COX15 p.Cys33=
c.99C>T · rs780790755 · VCV3006010
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | acceptor loss · deltas |
|---|---|---|
| Pangolin | Δ0.20 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 4.511 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,086 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000136%
Overall
0.000124%
2/1,614,088 alleles · very rare
exomes 2/1,461,776 · genomes 0/152,312 · joint denominator
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.Cys33=
- Coding
- c.99C>T
- MANE Select
- NM_078470
- dbSNP
- rs780790755
- Type
- single nucleotide variant
- Location
- chr10:99729726 (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-cys33 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown