YAP1 p.Phe96del
c.283TTC[1] · rs2496408254 · VCV2900514
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6.8 | GERP 0.69, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,878 alleles
Overall
6.2e-05%
1/1,613,338 alleles · very rare
exomes 1/1,461,030 · genomes 0/152,308 · joint denominator
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
- YAP1
- Protein
- p.Phe96del
- Coding
- c.283TTC[1]
- MANE Select
- NM_001130145
- dbSNP
- rs2496408254
- Type
- Microsatellite
- Location
- chr11:102111130 (GRCh38)
- Gene constraint
- LOEUF 0.212 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.46 · 41 PDB
- Residue 96
- the 'disordered' region; an α-helix
Similar variants
- YAP1 p.Ser274fs Uncertain significance ★★ same type
- YAP1 p.Asp399fs Likely pathogenic ★ same type
- YAP1 c.1277-16TG[2] Likely benign ★ 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/yap1-p-phe96del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown