COX10 p.Arg431=
c.1293G>A · rs781358995 · VCV2717925
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00334%, amr)
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 2.4 | GERP 0.099, phastCons 0.12 |
| Overall | ||
| CADD | 2.198 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00334%
Admixed American · 2/59,956 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000137%
2/1,455,948 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
- COX10
- Protein
- p.Arg431=
- Coding
- c.1293G>A
- MANE Select
- NM_001303
- dbSNP
- rs781358995
- Type
- single nucleotide variant
- Location
- chr17:14207174 (GRCh38)
- Gene constraint
- LOEUF 0.934 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.11
Similar variants
- COX10 p.Arg431Pro Likely benign ★★ ⚠ same residue
- COX10 p.Arg431Gln Uncertain significance ★ ⚠ same residue
- COX10 p.Arg431Trp Conflicting classifications of pathogenicity ★ ⚠ same residue
- COX10 p.Asp336Val Pathogenic/Likely pathogenic ★★ same type
- COX10 p.Gln230Ter Likely pathogenic ★★ same type
- COX10 p.Pro225Leu Likely pathogenic ★★ same type
- COX10 c.-89G>C Uncertain significance ★★ same type
- COX10 c.-89G>T 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/cox10-p-arg431 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown