CELF3 p.Ala342=
c.1026G>A · rs140590829 · VCV2639180
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.511%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.082 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.43 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -4.5 | GERP -4.8 |
| Overall | ||
| CADD | 8.896 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.511%
African / African-American · 374/73,198 alleles
Filtering AF
0.468%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.451%
Overall
0.0322%
500/1,553,274 alleles · rare
exomes 292/1,400,982 · genomes 208/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.511% | 196 |
| Remaining individualsnot grpmax-eligible | 0.0233% | 4,299 |
| Middle Eastern | 0.0188% | 5,320 |
| European (non-Finnish) | 0.00906% | 11,043 |
| Admixed American | 0.00586% | 17,053 |
| South Asian | 0.00356% | 28,109 |
| East Asian | 0.00244% | 41,020 |
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
- CELF3
- Protein
- p.Ala342=
- Coding
- c.1026G>A
- MANE Select
- NM_007185
- dbSNP
- rs140590829
- Type
- single nucleotide variant
- Location
- chr1:151706324 (GRCh38)
- Gene constraint
- LOEUF 0.662 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.04 · 1 PDB
Similar variants
- CELF3 p.Ala146Thr Uncertain significance ★ ⚠ same type
- CELF3 p.Ala206Ser Uncertain significance ★ ⚠ same type
- CELF3 p.Ala206Thr Uncertain significance ★ ⚠ same type
- CELF3 p.Ala216Glu Uncertain significance ★ ⚠ same type
- CELF3 p.Ala221Thr Uncertain significance ★ ⚠ same type
- CELF3 p.Ala276Thr Uncertain significance ★ ⚠ same type
- CELF3 p.Ala312Val Uncertain significance ★ ⚠ same type
- CELF3 p.Ala323Thr 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/celf3-p-ala342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown