Is BAP1 p.Cys320= (c.960C>T) pathogenic?

BAP1 p.Cys320= (c.960C>T) is classified Benign/Likely benign in BAP1 (ClinVar, Multiple submitters, 14 submitters; last evaluated 2026-02-04). Rare (popmax 0.731%, afr); Associated with melanoma, uveal, susceptibility to, 2.

What condition is associated with BAP1 p.Cys320= (c.960C>T)?

BAP1 p.Cys320= (c.960C>T) is associated with melanoma, uveal, susceptibility to, 2, BAP1-related tumor predisposition syndrome, hereditary neoplastic syndrome (ClinVar).

How common is BAP1 p.Cys320= (c.960C>T) in the general population?

BAP1 p.Cys320= (c.960C>T) is rare (popmax 0.731%, afr) (gnomAD).

BAP1 p.Cys320=

c.960C>T · rs143659795 · VCV240070

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 14 submitters

gnomAD v4.1

Rare

rare (popmax 0.731%, afr)

Conditions

melanoma, uveal, susceptibility to, 2

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
Constraint at this position
Conservation	phyloP 0.35	GERP -0.33, phastCons 0.007
Overall
CADD	5.664	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.731% African / African-American · 548/75,012 alleles

Filtering AF 0.68% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.66%

Overall 0.0437% 705/1,613,808 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.731%	137
Middle Eastern	0.132%	755
Remaining individualsnot grpmax-eligible	0.0528%	1,894
Admixed American	0.045%	2,223
European (non-Finnish)	0.00678%	14,750
South Asian	0.00659%	15,181
Finnishnot grpmax-eligible	0.00314%	31,863
East Asian	0.00223%	44,880

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: BAP1
Protein: p.Cys320=
Coding: c.960C>T
MANE Select: NM_007212 · reported on NM_004656
dbSNP: rs143659795
Type: single nucleotide variant
Location: chr3:52405266 (GRCh38)
Structure: AlphaFold pLDDT 78.27 · 28 PDB

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

Disease context

melanoma, uveal, susceptibility to, 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: BAP1-related tumor predisposition syndrome hereditary neoplastic syndrome

Similar variants

BAP1 p.Cys320Arg Uncertain significance ★★ ⚠ same residue
BAP1 p.Cys320Tyr Uncertain significance ★★ ⚠ same residue
BAP1 p.Cys320fs Pathogenic ★★ same residue
BAP1 p.Cys320Gly 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.122+5G>A Pathogenic/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-cys320 (accessed [today's date]).

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