Is COX10 p.Ser238Phe (c.713C>T) pathogenic?

COX10 p.Ser238Phe (c.713C>T) is classified Uncertain significance in COX10 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-31). AlphaMissense: likely benign (0.1677); Very rare (popmax 0.00549%, sas); Associated with Inborn genetic diseases.

What condition is associated with COX10 p.Ser238Phe (c.713C>T)?

COX10 p.Ser238Phe (c.713C>T) is associated with Inborn genetic diseases (ClinVar).

How common is COX10 p.Ser238Phe (c.713C>T) in the general population?

COX10 p.Ser238Phe (c.713C>T) is very rare (popmax 0.00549%, sas) (gnomAD).

What do computational predictors say about COX10 p.Ser238Phe (c.713C>T)?

AlphaMissense predicts likely benign (score 0.1677) — an in-silico prediction, not a clinical call.

COX10 p.Ser238Phe

c.713C>T · rs1279780509 · VCV2478916

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1677 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00549%, sas)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1677	likely benign
REVEL	0.559	indeterminate
SaProt	LLR -11.20	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP 1.5, phastCons 1
Regional constraint	o/e 0.76	unconstrained · MANE · 32 kb · p 0.048 · regional, not allelic
Overall
CADD	22.9	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

Grpmax group 0.00549% South Asian · 5/91,088 alleles

Filtering AF 0.0021% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00136%

Overall 0.000684% 10/1,461,888 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00549%	18,218
African / African-American	0.00133%	75,048
European (non-Finnish)	0.000339%	295,009

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.Ser238Phe
Coding: c.713C>T
MANE Select: NM_001303
dbSNP: rs1279780509
Type: single nucleotide variant
Location: chr17:14192006 (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.Ala175Ser Uncertain significance ★★ ⚠ same condition
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
COX10 p.Gly436Arg 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-ser238phe (accessed [today's date]).

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