YAP1 p.Arg124Ter
c.370C>T · rs587777249 · VCV120326
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
coloboma
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 9 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 42.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- YAP1
- Protein
- p.Arg124Ter
- Coding
- c.370C>T
- MANE Select
- NM_001130145
- dbSNP
- rs587777249
- Type
- single nucleotide variant
- Location
- chr11:102114192 (GRCh38)
- Gene constraint
- LOEUF 0.212 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.46 · 41 PDB
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-arg124ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown