Is CELF4 p.Val279= (c.837C>T) pathogenic?

CELF4 p.Val279= (c.837C>T) is classified Likely benign in CELF4 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-19). Rare (popmax 0.104%, nfe); Associated with CELF4-related disorder.

What condition is associated with CELF4 p.Val279= (c.837C>T)?

CELF4 p.Val279= (c.837C>T) is associated with CELF4-related disorder (ClinVar).

How common is CELF4 p.Val279= (c.837C>T) in the general population?

CELF4 p.Val279= (c.837C>T) is rare (popmax 0.104%, nfe) (gnomAD).

CELF4 p.Val279=

c.837C>T · rs142389555 · VCV3049299

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.104%, nfe)

Conditions

CELF4-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 -0.56	GERP -4, phastCons 0.001
Overall
CADD	7.841	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.104% European (non-Finnish) · 1,228/1,179,626 alleles

Filtering AF 0.0992% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0973%

Overall 0.0812% 1,310/1,613,236 alleles · rare exomes 1,230/1,461,008 · genomes 80/152,228 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.104%	961
Remaining individualsnot grpmax-eligible	0.0448%	2,231
Admixed American	0.035%	2,857
African / African-American	0.0213%	4,684
South Asian	0.0154%	6,502
Finnishnot grpmax-eligible	0.00314%	31,872
East Asian	0.00223%	44,864

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: CELF4
Protein: p.Val279=
Coding: c.837C>T
MANE Select: NM_020180
dbSNP: rs142389555
Type: single nucleotide variant
Location: chr18:37273128 (GRCh38)
Gene constraint: LOEUF 0.546 · pLI 0.84 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 62.70 · 2 PDB
Residue 279: the 'sufficient for rna-binding and mse-dependent splicing activity' region

Full CELF4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CELF4-related disorder

Similar variants

CELF4 c.801+1G>C Uncertain significance ★ same condition
CELF4 p.Gln414His Uncertain significance ⚠ same condition
CELF4 c.801+7G>A Benign same condition
CELF4 p.Ala310= Likely benign same condition
CELF4 p.Ala328= Benign same condition
CELF4 p.Asp69= Likely benign same condition
CELF4 p.Leu109= Likely benign same condition
CELF4 p.Phe358= Likely benign same condition

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/celf4-p-val279 (accessed [today's date]).

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