Is BAP1 p.Ser98= (c.294C>T) pathogenic?

BAP1 p.Ser98= (c.294C>T) is classified Benign/Likely benign in BAP1 (ClinVar, Multiple submitters, 14 submitters; last evaluated 2026-04-01). Ultra-rare (popmax 0.0758%, nfe); Associated with BAP1-related tumor predisposition syndrome.

What condition is associated with BAP1 p.Ser98= (c.294C>T)?

BAP1 p.Ser98= (c.294C>T) is associated with BAP1-related tumor predisposition syndrome, melanoma, uveal, susceptibility to, 2, hereditary neoplastic syndrome (ClinVar).

How common is BAP1 p.Ser98= (c.294C>T) in the general population?

BAP1 p.Ser98= (c.294C>T) is ultra-rare (popmax 0.0758%, nfe) (gnomAD).

How is BAP1-related tumor predisposition syndrome inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

BAP1 p.Ser98=

c.294C>T · rs140641333 · VCV259517

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 14 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0758%, nfe)

Conditions

BAP1-related tumor predisposition 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
Constraint at this position
Conservation	phyloP -1.3	GERP -3.5
Overall
CADD	6.745	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0758% European (non-Finnish) · 894/1,179,410 alleles

Filtering AF 0.0716% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.07%

Overall 0.059% 951/1,612,748 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0758%	1,319
Remaining individualsnot grpmax-eligible	0.04%	2,499
Admixed American	0.0334%	2,993
Middle Eastern	0.0165%	6,058
African / African-American	0.0107%	9,373
Finnishnot grpmax-eligible	0.00313%	31,955
South Asian	0.0011%	90,720

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.Ser98=
Coding: c.294C>T
MANE Select: NM_007212 · reported on NM_004656
dbSNP: rs140641333
Type: single nucleotide variant
Location: chr3:52408039 (GRCh38)
Structure: AlphaFold pLDDT 78.27 · 28 PDB
Residue 98: the 'interaction with hip2' region; the 'interaction with nucleosomes via an acidic patch on histone h2a and histone h2b' region; an α-helix

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

Disease context

Also linked: melanoma, uveal, susceptibility to, 2 hereditary neoplastic syndrome Kury-Isidor syndrome

For BAP1-related tumor predisposition syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Adult

Similar variants

BAP1 p.Ser98Arg Uncertain significance ★ ⚠ same residue
BAP1 p.Ser98fs Pathogenic ★ same residue
BAP1 p.Ser98Thr 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
BAP1 c.122+5G>C 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-ser98 (accessed [today's date]).

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