Is COX10 p.Ala175Ser (c.523G>T) pathogenic?

COX10 p.Ala175Ser (c.523G>T) is classified Uncertain significance in COX10 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-02-07). AlphaMissense: likely benign (0.1803); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with COX10 p.Ala175Ser (c.523G>T)?

COX10 p.Ala175Ser (c.523G>T) is associated with Inborn genetic diseases (ClinVar).

How common is COX10 p.Ala175Ser (c.523G>T) in the general population?

COX10 p.Ala175Ser (c.523G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about COX10 p.Ala175Ser (c.523G>T)?

AlphaMissense predicts likely benign (score 0.1803) — an in-silico prediction, not a clinical call.

COX10 p.Ala175Ser

c.523G>T · rs2508434421 · VCV2683409

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1803 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,708)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1803	likely benign
REVEL	0.704	pathogenic-leaning
SaProt	LLR -10.60	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.6, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 90 kb · p 0.97 · regional, not allelic
Overall
CADD	25.9	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,708). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: COX10
Protein: p.Ala175Ser
Coding: c.523G>T
MANE Select: NM_001303
dbSNP: rs2508434421
Type: single nucleotide variant
Location: chr17:14102141 (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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

COX10 p.Ala175Val Uncertain significance ★★ ⚠ same residue
COX10 p.Ala175Gly Uncertain significance ★ ⚠ same residue
COX10 p.Ala303Asp Uncertain significance ★★ ⚠ same condition
COX10 p.Arg334His Uncertain significance ★★ ⚠ same condition
COX10 p.Arg398Cys Uncertain significance ★★ ⚠ same condition
COX10 p.Asp308Asn Uncertain significance ★★ ⚠ same condition
COX10 p.Glu25Gly Uncertain significance ★★ ⚠ same condition
COX10 p.Gly434Arg Uncertain significance ★★ ⚠ same condition

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-ala175ser (accessed [today's date]).

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