COX20 p.Arg54=
c.162A>G · rs369757278 · VCV2894285
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00325%, 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 3.6 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 13.71 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00325%
European (non-Finnish) · 38/1,170,132 alleles
Filtering AF
0.00241%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00211%
Overall
0.00243%
39/1,602,652 alleles · very rare
exomes 36/1,450,556 · genomes 3/152,096 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00325% | 30,793 |
| African / African-American | 0.00134% | 74,640 |
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.Arg54=
- Coding
- c.162A>G
- MANE Select
- NM_198076
- dbSNP
- rs369757278
- Type
- single nucleotide variant
- Location
- chr1:244842199 (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.Arg54Gly 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.Ala3Thr Uncertain significance ★★ ⚠ same type
- COX20 p.Arg31Trp 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-arg54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown