Is CCNQ p.Ala3= (c.9C>T) pathogenic?

CCNQ p.Ala3= (c.9C>T) is classified Likely benign in CCNQ (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-09-28). Very rare (popmax 0.00435%, eas); Associated with CCNQ-related disorder.

What condition is associated with CCNQ p.Ala3= (c.9C>T)?

CCNQ p.Ala3= (c.9C>T) is associated with CCNQ-related disorder (ClinVar).

How common is CCNQ p.Ala3= (c.9C>T) in the general population?

CCNQ p.Ala3= (c.9C>T) is very rare (popmax 0.00435%, eas) (gnomAD).

CCNQ p.Ala3=

c.9C>T · rs1166475022 · VCV3047262

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00435%, eas)

Conditions

CCNQ-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.49	GERP 0.99
Overall
CADD	8.037	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00435% East Asian · 1/23,006 alleles

Filtering AF 0.000728% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000532%

Overall 0.00115% 12/1,043,504 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00435%	23,006
European (non-Finnish)	0.00136%	73,696

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.Ala3=
Coding: c.9C>T
MANE Select: NM_152274
dbSNP: rs1166475022
Type: single nucleotide variant
Location: chrX:153599065 (GRCh38)
Structure: AlphaFold pLDDT 88.81
Residue 3: the 'disordered' region

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

Disease context

CCNQ-related disorder

Similar variants

CCNQ p.Gly9= Benign ★ same condition
CCNQ p.Tyr241Cys Likely benign ★ same condition
CCNQ c.297-4G>A Likely benign same condition
CCNQ c.-5G>A Likely benign same condition
CCNQ p.Ala66fs Likely pathogenic ★ same condition
CCNQ c.113-85T>C Benign ★★ same type
CCNQ c.296+72C>T Benign ★★ same type
CCNQ c.297-320A>G 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-ala3 (accessed [today's date]).

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