Is CEP44 p.Arg11Gln (c.32G>A) pathogenic?

CEP44 p.Arg11Gln (c.32G>A) is classified Uncertain significance in CEP44 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-03). AlphaMissense: ambiguous (0.5239); Rare (popmax 0.5%, afr).

How common is CEP44 p.Arg11Gln (c.32G>A) in the general population?

CEP44 p.Arg11Gln (c.32G>A) is rare (popmax 0.5%, afr) (gnomAD).

What do computational predictors say about CEP44 p.Arg11Gln (c.32G>A)?

AlphaMissense predicts ambiguous (score 0.5239) — an in-silico prediction, not a clinical call.

CEP44 p.Arg11Gln

c.32G>A · VCV4226318

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5239 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.5%, afr)

Computational evidence

Protein change
AlphaMissense	0.5239	ambiguous
REVEL	0.327	indeterminate
SaProt	LLR -8.32	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.9	GERP 1.8, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 18 kb · p 0.48 · regional, not allelic
Overall
CADD	33.0	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 0.5% African / African-American · 375/75,036 alleles

Filtering AF 0.458% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.442%

Overall 0.0324% 522/1,613,580 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.5%	200
Remaining individualsnot grpmax-eligible	0.0384%	2,603
Admixed American	0.0367%	2,727
European (non-Finnish)	0.00831%	12,037
South Asian	0.0033%	30,347

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: CEP44
Protein: p.Arg11Gln
Coding: c.32G>A
MANE Select: NM_001040157
Type: single nucleotide variant
Location: chr4:174299153 (GRCh38)
Gene constraint: LOEUF 1.34 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.41 · 1 PDB
Residue 11: the 'binds with microtubules and centrioles' region; an α-helix

Full CEP44 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP44 p.Ala102Gly Uncertain significance ★ ⚠ same type
CEP44 p.Ala155Thr Uncertain significance ★ ⚠ same type
CEP44 p.Ala172Ser Uncertain significance ★ ⚠ same type
CEP44 p.Ala172Thr Uncertain significance ★ ⚠ same type
CEP44 p.Ala172Val Uncertain significance ★ ⚠ same type
CEP44 p.Ala349Gly Uncertain significance ★ ⚠ same type
CEP44 p.Arg176Cys Uncertain significance ★ ⚠ same type
CEP44 p.Arg72His Uncertain significance ★ ⚠ 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/cep44-p-arg11gln (accessed [today's date]).

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