Is YAP1 p.Gly293= (c.879C>T) pathogenic?

YAP1 p.Gly293= (c.879C>T) is classified Likely benign in YAP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-16). Ultra-rare (popmax 0.0223%, eas); Associated with YAP1-related disorder.

What condition is associated with YAP1 p.Gly293= (c.879C>T)?

YAP1 p.Gly293= (c.879C>T) is associated with YAP1-related disorder (ClinVar).

How common is YAP1 p.Gly293= (c.879C>T) in the general population?

YAP1 p.Gly293= (c.879C>T) is ultra-rare (popmax 0.0223%, eas) (gnomAD).

YAP1 p.Gly293=

c.879C>T · rs756175059 · VCV3059192

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0223%, eas)

Conditions

YAP1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.012	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.4	GERP -4.4
Overall
CADD	7.182	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0223% East Asian · 10/44,882 alleles

Filtering AF 0.012% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00916%

Overall 0.00155% 25/1,613,418 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0223%	4,488
Admixed American	0.00167%	59,990
Remaining individualsnot grpmax-eligible	0.0016%	62,436
African / African-American	0.00133%	74,908
European (non-Finnish)	0.00102%	98,323

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.Gly293=
Coding: c.879C>T
MANE Select: NM_001130145
dbSNP: rs756175059
Type: single nucleotide variant
Location: chr11:102205969 (GRCh38)
Gene constraint: LOEUF 0.212 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 58.46 · 41 PDB
Residue 293: the 'disordered' region; the 'transactivation domain' region

Full YAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

YAP1-related disorder

Similar variants

YAP1 p.Ser105Pro Uncertain significance ★★ ⚠ same condition
YAP1 p.Arg394Ter Pathogenic ★ same condition
YAP1 c.321+8C>T Likely benign same condition
YAP1 p.Tyr247fs Uncertain significance same condition
YAP1 p.Gln238Ter 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

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-gly293 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown