PALB2 p.Pro713=
c.2139T>A · rs2142380112 · VCV1786524
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
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 -1.2 | GERP -3.4 |
| Overall | ||
| CADD | 0.485 | PHRED · no single calibrated threshold — expert panels disagree |
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.Pro713=
- Coding
- c.2139T>A
- MANE Select
- NM_024675
- dbSNP
- rs2142380112
- Type
- single nucleotide variant
- Location
- chr16:23630015 (GRCh38)
- Gene constraint
- LOEUF 0.9 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.07 · 4 PDB
- Residue 713
- a UniProt-annotated variant site (risk factor for brovca5); a UniProt-annotated variant site (in fancn; risk factor for brovca5)
Similar variants
- PALB2 p.Pro713Ser Uncertain significance ★★ ⚠ same residue
- PALB2 p.Pro713Thr 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
- PALB2 p.Gln692Ter Likely pathogenic ★★★ same condition
- PALB2 p.Glu3Ter Pathogenic ★★★ same condition
- PALB2 p.Gly853= 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/palb2-p-pro713 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown