Is COX7B p.Gln19Ter (c.55C>T) pathogenic?

COX7B p.Gln19Ter (c.55C>T) is classified Pathogenic in COX7B (ClinVar, No assertion criteria, 2 submitters; last evaluated 2012-11-02). Absent from gnomAD v4.1; Associated with linear skin defects with multiple congenital anomalies 2.

What condition is associated with COX7B p.Gln19Ter (c.55C>T)?

COX7B p.Gln19Ter (c.55C>T) is associated with linear skin defects with multiple congenital anomalies 2 (ClinVar).

How common is COX7B p.Gln19Ter (c.55C>T) in the general population?

COX7B p.Gln19Ter (c.55C>T) is absent from gnomAD v4.1 (gnomAD).

COX7B p.Gln19Ter

c.55C>T · rs397514585 · VCV39769

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

linear skin defects with multiple congenital anomalies 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 3
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.8	GERP 2.3, phastCons 1
Overall
CADD	36.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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.Gln19Ter
Coding: c.55C>T
MANE Select: NM_001866
dbSNP: rs397514585
Type: single nucleotide variant
Location: chrX:77902657 (GRCh38)
Structure: AlphaFold pLDDT 90.15 · 3 PDB

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

Disease context

linear skin defects with multiple congenital anomalies 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

COX7B p.Arg29His Uncertain significance ★★ ⚠ same condition
COX7B p.Thr73Ala Uncertain significance ★ ⚠ same condition
COX7B p.Val69Ala Uncertain significance ★ ⚠ same condition
COX7B c.41-2A>G Pathogenic same condition
COX7B p.Leu66fs Pathogenic same condition
COX7B c.165+10A>G Benign ★★ same type
COX7B c.*82G>T Likely benign ★★ same type
COX7B p.Ser16Arg 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-gln19ter (accessed [today's date]).

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