CELF4 p.Pro406=
c.1218G>A · rs78311159 · VCV728639
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.892%, eas)
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 0.58 | GERP -4.7, phastCons 1 |
| Overall | ||
| CADD | 12.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.892%
East Asian · 387/43,372 alleles
Filtering AF
0.819%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.79%
Overall
0.0466%
737/1,579,972 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.892% | 112 |
| Admixed American | 0.142% | 702 |
| Middle Eastern | 0.133% | 751 |
| Remaining individualsnot grpmax-eligible | 0.108% | 927 |
| African / African-American | 0.0551% | 1,814 |
| European (non-Finnish) | 0.013% | 7,697 |
| South Asian | 0.00349% | 28,684 |
| Finnishnot grpmax-eligible | 0.00325% | 30,778 |
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.Pro406=
- Coding
- c.1218G>A
- MANE Select
- NM_020180
- dbSNP
- rs78311159
- Type
- single nucleotide variant
- Location
- chr18:37264705 (GRCh38)
- Gene constraint
- LOEUF 0.546 · pLI 0.84 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.70 · 2 PDB
- Residue 406
- the rrm 3 domain
Similar variants
- CELF4 p.Pro406Leu Uncertain significance ★ ⚠ same residue
- CELF4 p.Gly193Val Uncertain significance ★★ ⚠ same type
- CELF4 p.Ala381= Benign/Likely benign ★★ same type
- CELF4 p.Pro127= 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-pro406 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown