Is COX10 p.Gln322Pro (c.965A>C) pathogenic?

COX10 p.Gln322Pro (c.965A>C) is classified Uncertain significance in COX10 (ClinVar, Single submitter, 2 submitters; last evaluated 2024-10-29). AlphaMissense: likely pathogenic (0.9817); Absent from gnomAD v4.1.

How common is COX10 p.Gln322Pro (c.965A>C) in the general population?

COX10 p.Gln322Pro (c.965A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about COX10 p.Gln322Pro (c.965A>C)?

AlphaMissense predicts likely pathogenic (score 0.9817) — an in-silico prediction, not a clinical call.

COX10 p.Gln322Pro

c.965A>C · rs2508550992 · VCV1973811

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9817 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9817	likely pathogenic
REVEL	0.961	strongly pathogenic-leaning
SaProt	LLR -13.29	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.5, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 372 bp · p 0.13 · regional, not allelic
Overall
CADD	28.9	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: COX10
Protein: p.Gln322Pro
Coding: c.965A>C
MANE Select: NM_001303
dbSNP: rs2508550992
Type: single nucleotide variant
Location: chr17:14206846 (GRCh38)
Gene constraint: LOEUF 0.934 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 77.11

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

Similar variants

COX10 p.Asp336Val Pathogenic/Likely pathogenic ★★ same type
COX10 p.Gln230Ter Likely pathogenic ★★ same type
COX10 p.Pro225Leu Likely pathogenic ★★ same type
COX10 c.-89G>C Uncertain significance ★★ same type
COX10 c.-89G>T Uncertain significance ★★ same type
COX10 p.Ala174Thr Uncertain significance ★★ ⚠ same type
COX10 p.Ala175Ser Uncertain significance ★★ ⚠ same type
COX10 p.Ala175Val 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/cox10-p-gln322pro (accessed [today's date]).

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