Is CTAGE9 p.Ala122Val (c.365C>T) pathogenic?

CTAGE9 p.Ala122Val (c.365C>T) is classified Uncertain significance in CTAGE9 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-07). AlphaMissense: likely benign (0.1162); Absent from gnomAD v4.1.

How common is CTAGE9 p.Ala122Val (c.365C>T) in the general population?

CTAGE9 p.Ala122Val (c.365C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CTAGE9 p.Ala122Val (c.365C>T)?

AlphaMissense predicts likely benign (score 0.1162) — an in-silico prediction, not a clinical call.

CTAGE9 p.Ala122Val

c.365C>T · rs2483187499 · VCV2332297

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1162 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1162	likely benign
REVEL	0.025	moderately benign-leaning
SaProt	LLR -6.10	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 1.3	GERP -2.4, phastCons 0.18
Regional constraint	o/e 0.30	constrained · MANE · 241 bp · p 3.8e-11 · regional, not allelic
Overall
CADD	8.103	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: CTAGE9
Protein: p.Ala122Val
Coding: c.365C>T
MANE Select: NM_001145659
dbSNP: rs2483187499
Type: single nucleotide variant
Location: chr6:131710653 (GRCh38)
Gene constraint: LOEUF 1.713 · pLI 0.41 (gnomAD)
Structure: AlphaFold pLDDT 69.37

Full CTAGE9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CTAGE9 p.Ala120Thr Uncertain significance ★ ⚠ same type
CTAGE9 p.Ala120Val Uncertain significance ★ ⚠ same type
CTAGE9 p.Ala168Val Uncertain significance ★ ⚠ same type
CTAGE9 p.Ala208Val Uncertain significance ★ ⚠ same type
CTAGE9 p.Ala280Val Uncertain significance ★ ⚠ same type
CTAGE9 p.Ala321Thr Uncertain significance ★ ⚠ same type
CTAGE9 p.Ala48Pro Uncertain significance ★ ⚠ same type
CTAGE9 p.Ala748Val 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/ctage9-p-ala122val (accessed [today's date]).

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