Is CCNQ p.Ala172Gly (c.515C>G) pathogenic?

CCNQ p.Ala172Gly (c.515C>G) is classified Uncertain significance in CCNQ (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-22). AlphaMissense: likely benign (0.3394); Absent from gnomAD v4.1.

How common is CCNQ p.Ala172Gly (c.515C>G) in the general population?

CCNQ p.Ala172Gly (c.515C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCNQ p.Ala172Gly (c.515C>G)?

AlphaMissense predicts likely benign (score 0.3394) — an in-silico prediction, not a clinical call.

CCNQ p.Ala172Gly

c.515C>G · rs2521899540 · VCV2549409

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3394 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3394	likely benign
REVEL	0.225	benign-leaning
SaProt	LLR -7.06	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 6.5	GERP 0.66, phastCons 1
Regional constraint	o/e 0.66	unconstrained · MANE · 11 kb · p 2.8e-07 · regional, not allelic
Overall
CADD	24.7	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: CCNQ
Protein: p.Ala172Gly
Coding: c.515C>G
MANE Select: NM_152274
dbSNP: rs2521899540
Type: single nucleotide variant
Location: chrX:153592648 (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-ala172gly (accessed [today's date]).

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