Is CTAGE1 p.Val26Asp (c.77T>A) pathogenic?

CTAGE1 p.Val26Asp (c.77T>A) is classified Uncertain significance in CTAGE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-25). AlphaMissense: likely pathogenic (0.7185); Absent from gnomAD v4.1.

How common is CTAGE1 p.Val26Asp (c.77T>A) in the general population?

CTAGE1 p.Val26Asp (c.77T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CTAGE1 p.Val26Asp (c.77T>A)?

AlphaMissense predicts likely pathogenic (score 0.7185) — an in-silico prediction, not a clinical call.

CTAGE1 p.Val26Asp

c.77T>A · rs2510645937 · VCV2318878

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7185 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.7185	likely pathogenic · top 1% in CTAGE1
REVEL	0.304	indeterminate
SaProt	LLR -11.09	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3	GERP -0.97, phastCons 0.013
Regional constraint	o/e 1.13	unconstrained · MANE · 2,234 bp · p 0.00025 · regional, not allelic
Overall
CADD	19.57	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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: CTAGE1
Protein: p.Val26Asp
Coding: c.77T>A
MANE Select: NM_172241
dbSNP: rs2510645937
Type: single nucleotide variant
Location: chr18:22417735 (GRCh38)
Structure: AlphaFold pLDDT 70.45

Full CTAGE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CTAGE1 p.Ala169= Benign ★★ same type
CTAGE1 p.Ile682Met Benign ★★ same type
CTAGE1 p.Pro686Thr Benign ★★ ⚠ same type
CTAGE1 p.Val696Met Benign ★★ same type
CTAGE1 p.Ala181Val Uncertain significance ★ ⚠ same type
CTAGE1 p.Ala19Thr Uncertain significance ★ ⚠ same type
CTAGE1 p.Ala282Asp Uncertain significance ★ ⚠ same type
CTAGE1 p.Ala332Thr 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/ctage1-p-val26asp (accessed [today's date]).

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