Is CELF2 p.Ser313fs (c.938_939del) pathogenic?

CELF2 p.Ser313fs (c.938939del) is classified Likely pathogenic in CELF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-25). Associated with developmental and epileptic encephalopathy 97.

What condition is associated with CELF2 p.Ser313fs (c.938_939del)?

CELF2 p.Ser313fs (c.938_939del) is associated with developmental and epileptic encephalopathy 97 (ClinVar).

CELF2 p.Ser313fs

c.938_939del · VCV3338598

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

developmental and epileptic encephalopathy 97

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 9 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 1.5, phastCons 1

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

Variant & gene context

Gene: CELF2
Protein: p.Ser313fs
Coding: c.938_939del
MANE Select: NM_001326342
Type: Microsatellite
Location: chr10:11288508 (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

Disease context

developmental and epileptic encephalopathy 97 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CELF2 p.Arg513His Likely pathogenic ★★ same condition
CELF2 p.Gln237Ter Pathogenic/Likely pathogenic ★★ same condition
CELF2 c.355-6858_403+3281del Pathogenic ★ same condition
CELF2 p.Ala295fs Pathogenic ★ same condition
CELF2 p.Arg506His Pathogenic ★ same condition
CELF2 p.Arg513Cys Likely pathogenic ★ same condition
CELF2 p.Asp451fs Pathogenic ★ same condition
CELF2 p.Gln88fs Likely pathogenic ★ 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/celf2-p-ser313fs (accessed [today's date]).

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