Is CELF2 p.Asp451fs (c.1353del) pathogenic?

CELF2 p.Asp451fs (c.1353del) is classified Pathogenic in CELF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-04). Absent from gnomAD; Associated with developmental and epileptic encephalopathy 97.

What condition is associated with CELF2 p.Asp451fs (c.1353del)?

CELF2 p.Asp451fs (c.1353del) is associated with developmental and epileptic encephalopathy 97 (ClinVar).

How common is CELF2 p.Asp451fs (c.1353del) in the general population?

CELF2 p.Asp451fs (c.1353del) is absent from gnomAD (gnomAD).

CELF2 p.Asp451fs

c.1353del · rs2132555667 · VCV1685612

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 12 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.7, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: CELF2
Protein: p.Asp451fs
Coding: c.1353del
MANE Select: NM_001326342
dbSNP: rs2132555667
Type: Deletion
Location: chr10:11325894 (GRCh38)
Gene constraint: LOEUF 0.294 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 66.26 · 7 PDB
Residue 451: the rrm 3 domain; a β-strand; the 'necessary for rna-binding, tnnt2 exon 5 and nmda r1 exon 21 inclusion' region

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 c.355-6858_403+3281del Pathogenic ★ same condition
CELF2 p.Ala295fs Pathogenic ★ same condition
CELF2 p.Lys466fs Likely pathogenic ★ same condition
CELF2 p.Lys471fs Likely pathogenic ★ same condition
CELF2 p.Met13fs Likely pathogenic ★ same condition
CELF2 c.355-48_403+52del Uncertain significance ★ same condition
CELF2 p.Ala363_Leu364insTer Uncertain significance ★ same condition
CELF2 p.Arg513His 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-asp451fs (accessed [today's date]).

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