Is CELF2 p.Asn308Ser (c.923A>G) pathogenic?

CELF2 p.Asn308Ser (c.923A>G) is classified Likely benign in CELF2 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-12-01). AlphaMissense: likely benign (0.0442); Rare (popmax 0.14%, nfe).

How common is CELF2 p.Asn308Ser (c.923A>G) in the general population?

CELF2 p.Asn308Ser (c.923A>G) is rare (popmax 0.14%, nfe) (gnomAD).

What do computational predictors say about CELF2 p.Asn308Ser (c.923A>G)?

AlphaMissense predicts likely benign (score 0.0442) — an in-silico prediction, not a clinical call.

CELF2 p.Asn308Ser

c.923A>G · rs41291249 · VCV2640299

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0442 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.14%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0442	likely benign
REVEL	0.078	moderately benign-leaning
SaProt	LLR -4.17	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 7.9	GERP 0.72, phastCons 1
Regional constraint	o/e 0.50	unconstrained · MANE · 156 kb · p 7.3e-29 · regional, not allelic
Overall
CADD	23.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM N301S vs ClinVar N308S) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.14% European (non-Finnish) · 1,656/1,180,024 alleles

Filtering AF 0.135% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.132%

Overall 0.115% 1,862/1,613,952 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.14%	713
Remaining individualsnot grpmax-eligible	0.096%	1,042
Finnishnot grpmax-eligible	0.0956%	1,047
Admixed American	0.0716%	1,396
African / African-American	0.0253%	3,949
South Asian	0.0253%	3,960

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: CELF2
Protein: p.Asn308Ser
Coding: c.923A>G
MANE Select: NM_001326342
dbSNP: rs41291249
Type: single nucleotide variant
Location: chr10:11288499 (GRCh38)
Gene constraint: LOEUF 0.294 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 66.26 · 7 PDB

Full CELF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CELF2 p.Arg506Cys Pathogenic/Likely pathogenic ★★ same type
CELF2 p.Arg513His Likely pathogenic ★★ same type
CELF2 p.Gln237Ter Pathogenic/Likely pathogenic ★★ same type
CELF2 p.Ala135Thr Uncertain significance ★★ ⚠ same type
CELF2 p.Val95Leu Uncertain significance ★★ ⚠ same type
CELF2 p.Arg506His Pathogenic ★ same type
CELF2 p.Arg506Leu Pathogenic ★ same type
CELF2 p.Arg513Cys Likely pathogenic ★ 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/celf2-p-asn308ser (accessed [today's date]).

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