Is CELF4 p.Asp434= (c.1302C>T) pathogenic?

CELF4 p.Asp434= (c.1302C>T) is classified Likely benign in CELF4 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-03-01). Ultra-rare (popmax 0.0213%, sas).

How common is CELF4 p.Asp434= (c.1302C>T) in the general population?

CELF4 p.Asp434= (c.1302C>T) is ultra-rare (popmax 0.0213%, sas) (gnomAD).

CELF4 p.Asp434=

c.1302C>T · VCV4820862

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0213%, sas)

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 4.8	GERP -1, phastCons 1
Overall
CADD	13.76	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0213% South Asian · 19/89,372 alleles

Filtering AF 0.0139% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0116%

Overall 0.00497% 73/1,470,028 alleles · ultra-rare exomes 63/1,326,746 · genomes 10/143,282 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0213%	4,704
East Asian	0.00975%	10,257
African / African-American	0.00722%	13,860
European (non-Finnish)	0.00403%	24,799
Remaining individualsnot grpmax-eligible	0.00372%	26,865

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.Asp434=
Coding: c.1302C>T
MANE Select: NM_020180
Type: single nucleotide variant
Location: chr18:37259212 (GRCh38)
Gene constraint: LOEUF 0.546 · pLI 0.84 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 62.70 · 2 PDB
Residue 434: the rrm 3 domain

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

Similar variants

CELF4 p.Gly193Val Uncertain significance ★★ ⚠ same type
CELF4 p.Ala381= Benign/Likely benign ★★ same type
CELF4 p.Pro127= Benign ★★ same type
CELF4 p.Pro406= Benign ★★ same type
CELF4 p.Glu76Ter Pathogenic ★ same type
CELF4 c.1165+2T>C Uncertain significance ★ same type
CELF4 c.370-67640C>A Uncertain significance ★ same type
CELF4 c.577+2T>G Uncertain significance ★ 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/celf4-p-asp434 (accessed [today's date]).

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