Is CELF3 p.Arg32Gln (c.95G>A) pathogenic?

CELF3 p.Arg32Gln (c.95G>A) is classified Uncertain significance in CELF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-25). AlphaMissense: likely benign (0.1081); Very rare (popmax 0.00667%, amr).

How common is CELF3 p.Arg32Gln (c.95G>A) in the general population?

CELF3 p.Arg32Gln (c.95G>A) is very rare (popmax 0.00667%, amr) (gnomAD).

What do computational predictors say about CELF3 p.Arg32Gln (c.95G>A)?

AlphaMissense predicts likely benign (score 0.1081) — an in-silico prediction, not a clinical call.

CELF3 p.Arg32Gln

c.95G>A · VCV3831298

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1081 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00667%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1081	likely benign
REVEL	0.135	moderately benign-leaning
SaProt	LLR -8.31	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 7.7	GERP 0.17, phastCons 1
Regional constraint	o/e 0.59	unconstrained · MANE · 8,731 bp · p 6.5e-15 · regional, not allelic
Overall
CADD	29.2	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

Grpmax group 0.00667% Admixed American · 4/59,996 alleles

Filtering AF 0.00226% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00135%

Overall 0.000558% 9/1,614,022 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00667%	14,999
African / African-American	0.00267%	37,470
European (non-Finnish)	0.000254%	393,337

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: CELF3
Protein: p.Arg32Gln
Coding: c.95G>A
MANE Select: NM_007185
Type: single nucleotide variant
Location: chr1:151715926 (GRCh38)
Gene constraint: LOEUF 0.662 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.04 · 1 PDB
Residue 32: the rrm 1 domain

Full CELF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CELF3 p.Ala146Thr Uncertain significance ★ ⚠ same type
CELF3 p.Ala206Ser Uncertain significance ★ ⚠ same type
CELF3 p.Ala206Thr Uncertain significance ★ ⚠ same type
CELF3 p.Ala216Glu Uncertain significance ★ ⚠ same type
CELF3 p.Ala221Thr Uncertain significance ★ ⚠ same type
CELF3 p.Ala276Thr Uncertain significance ★ ⚠ same type
CELF3 p.Ala312Val Uncertain significance ★ ⚠ same type
CELF3 p.Ala323Thr 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/celf3-p-arg32gln (accessed [today's date]).

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