Is BAP1 p.Trp196Ter (c.588G>A) pathogenic?

BAP1 p.Trp196Ter (c.588G>A) is classified Pathogenic in BAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with BAP1 p.Trp196Ter (c.588G>A)?

BAP1 p.Trp196Ter (c.588G>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BAP1 p.Trp196Ter (c.588G>A) in the general population?

BAP1 p.Trp196Ter (c.588G>A) is absent from gnomAD v4.1 (gnomAD).

BAP1 p.Trp196Ter

c.588G>A · rs1193212091 · VCV1750309

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,571,620)

Conditions

hereditary neoplastic syndrome

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 haploinsufficient gene (ClinGen); NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.1, phastCons 1
Overall
CADD	37.0	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

No allele count reported in gnomAD v4.1 (AN 1,571,620). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BAP1
Protein: p.Trp196Ter
Coding: c.588G>A
MANE Select: NM_007212 · reported on NM_004656
dbSNP: rs1193212091
Type: single nucleotide variant
Location: chr3:52406900 (GRCh38)
Structure: AlphaFold pLDDT 78.27 · 28 PDB
Residue 196: the 'disordered' region

Full BAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BAP1 p.Trp196Ser Uncertain significance ★★ ⚠ same residue
BAP1 p.Trp196Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
BAP1 p.Trp196Leu Uncertain significance ★ ⚠ same residue
BAP1 p.Trp196Arg Uncertain significance ★ ⚠ same residue
BAP1 c.1117-1G>A Likely pathogenic ★★ same condition
BAP1 c.122+1G>A Pathogenic ★★ same condition
BAP1 c.122+1G>T Pathogenic/Likely pathogenic ★★ same condition
BAP1 c.1251-1G>A Likely pathogenic ★★ same condition

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/bap1-p-trp196ter (accessed [today's date]).

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