Is COX7B p.Thr47Ile (c.140C>T) pathogenic?

COX7B p.Thr47Ile (c.140C>T) is classified Uncertain significance in COX7B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-30). AlphaMissense: likely benign (0.1026); Absent from gnomAD v4.1.

How common is COX7B p.Thr47Ile (c.140C>T) in the general population?

COX7B p.Thr47Ile (c.140C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about COX7B p.Thr47Ile (c.140C>T)?

AlphaMissense predicts likely benign (score 0.1026) — an in-silico prediction, not a clinical call.

COX7B p.Thr47Ile

c.140C>T · rs781928139 · VCV2764680

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1026 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1026	likely benign
REVEL	0.012	strongly benign-leaning
SaProt	LLR -7.72	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 0.99	GERP 0.52, phastCons 0.85
Regional constraint	o/e 0.86	unconstrained · MANE · 5,704 bp · p 0.27 · regional, not allelic
Overall
CADD	14.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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: COX7B
Protein: p.Thr47Ile
Coding: c.140C>T
MANE Select: NM_001866
dbSNP: rs781928139
Type: single nucleotide variant
Location: chrX:77902742 (GRCh38)
Structure: AlphaFold pLDDT 90.15 · 3 PDB

Full COX7B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COX7B p.Arg29His Uncertain significance ★★ ⚠ same type
COX7B c.165+10A>G Benign ★★ same type
COX7B c.*82G>T Likely benign ★★ same type
COX7B p.Ser16Arg Benign ★★ ⚠ same type
COX7B c.40+5G>C Likely pathogenic ★ same type
COX7B p.Ala57Ser Uncertain significance ★ ⚠ same type
COX7B p.Asn79Asp Uncertain significance ★ ⚠ same type
COX7B p.Leu66Val 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/cox7b-p-thr47ile (accessed [today's date]).

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