Is BAP1 p.Ser628Ter (c.1883C>A) pathogenic?

BAP1 p.Ser628Ter (c.1883C>A) is classified Pathogenic in BAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-10-20). No allele count reported in gnomAD v4.1 (AN 1,613,478); Associated with BAP1-related tumor predisposition syndrome.

What condition is associated with BAP1 p.Ser628Ter (c.1883C>A)?

BAP1 p.Ser628Ter (c.1883C>A) is associated with BAP1-related tumor predisposition syndrome (ClinVar).

How common is BAP1 p.Ser628Ter (c.1883C>A) in the general population?

BAP1 p.Ser628Ter (c.1883C>A) is no allele count reported in gnomAD v4.1 (AN 1,613,478) (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.Ser628Ter

c.1883C>A · rs2153226434 · VCV1070605

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 1,613,478)

Conditions

BAP1-related tumor predisposition 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 LoF-intolerant gene
NMD	predicted	premature termination codon in exon 14 of 17
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2, phastCons 1
Overall
CADD	41.0	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 1,613,478). 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.Ser628Ter
Coding: c.1883C>A
MANE Select: NM_004656
dbSNP: rs2153226434
Type: single nucleotide variant
Location: chr3:52403145 (GRCh38)
Gene constraint: LOEUF 0.324 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.87 · 4 PDB
Residue 628: a UniProt-annotated variant site (in tpds1); the 'interaction with brca1' region

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

Disease context

BAP1-related tumor predisposition syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For BAP1-related tumor predisposition syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Adult

Similar variants

BAP1 p.Ser628Leu Uncertain significance ★★ ⚠ same residue
BAP1 p.Ser628= Likely benign ★ same residue
BAP1 p.Ser628fs Pathogenic ★★ same residue
BAP1 p.Ser628Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
BAP1 p.Ser628Pro 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

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-ser628ter (accessed [today's date]).

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