Is CTAG2 p.Glu89Gln (c.265G>C) pathogenic?

CTAG2 p.Glu89Gln (c.265G>C) is classified Benign in CTAG2 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-08-16). AlphaMissense: likely benign (0.0891); Common (popmax 77.2%, eas) — too common for a highly-penetrant pathogenic allele.

What do computational predictors say about CTAG2 p.Glu89Gln (c.265G>C)?

AlphaMissense predicts likely benign (score 0.0891) — an in-silico prediction, not a clinical call.

CTAG2 p.Glu89Gln

Q: How common is CTAG2 p.Glu89Gln (c.265G>C) in the general population?

CTAG2 p.Glu89Gln (c.265G>C) is common (popmax 77.2%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.265G>C · rs17328091 · VCV770030

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0891 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 77.2%, eas) — too common for a highly-penetrant pathogenic allele

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.0891	likely benign
SaProt	LLR -6.54	tolerated
⇒ AlphaMissense and SaProt both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.6	GERP -1.7
Regional constraint	o/e 0.97	unconstrained · MANE · 1,329 bp · p 0.74 · regional, not allelic
Overall
CADD	0.015	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 77.2% East Asian · 25,849/33,477 alleles

Filtering AF 76.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 76.1%

Overall 59.6% 717,068/1,203,514 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	77.2%	1
Amishnot grpmax-eligible	68.5%	1
Finnishnot grpmax-eligible	63.7%	2
European (non-Finnish)	62.6%	2
Ashkenazi Jewishnot grpmax-eligible	60%	2
Remaining individualsnot grpmax-eligible	58%	2
Middle Eastern	57.6%	2
Admixed American	53.9%	2
South Asian	45.8%	2
African / African-American	17.5%	6

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: CTAG2
Protein: p.Glu89Gln
Coding: c.265G>C
MANE Select: NM_172377
dbSNP: rs17328091
Type: single nucleotide variant
Location: chrX:154653251 (GRCh38)
Structure: AlphaFold pLDDT 47.90
Residue 89: a UniProt-annotated variant site (in)

Full CTAG2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CTAG2 c.405-28T>C Likely benign ★★ same type
CTAG2 c.405-93G>C Benign ★★ same type
CTAG2 p.Met94Val Benign ★★ same type
CTAG2 p.Pro99Ala Benign ★★ same type
CTAG2 c.404+107C>A Uncertain significance ★ ⚠ same type
CTAG2 c.404+21G>C Uncertain significance ★ ⚠ same type
CTAG2 c.404+35C>T Uncertain significance ★ ⚠ same type
CTAG2 c.404+42G>A 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/ctag2-p-glu89gln (accessed [today's date]).

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