Is BAP1 p.Pro42= (c.126T>A) pathogenic?

BAP1 p.Pro42= (c.126T>A) is classified Likely benign in BAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-09). No allele count reported in gnomAD v4.1 (AN 1,609,092); Associated with hereditary neoplastic syndrome.

What condition is associated with BAP1 p.Pro42= (c.126T>A)?

BAP1 p.Pro42= (c.126T>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BAP1 p.Pro42= (c.126T>A) in the general population?

BAP1 p.Pro42= (c.126T>A) is no allele count reported in gnomAD v4.1 (AN 1,609,092) (gnomAD).

BAP1 p.Pro42=

c.126T>A · rs1156967472 · VCV1765176

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,609,092)

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
Constraint at this position
Conservation	phyloP -1.3	GERP -3.5
Overall
CADD	11.45	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,609,092). 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.Pro42=
Coding: c.126T>A
MANE Select: NM_004656
dbSNP: rs1156967472
Type: single nucleotide variant
Location: chr3:52408603 (GRCh38)
Gene constraint: LOEUF 0.324 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.87 · 4 PDB
Residue 42: the uch catalytic domain

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.Pro42Leu Uncertain significance ★★ ⚠ same residue
BAP1 p.Pro42Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
BAP1 p.Pro42Thr Uncertain significance ★ ⚠ same residue
BAP1 p.Pro42Arg Uncertain significance ★ ⚠ same residue
BAP1 p.Pro42His 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-pro42 (accessed [today's date]).

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