Is CELF4 p.Phe358= (c.1074C>T) pathogenic?

CELF4 p.Phe358= (c.1074C>T) is classified Likely benign in CELF4 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-15). Very rare (popmax 0.00668%, eas); Associated with CELF4-related disorder.

What condition is associated with CELF4 p.Phe358= (c.1074C>T)?

CELF4 p.Phe358= (c.1074C>T) is associated with CELF4-related disorder (ClinVar).

How common is CELF4 p.Phe358= (c.1074C>T) in the general population?

CELF4 p.Phe358= (c.1074C>T) is very rare (popmax 0.00668%, eas) (gnomAD).

CELF4 p.Phe358=

c.1074C>T · rs765790379 · VCV3053005

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00668%, eas)

Conditions

CELF4-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.25 · evaluated, not missing
Constraint at this position
Conservation	phyloP 5.4	GERP -0.87, phastCons 1
Overall
CADD	14.57	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00668% East Asian · 3/44,886 alleles

Filtering AF 0.00177% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.00186% 30/1,613,852 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00668%	14,962
African / African-American	0.004%	24,981
European (non-Finnish)	0.00186%	53,636
Remaining individualsnot grpmax-eligible	0.0016%	62,486
South Asian	0.0011%	91,066

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.Phe358=
Coding: c.1074C>T
MANE Select: NM_020180
dbSNP: rs765790379
Type: single nucleotide variant
Location: chr18:37270793 (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

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.Asp69= Likely benign same condition
CELF4 p.Leu109= 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-phe358 (accessed [today's date]).

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