Is COX10 p.Ala302= (c.906G>A) pathogenic?

COX10 p.Ala302= (c.906G>A) is classified Likely benign in COX10 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-01). Very rare (popmax 0.00534%, nfe).

How common is COX10 p.Ala302= (c.906G>A) in the general population?

COX10 p.Ala302= (c.906G>A) is very rare (popmax 0.00534%, nfe) (gnomAD).

COX10 p.Ala302=

c.906G>A · rs781027968 · VCV444400

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00534%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -8	GERP -2.8
Overall
CADD	1.083	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00534% European (non-Finnish) · 63/1,179,994 alleles

Filtering AF 0.00426% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00387%

Overall 0.00434% 70/1,614,084 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00534%	18,730
Remaining individualsnot grpmax-eligible	0.0048%	20,825
Admixed American	0.00333%	30,007
Finnishnot grpmax-eligible	0.00156%	64,038
African / African-American	0.00133%	74,964

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: COX10
Protein: p.Ala302=
Coding: c.906G>A
dbSNP: rs781027968
Type: single nucleotide variant
Location: chr17:14192199 (GRCh38)

Full COX10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/cox10-p-ala302 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown