Is CELF4 p.Asp69= (c.207C>T) pathogenic?

CELF4 p.Asp69= (c.207C>T) is classified Likely benign in CELF4 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-08). Very rare (popmax 0.00873%, nfe); Associated with CELF4-related disorder.

What condition is associated with CELF4 p.Asp69= (c.207C>T)?

CELF4 p.Asp69= (c.207C>T) is associated with CELF4-related disorder (ClinVar).

How common is CELF4 p.Asp69= (c.207C>T) in the general population?

CELF4 p.Asp69= (c.207C>T) is very rare (popmax 0.00873%, nfe) (gnomAD).

CELF4 p.Asp69=

c.207C>T · rs780570053 · VCV3041530

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00873%, 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 6.6	GERP 2.3, phastCons 1
Overall
CADD	13.24	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00873% European (non-Finnish) · 103/1,179,908 alleles

Filtering AF 0.00733% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00684%

Overall 0.00669% 108/1,613,772 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00873%	11,455
Admixed American	0.00333%	29,989
Remaining individualsnot grpmax-eligible	0.0032%	31,236
African / African-American	0.00133%	74,908

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.Asp69=
Coding: c.207C>T
MANE Select: NM_020180
dbSNP: rs780570053
Type: single nucleotide variant
Location: chr18:37565435 (GRCh38)
Gene constraint: LOEUF 0.546 · pLI 0.84 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 62.70 · 2 PDB
Residue 69: the rrm 1 domain; an α-helix; 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.Leu109= Likely benign same condition
CELF4 p.Phe358= Likely benign same condition
CELF4 p.Val279= 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-asp69 (accessed [today's date]).

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