YAP1 p.Arg106=
c.316C>A · rs529940453 · VCV726526
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.201%, sas)
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 2.7 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 14.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.201%
South Asian · 183/91,066 alleles
Filtering AF
0.177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.168%
Overall
0.0123%
199/1,612,716 alleles · rare
exomes 191/1,460,448 · genomes 8/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.201% | 498 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,206 |
| Admixed American | 0.005% | 20,005 |
| European (non-Finnish) | 8.48e-05% | 1,179,709 |
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.Arg106=
- Coding
- c.316C>A
- MANE Select
- NM_001130145
- dbSNP
- rs529940453
- Type
- single nucleotide variant
- Location
- chr11:102111164 (GRCh38)
- Gene constraint
- LOEUF 0.212 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.46 · 41 PDB
- Residue 106
- the 'disordered' region
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-arg106 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown