Is PALB2 p.Phe588Val (c.1762T>G) pathogenic?

PALB2 p.Phe588Val (c.1762T>G) is classified Likely benign in PALB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-05-06). AlphaMissense: likely benign (0.0954); Very rare (popmax 0.00149%); Associated with hereditary neoplastic syndrome.

What condition is associated with PALB2 p.Phe588Val (c.1762T>G)?

PALB2 p.Phe588Val (c.1762T>G) is associated with hereditary neoplastic syndrome (ClinVar).

How common is PALB2 p.Phe588Val (c.1762T>G) in the general population?

PALB2 p.Phe588Val (c.1762T>G) is very rare (popmax 0.00149%) (gnomAD).

What do computational predictors say about PALB2 p.Phe588Val (c.1762T>G)?

AlphaMissense predicts likely benign (score 0.0954) — an in-silico prediction, not a clinical call.

PALB2 p.Phe588Val

c.1762T>G · VCV4861494

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0954 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00149%)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.0954	likely benign
REVEL	0.098	moderately benign-leaning
SaProt	LLR -5.79	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.86	GERP -3.6, phastCons 0.008
Regional constraint	o/e 1.00	unconstrained · MANE · 38 kb · p 0.87 · regional, not allelic
Overall
CADD	11.85	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

Grpmax group 0.00149%

Overall 0.00149% 24/1,614,072 alleles · very rare exomes 15/1,461,826 · genomes 9/152,246 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.0359%	2,784
Remaining individualsnot grpmax-eligible	0.0016%	62,488

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PALB2
Protein: p.Phe588Val
Coding: c.1762T>G
MANE Select: NM_024675
Type: single nucleotide variant
Location: chr16:23630392 (GRCh38)
Gene constraint: LOEUF 0.9 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 54.07 · 4 PDB
Residue 588: a UniProt-annotated variant site (risk factor for brovca5); a UniProt-annotated variant site (in fancn; risk factor for brovca5)

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.Phe588Leu 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
PALB2 p.Trp1038Ter 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-phe588val (accessed [today's date]).

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