YAP1 p.Ile193=
c.579C>T · rs537251084 · VCV2713761
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.022%, sas)
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 · C>A here scores Δ0.28 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.4 | GERP -5 |
| Overall | ||
| CADD | 8.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.022%
South Asian · 20/91,068 alleles
Filtering AF
0.0145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0121%
Overall
0.00186%
30/1,613,790 alleles · ultra-rare
exomes 30/1,461,510 · genomes 0/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.022% | 4,553 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| European (non-Finnish) | 0.000593% | 168,533 |
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.Ile193=
- Coding
- c.579C>T
- MANE Select
- NM_001130145
- dbSNP
- rs537251084
- Type
- single nucleotide variant
- Location
- chr11:102162462 (GRCh38)
- Gene constraint
- LOEUF 0.212 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.46 · 41 PDB
- Residue 193
- the ww 1 domain; a turn
Similar variants
- YAP1 p.Gln238Ter Uncertain significance ★★ same type
- YAP1 p.Ser105Pro Uncertain significance ★★ ⚠ same type
- YAP1 p.Thr145Ser Uncertain significance ★★ ⚠ same type
- YAP1 p.Val55Leu Uncertain significance ★★ ⚠ same type
- YAP1 c.1276+42G>C Benign ★★ same type
- YAP1 c.322-157A>G Benign ★★ same type
- YAP1 c.322-247C>T Benign ★★ same type
- YAP1 c.802+206C>A 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-ile193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown