Is COX7B p.Lys36Arg (c.107A>G) pathogenic?

COX7B p.Lys36Arg (c.107A>G) is classified Conflicting classifications of pathogenicity in COX7B (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2024-10-19). AlphaMissense: likely benign (0.0991); Very rare (popmax 0.00716%, nfe); Associated with Inborn genetic diseases.

What condition is associated with COX7B p.Lys36Arg (c.107A>G)?

COX7B p.Lys36Arg (c.107A>G) is associated with Inborn genetic diseases (ClinVar).

How common is COX7B p.Lys36Arg (c.107A>G) in the general population?

COX7B p.Lys36Arg (c.107A>G) is very rare (popmax 0.00716%, nfe) (gnomAD).

What do computational predictors say about COX7B p.Lys36Arg (c.107A>G)?

AlphaMissense predicts likely benign (score 0.0991) — an in-silico prediction, not a clinical call.

COX7B p.Lys36Arg

c.107A>G · rs782304953 · VCV2660959

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0991 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00716%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0991	likely benign
REVEL	0.252	benign-leaning
SaProt	LLR -8.59	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.9	GERP 1.1, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 5,704 bp · p 0.27 · regional, not allelic
Overall
CADD	22.5	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 0.00716% European (non-Finnish) · 64/893,282 alleles

Filtering AF 0.00574% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00522%

Overall 0.00539% 65/1,206,850 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00716%	13,958
Remaining individualsnot grpmax-eligible	0.00211%	47,421

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.Lys36Arg
Coding: c.107A>G
MANE Select: NM_001866
dbSNP: rs782304953
Type: single nucleotide variant
Location: chrX:77902709 (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.Leu66Val Uncertain significance ★ ⚠ 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.Arg29Cys Likely benign ★ ⚠ same condition
COX7B p.Lys6Arg Likely benign ★ same condition
COX7B p.Arg29His Uncertain significance ★★ ⚠ same type
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-lys36arg (accessed [today's date]).

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