Is PALB2 p.Pro1097fs (c.3290_3292delinsAT) pathogenic?

PALB2 p.Pro1097fs (c.32903292delinsAT) is classified Likely pathogenic in PALB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-19). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with PALB2 p.Pro1097fs (c.3290_3292delinsAT)?

PALB2 p.Pro1097fs (c.3290_3292delinsAT) is associated with hereditary neoplastic syndrome (ClinVar).

How common is PALB2 p.Pro1097fs (c.3290_3292delinsAT) in the general population?

PALB2 p.Pro1097fs (c.3290_3292delinsAT) is absent from gnomAD (gnomAD).

PALB2 p.Pro1097fs

c.3290_3292delinsAT · rs2506215712 · VCV1729842

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 12 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.8	GERP 1.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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: PALB2
Protein: p.Pro1097fs
Coding: c.3290_3292delinsAT
MANE Select: NM_024675
dbSNP: rs2506215712
Type: Indel
Location: chr16:23607922 (GRCh38)
Gene constraint: LOEUF 0.9 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 54.07 · 4 PDB
Residue 1097: a turn; the 'required for interaction with polh and polh dna synthesis stimulation' region; the 'interaction with rad51, brca2 and polh' region; a UniProt-annotated variant site (risk factor for brovca5); a UniProt-annotated variant site (in fancn; risk factor for brovca5); a UniProt-annotated variant site (risk factor for brovca5; risk factor for pnca3)

Full PALB2 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

PALB2 p.Pro1097Arg Uncertain significance ★★ ⚠ same residue
PALB2 p.Pro1097Leu Uncertain significance ★★ ⚠ same residue
PALB2 p.Pro1097Thr Uncertain significance ★★ ⚠ same residue
PALB2 p.Pro1097= Benign/Likely benign ★★ same residue
PALB2 p.Pro1097_Lys1098insTer Pathogenic ★ same residue
PALB2 p.Pro1097His Uncertain significance ★ ⚠ same residue
PALB2 p.Ala842fs Pathogenic ★★★ same condition
PALB2 c.2223_2224delinsG 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/palb2-p-pro1097fs (accessed [today's date]).

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