COX20 p.Ala3=
c.9C>T · rs1445158730 · VCV1644151
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00627%, nfe)
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 -4.5 | GERP -3.1 |
| Overall | ||
| CADD | 5.341 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00627%
European (non-Finnish) · 63/1,004,536 alleles
Filtering AF
0.00501%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00455%
Overall
0.00497%
63/1,268,490 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
- COX20
- Protein
- p.Ala3=
- Coding
- c.9C>T
- MANE Select
- NM_198076
- dbSNP
- rs1445158730
- Type
- single nucleotide variant
- Location
- chr1:244835723 (GRCh38)
- Gene constraint
- LOEUF 1.927 · pLI 0.06 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 66.42
Similar variants
- COX20 p.Ala3Thr Uncertain significance ★★ ⚠ same residue
- COX20 p.Ala3Ser Benign/Likely benign ★★ same residue
- COX20 p.Ala3Val Uncertain significance ★ ⚠ same residue
- COX20 c.157+3G>C Pathogenic/Likely pathogenic ★★ same type
- COX20 p.Lys14Arg Pathogenic ★★ ⚠ same type
- COX20 p.Tyr36Ter Likely pathogenic ★★ same type
- COX20 p.Arg31Trp Uncertain significance ★★ ⚠ same type
- COX20 p.Arg54Gly 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/cox20-p-ala3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown