COX20 p.Pro10=
c.30C>G · rs924119045 · VCV509566
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0252%, mid)
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 -0.084 | GERP 0.63, phastCons 0.002 |
| Overall | ||
| CADD | 7.874 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0252%
Middle Eastern · 1/3,970 alleles
Filtering AF
0.00551%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0036%
Overall
0.00197%
25/1,271,152 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0252% | 3,970 |
| South Asian | 0.0142% | 7,045 |
| Remaining individualsnot grpmax-eligible | 0.00636% | 15,731 |
| Admixed American | 0.00372% | 26,878 |
| European (non-Finnish) | 0.00149% | 67,007 |
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.Pro10=
- Coding
- c.30C>G
- MANE Select
- NM_198076
- dbSNP
- rs924119045
- Type
- single nucleotide variant
- Location
- chr1:244835744 (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 c.157+3G>C Pathogenic/Likely pathogenic ★★ same type
- COX20 p.Lys14Arg Pathogenic ★★ ⚠ same type
- COX20 p.Tyr36Ter Likely pathogenic ★★ same type
- COX20 p.Ala3Thr Uncertain significance ★★ ⚠ same type
- COX20 p.Arg31Trp Uncertain significance ★★ ⚠ same type
- COX20 p.Arg54Gly Uncertain significance ★★ ⚠ same type
- COX20 p.Asp107Asn Uncertain significance ★★ ⚠ same type
- COX20 p.Asp107His 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-pro10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown