Is CCNQ p.Val96Ala (c.287T>C) pathogenic?

CCNQ p.Val96Ala (c.287T>C) is classified Uncertain significance in CCNQ (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-21). AlphaMissense: likely pathogenic (0.9275); Absent from gnomAD v4.1.

How common is CCNQ p.Val96Ala (c.287T>C) in the general population?

CCNQ p.Val96Ala (c.287T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCNQ p.Val96Ala (c.287T>C)?

AlphaMissense predicts likely pathogenic (score 0.9275) — an in-silico prediction, not a clinical call.

CCNQ p.Val96Ala

c.287T>C · VCV3632697

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9275 · 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	0.9275	likely pathogenic
REVEL	0.369	indeterminate
SaProt	LLR -11.38	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 9.1	GERP 1.8, phastCons 1
Regional constraint	o/e 0.66	unconstrained · MANE · 11 kb · p 2.8e-07 · regional, not allelic
Overall
CADD	26.4	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: CCNQ
Protein: p.Val96Ala
Coding: c.287T>C
MANE Select: NM_152274
Type: single nucleotide variant
Location: chrX:153596013 (GRCh38)
Structure: AlphaFold pLDDT 88.81

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

Similar variants

CCNQ c.113-85T>C Benign ★★ same type
CCNQ c.296+72C>T Benign ★★ same type
CCNQ c.297-320A>G Benign ★★ same type
CCNQ c.429+171C>T Benign ★★ same type
CCNQ c.429+8C>T Benign ★★ same type
CCNQ c.430-12G>A Benign/Likely benign ★★ same type
CCNQ c.657+144C>T Benign ★★ same type
CCNQ p.Ala209= Benign/Likely 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/ccnq-p-val96ala (accessed [today's date]).

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