Is PALB2 p.Thr413Pro (c.1237A>C) pathogenic?

PALB2 p.Thr413Pro (c.1237A>C) is classified Uncertain significance in PALB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-08-26). AlphaMissense: ambiguous (0.4153); Absent from gnomAD v4.1; Associated with hereditary breast carcinoma.

What condition is associated with PALB2 p.Thr413Pro (c.1237A>C)?

PALB2 p.Thr413Pro (c.1237A>C) is associated with hereditary breast carcinoma (ClinVar).

How common is PALB2 p.Thr413Pro (c.1237A>C) in the general population?

PALB2 p.Thr413Pro (c.1237A>C) is absent from gnomAD v4.1 (gnomAD).

How is Hereditary breast cancer inherited?

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

What do computational predictors say about PALB2 p.Thr413Pro (c.1237A>C)?

AlphaMissense predicts ambiguous (score 0.4153) — an in-silico prediction, not a clinical call.

PALB2 p.Thr413Pro

c.1237A>C · rs1335631200 · VCV655733

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4153 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary breast carcinoma

Computational evidence

Protein change
AlphaMissense	0.4153	ambiguous
REVEL	0.418	indeterminate
SaProt	LLR -3.26	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 1.7, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 38 kb · p 0.87 · regional, not allelic
Overall
CADD	25.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PALB2
Protein: p.Thr413Pro
Coding: c.1237A>C
MANE Select: NM_024675
dbSNP: rs1335631200
Type: single nucleotide variant
Location: chr16:23635309 (GRCh38)
Gene constraint: LOEUF 0.9 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 54.07 · 4 PDB
Residue 413: the 'cham (chromatin-association motif); required for chromatin association, mediates nucleosome association' region; a UniProt-annotated variant site (risk factor for brovca5); the 'dna-binding (with the preference d loop > dsdna > ssdna)' region

Full PALB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary breast carcinoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hereditary breast cancer (Orphanet):

Inheritance: Autosomal dominant, Multigenic/multifactorial
Onset: Adult, Elderly

Similar variants

PALB2 p.Thr413Arg Uncertain significance ★★ same residue
PALB2 p.Thr413= Likely benign ★ same residue
PALB2 p.Thr413Ala Uncertain significance ★ ⚠ same residue
PALB2 p.Thr413Ile Uncertain significance ★ ⚠ same residue
PALB2 p.Thr413Lys Uncertain significance ★ same residue
PALB2 c.3350+4A>G Likely pathogenic ★★★ same condition
PALB2 p.Arg1117Lys Pathogenic ★★★ ⚠ same condition
PALB2 p.Gln228Ter 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-thr413pro (accessed [today's date]).

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