Is BAP1 p.Lys187Arg (c.560A>G) pathogenic?

BAP1 p.Lys187Arg (c.560A>G) is classified Uncertain significance in BAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-12). AlphaMissense: likely pathogenic (0.745); Absent from gnomAD v4.1.

How common is BAP1 p.Lys187Arg (c.560A>G) in the general population?

BAP1 p.Lys187Arg (c.560A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BAP1 p.Lys187Arg (c.560A>G)?

AlphaMissense predicts likely pathogenic (score 0.745) — an in-silico prediction, not a clinical call.

BAP1 p.Lys187Arg

c.560A>G · rs2153227782 · VCV2499176

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.745 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.745	likely pathogenic
REVEL	0.445	indeterminate
SaProt	LLR -8.24	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 2.1, phastCons 1
Overall
CADD	29.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: BAP1
Protein: p.Lys187Arg
Coding: c.560A>G
MANE Select: NM_004656
dbSNP: rs2153227782
Type: single nucleotide variant
Location: chr3:52407194 (GRCh38)
Gene constraint: LOEUF 0.324 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.87 · 4 PDB
Residue 187: the uch catalytic domain; a β-strand

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

Similar variants

BAP1 p.Lys187= Likely benign ★★ same residue
BAP1 c.1117-1G>A Likely pathogenic ★★ same type
BAP1 c.122+1G>A Pathogenic ★★ same type
BAP1 c.122+1G>T Pathogenic/Likely pathogenic ★★ same type
BAP1 c.122+5G>A Pathogenic/Likely pathogenic ★★ same type
BAP1 c.122+5G>C Likely pathogenic ★★ same type
BAP1 c.1251-1G>A Likely pathogenic ★★ same type
BAP1 c.1251-1G>C Likely pathogenic ★★ 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/bap1-p-lys187arg (accessed [today's date]).

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