Is CCNQ p.Val168Phe (c.502G>T) pathogenic?

CCNQ p.Val168Phe (c.502G>T) is classified Likely benign in CCNQ (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-08). AlphaMissense: likely benign (0.2531); Very rare (popmax 0.00706%, sas).

How common is CCNQ p.Val168Phe (c.502G>T) in the general population?

CCNQ p.Val168Phe (c.502G>T) is very rare (popmax 0.00706%, sas) (gnomAD).

What do computational predictors say about CCNQ p.Val168Phe (c.502G>T)?

AlphaMissense predicts likely benign (score 0.2531) — an in-silico prediction, not a clinical call.

CCNQ p.Val168Phe

c.502G>T · rs370810560 · VCV1947874

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2531 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00706%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2531	likely benign
REVEL	0.128	moderately benign-leaning
SaProt	LLR -8.14	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 -2.1	GERP -0.64
Regional constraint	o/e 0.66	unconstrained · MANE · 11 kb · p 2.8e-07 · regional, not allelic
Overall
CADD	14.15	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 0.00706% South Asian · 4/56,691 alleles

Filtering AF 0.00235% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00141%

Overall 0.000661% 8/1,210,384 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00706%	14,173
African / African-American	0.0052%	19,230
Remaining individualsnot grpmax-eligible	0.0021%	47,581

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: CCNQ
Protein: p.Val168Phe
Coding: c.502G>T
MANE Select: NM_152274
dbSNP: rs370810560
Type: single nucleotide variant
Location: chrX:153592661 (GRCh38)
Structure: AlphaFold pLDDT 88.81

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

Similar variants

CCNQ p.Val168Ile Uncertain significance ★ ⚠ same residue
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

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-val168phe (accessed [today's date]).

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