Is BAP1 p.Gly560= (c.1680C>T) pathogenic?

BAP1 p.Gly560= (c.1680C>T) is classified Uncertain significance in BAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-29). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with BAP1 p.Gly560= (c.1680C>T)?

BAP1 p.Gly560= (c.1680C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BAP1 p.Gly560= (c.1680C>T) in the general population?

BAP1 p.Gly560= (c.1680C>T) is absent from gnomAD v4.1 (gnomAD).

BAP1 p.Gly560=

c.1680C>T · rs2153226598 · VCV3224437

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

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
Pangolin	Δ0.31	gain · loss 0.05 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 2.5	GERP -1.5, phastCons 1
Overall
CADD	19.65	PHRED · no single calibrated threshold — expert panels disagree

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.Gly560=
Coding: c.1680C>T
MANE Select: NM_004656
dbSNP: rs2153226598
Type: single nucleotide variant
Location: chr3:52403465 (GRCh38)
Gene constraint: LOEUF 0.324 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.87 · 4 PDB
Residue 560: a UniProt-annotated variant site (in tpds1)

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.Gly560Asp Uncertain significance ★★ ⚠ same residue
BAP1 p.Gly560Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
BAP1 p.Gly560Arg Uncertain significance ★ ⚠ same residue
BAP1 p.Gly560Cys 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-gly560 (accessed [today's date]).

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