COX15 p.Pro302=
c.906G>A · rs143079914 · VCV736880
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00549%, sas)
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 -0.28 | GERP -3.4, phastCons 0.44 |
| Overall | ||
| CADD | 13.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00549%
South Asian · 5/91,084 alleles
Filtering AF
0.00358%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00321%
Overall
0.0039%
63/1,613,928 alleles · very rare
exomes 58/1,461,876 · genomes 5/152,052 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00549% | 18,217 |
| European (non-Finnish) | 0.00458% | 21,852 |
| African / African-American | 0.00401% | 24,952 |
| Finnishnot grpmax-eligible | 0.00156% | 64,034 |
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
- COX15
- Protein
- p.Pro302=
- Coding
- c.906G>A
- MANE Select
- NM_078470
- dbSNP
- rs143079914
- Type
- single nucleotide variant
- Location
- chr10:99718427 (GRCh38)
- Gene constraint
- LOEUF 1.198 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 85.29
Similar variants
- COX15 c.272+2T>G Pathogenic/Likely pathogenic ★★ same type
- COX15 c.750+1G>A Likely pathogenic ★★ same type
- COX15 c.750+1G>T Likely pathogenic ★★ same type
- COX15 p.Arg153Ter Pathogenic/Likely pathogenic ★★ same type
- COX15 p.Arg217Trp Pathogenic ★★ same type
- COX15 p.Ser151Ter Pathogenic/Likely pathogenic ★★ same type
- COX15 p.Ser229Ter Pathogenic/Likely pathogenic ★★ same type
- COX15 p.Ser277Ter Pathogenic/Likely pathogenic ★★ 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/cox15-p-pro302 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown