Is CCNQ p.Arg113His (c.338G>A) pathogenic?

CCNQ p.Arg113His (c.338G>A) is classified Likely benign in CCNQ (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-15). AlphaMissense: likely benign (0.0659); Rare (popmax 0.464%, mid); Associated with neutropenia.

What condition is associated with CCNQ p.Arg113His (c.338G>A)?

CCNQ p.Arg113His (c.338G>A) is associated with neutropenia, lymphopenia (ClinVar).

How common is CCNQ p.Arg113His (c.338G>A) in the general population?

CCNQ p.Arg113His (c.338G>A) is rare (popmax 0.464%, mid) (gnomAD).

What do computational predictors say about CCNQ p.Arg113His (c.338G>A)?

AlphaMissense predicts likely benign (score 0.0659) — an in-silico prediction, not a clinical call.

CCNQ p.Arg113His

c.338G>A · rs150562029 · VCV703138

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.0659 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.464%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

neutropenia

Computational evidence

Protein change
AlphaMissense	0.0659	likely benign
REVEL	0.029	moderately benign-leaning
SaProt	LLR -6.69	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 0.24	GERP -1.9, phastCons 0.96
Regional constraint	o/e 0.66	unconstrained · MANE · 11 kb · p 2.8e-07 · regional, not allelic
Overall
CADD	11.51	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 0.464% Middle Eastern · 20/4,306 alleles

Filtering AF 0.431% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.426%

Overall 0.351% 4,252/1,210,043 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.464%	215
European (non-Finnish)	0.443%	226
Remaining individualsnot grpmax-eligible	0.294%	340
Finnishnot grpmax-eligible	0.0902%	1,109
Admixed American	0.0872%	1,146
African / African-American	0.0558%	1,791
Ashkenazi Jewishnot grpmax-eligible	0.0545%	1,836
South Asian	0.00528%	18,948

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.Arg113His
Coding: c.338G>A
MANE Select: NM_152274
dbSNP: rs150562029
Type: single nucleotide variant
Location: chrX:153594638 (GRCh38)
Structure: AlphaFold pLDDT 88.81

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

Disease context

neutropenia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: lymphopenia

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-arg113his (accessed [today's date]).

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