Is COX7B p.Arg29Cys (c.85C>T) pathogenic?

COX7B p.Arg29Cys (c.85C>T) is classified Likely benign in COX7B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-24). AlphaMissense: likely benign (0.1053); Very rare (popmax 0.00874%, afr); Associated with Inborn genetic diseases.

What condition is associated with COX7B p.Arg29Cys (c.85C>T)?

COX7B p.Arg29Cys (c.85C>T) is associated with Inborn genetic diseases (ClinVar).

How common is COX7B p.Arg29Cys (c.85C>T) in the general population?

COX7B p.Arg29Cys (c.85C>T) is very rare (popmax 0.00874%, afr) (gnomAD).

What do computational predictors say about COX7B p.Arg29Cys (c.85C>T)?

AlphaMissense predicts likely benign (score 0.1053) — an in-silico prediction, not a clinical call.

COX7B p.Arg29Cys

c.85C>T · rs367723477 · VCV3076487

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1053 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00874%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1053	likely benign
REVEL	0.113	moderately benign-leaning
SaProt	LLR -8.71	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.57 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.88	GERP -2.4, phastCons 0.94
Regional constraint	o/e 0.86	unconstrained · MANE · 5,704 bp · p 0.27 · regional, not allelic
Overall
CADD	15.66	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 0.00874% African / African-American · 5/57,222 alleles

Filtering AF 0.00338% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00215%

Overall 0.000497% 6/1,207,316 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00874%	11,444
Admixed American	0.00219%	45,734

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: COX7B
Protein: p.Arg29Cys
Coding: c.85C>T
MANE Select: NM_001866
dbSNP: rs367723477
Type: single nucleotide variant
Location: chrX:77902687 (GRCh38)
Structure: AlphaFold pLDDT 90.15 · 3 PDB

Full COX7B 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

COX7B p.Arg29His Uncertain significance ★★ ⚠ same residue
COX7B p.Leu66Val Uncertain significance ★ ⚠ same condition
COX7B p.Lys36Arg Conflicting classifications of pathogenicity ★ ⚠ same condition
COX7B p.Ser7Arg Conflicting classifications of pathogenicity ★ ⚠ same condition
COX7B p.Thr54Ala Conflicting classifications of pathogenicity ★ ⚠ same condition
COX7B p.Thr73Ile Uncertain significance ★ ⚠ same condition
COX7B p.Lys6Arg Likely benign ★ same condition
COX7B c.165+10A>G Benign ★★ 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/cox7b-p-arg29cys (accessed [today's date]).

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