Is CELF4 p.Pro346fs (c.1037del) pathogenic?

CELF4 p.Pro346fs (c.1037del) is classified Conflicting classifications of pathogenicity in CELF4 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-05-05). Absent from gnomAD v4.1; Associated with neurodevelopmental disorder.

What condition is associated with CELF4 p.Pro346fs (c.1037del)?

CELF4 p.Pro346fs (c.1037del) is associated with neurodevelopmental disorder (ClinVar).

How common is CELF4 p.Pro346fs (c.1037del) in the general population?

CELF4 p.Pro346fs (c.1037del) is absent from gnomAD v4.1 (gnomAD).

CELF4 p.Pro346fs

c.1037del · VCV3362794

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,782)

Conditions

neurodevelopmental disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 8 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.5	GERP -1.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,782). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CELF4
Protein: p.Pro346fs
Coding: c.1037del
MANE Select: NM_020180
Type: Deletion
Location: chr18:37270830 (GRCh38)
Gene constraint: LOEUF 0.546 · pLI 0.84 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 62.70 · 2 PDB

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

Disease context

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

Similar variants

CELF4 c.287-5_300del Uncertain significance ★ same condition
CELF4 p.Pro346Ser Uncertain significance ★ ⚠ same residue
CELF4 p.Gly193Val Uncertain significance ★★ ⚠ same condition
CELF4 c.370-67640C>A Uncertain significance ★ same condition
CELF4 c.577+2T>G Uncertain significance ★ same condition
CELF4 p.Arg138Ter Uncertain significance ★ same condition
CELF4 p.Cys194Ter Uncertain significance ★ same condition
CELF4 p.Gln271Ter Uncertain significance ★ 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-pro346fs (accessed [today's date]).

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