-val49ile (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown