Is BAP1 p.Leu709Ile (c.2124_2125delinsTA) pathogenic?

BAP1 p.Leu709Ile (c.21242125delinsTA) is classified Uncertain significance in BAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-02-13). Absent from gnomAD; Associated with BAP1-related tumor predisposition syndrome.

What condition is associated with BAP1 p.Leu709Ile (c.2124_2125delinsTA)?

BAP1 p.Leu709Ile (c.2124_2125delinsTA) is associated with BAP1-related tumor predisposition syndrome (ClinVar).

How common is BAP1 p.Leu709Ile (c.2124_2125delinsTA) in the general population?

BAP1 p.Leu709Ile (c.2124_2125delinsTA) is absent from gnomAD (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.Leu709Ile

c.2124_2125delinsTA · rs1704983742 · VCV1002809

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 · substitutions only
Constraint at this position
Conservation	phyloP 9.9	GERP 1.9, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Leu709Ile
Coding: c.2124_2125delinsTA
MANE Select: NM_007212 · reported on NM_004656
dbSNP: rs1704983742
Type: Indel
Location: chr3:52402353 (GRCh38)
Structure: AlphaFold pLDDT 78.27 · 28 PDB

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.Leu709= Benign/Likely benign ★★ same residue
BAP1 p.Ala304Asn Uncertain significance ★★ same condition
BAP1 p.Ala378Leu Uncertain significance ★★ same condition
BAP1 p.Ala471Ile Uncertain significance ★★ same condition
BAP1 p.Glu198Leu Uncertain significance ★★ same condition
BAP1 p.Gly4fs Pathogenic ★ same condition
BAP1 p.Ile461fs Pathogenic ★ same condition
BAP1 p.Lys291fs 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-leu709ile (accessed [today's date]).

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