COX5A p.Asp90=
c.270T>C · rs773949037 · VCV746574
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00833%, 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 3.5 | phastCons 1 |
| Overall | ||
| CADD | 9.13 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00833%
Admixed American · 5/59,994 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00041%
6/1,461,710 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00833% | 11,999 |
| European (non-Finnish) | 8.47e-05% | 1,179,944 |
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
- COX5A
- Protein
- p.Asp90=
- Coding
- c.270T>C
- MANE Select
- NM_004255
- dbSNP
- rs773949037
- Type
- single nucleotide variant
- Location
- chr15:74926835 (GRCh38)
- Gene constraint
- LOEUF 0.82 · pLI 0.65 (gnomAD)
- Structure
- AlphaFold pLDDT 88.21 · 3 PDB
Similar variants
- COX5A p.Ser25Cys Likely benign ★★ same type
- COX5A p.Ala13Thr Uncertain significance ★ ⚠ same type
- COX5A p.Ala32Asp Uncertain significance ★ ⚠ same type
- COX5A p.Ala32Thr Uncertain significance ★ ⚠ same type
- COX5A p.Ala54Gly Uncertain significance ★ ⚠ same type
- COX5A p.Arg107Ser Uncertain significance ★ ⚠ same type
- COX5A p.Arg55Cys Uncertain significance ★ ⚠ same type
- COX5A p.Arg94Gln 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/cox5a-p-asp90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown