Is PTEN p.Arg159Lys (c.476G>A) pathogenic?

PTEN p.Arg159Lys (c.476G>A) is classified Pathogenic in PTEN (ClinVar, Expert panel, 4 submitters; last evaluated 2025-10-03). AlphaMissense: likely pathogenic (0.9976); Absent from gnomAD v4.1; Associated with PTEN hamartoma tumor syndrome.

What condition is associated with PTEN p.Arg159Lys (c.476G>A)?

PTEN p.Arg159Lys (c.476G>A) is associated with PTEN hamartoma tumor syndrome, prostate cancer, hereditary, 1 (ClinVar).

How common is PTEN p.Arg159Lys (c.476G>A) in the general population?

PTEN p.Arg159Lys (c.476G>A) is absent from gnomAD v4.1 (gnomAD).

How is PTEN hamartoma tumor syndrome inherited?

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

What do computational predictors say about PTEN p.Arg159Lys (c.476G>A)?

AlphaMissense predicts likely pathogenic (score 0.9976) — an in-silico prediction, not a clinical call.

PTEN p.Arg159Lys

c.476G>A · rs1114167673 · VCV646006

Pathogenic Expert panel

Classification

Pathogenic

ClinVar

Review

Expert panel ★★★☆

ClinVar · 4 submitters

AlphaMissense

likely pathogenic

0.9976 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

PTEN hamartoma tumor syndrome

ClinGen expert panel — PTEN VCEP

Pathogenic for PTEN hamartoma tumor syndrome. Applied ACMG criteria (verbatim):

PM2_Supporting PM6_Strong PS3_Moderate PS4_Moderate PP2 PP3

Curation rationale (ClinGen, verbatim)

PTEN c.476G>A (p.Arg159Lys) meets criteria to be classified as Pathogenic for PTEN hamartoma tumor syndrome in a autossomal dominant manner under ACMG criteria for PTEN gene v3 (PMID:30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PS3_M: Phosphatase activity <-1.11 per Mighell et al. 2018 (PMID: 29706350). PP2: PTEN classified as a gene with missense variants that have low rate of benign missense variation and where missense variants are common mechanisms of disease. PP3: REVEL score (0.961) greater than 0.7. PM2_P: Variant absent on gnomad (v4). PM6_S: Assumed de novo case with strong PTEN-specific phenotype in patient (reported with extreme macrocephaly, autism and developmental delay, and seizures (Pediatric score +5) (internal laboratory contributor). PS4_M: Pediatric patient reported in Tuli et al. (PMID: 34184188) to have neonatal overgrowth, macrocephaly (+5.6 SD), developmental delay and periventricular leukomalacia.(Pediatric score +5. +1 proband point). Pediatric patient reported with developmental delay, macrocephaly and polymicrogyria. (Pediatric score +6, +1 proband point) (Internal laboratory contributor).

ClinGen Evidence Repository → · reported verbatim, not re-tallied by Sugi Variant.

Computational evidence

Protein change
AlphaMissense	0.9976	likely pathogenic ✓ concordant with ClinVar
REVEL	0.961	strongly pathogenic-leaning
SaProt	LLR -12.33	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.4, phastCons 1
Regional constraint	o/e 0.51	unconstrained · MANE · 32 kb · p 4.1e-17 · regional, not allelic
Overall
CADD	33.0	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: PTEN
Protein: p.Arg159Lys
Coding: c.476G>A
MANE Select: NM_000314
dbSNP: rs1114167673
Type: single nucleotide variant
Location: chr10:87933235 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI 0.05 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 83.76 · 12 PDB
Residue 159: an α-helix; the phosphatase tensin-type domain; a UniProt-annotated variant site (in mcephas)

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

Disease context

PTEN hamartoma tumor syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: prostate cancer, hereditary, 1

For PTEN hamartoma tumor syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: All ages
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

PTEN p.Arg159Gly Pathogenic/Likely pathogenic ★★ same residue
PTEN p.Arg159Trp Pathogenic/Likely pathogenic ★★ same residue
PTEN p.Arg159Met Conflicting classifications of pathogenicity ★ ⚠ same residue
PTEN p.Arg159Ser Uncertain significance ★ ⚠ same residue
PTEN p.Arg159Thr Uncertain significance ★ ⚠ same residue
PTEN p.Arg159= Likely benign ★ same residue
PTEN c.1026+1G>A Pathogenic ★★★ same condition
PTEN c.1027-1852A>G 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/pten-p-arg159lys (accessed [today's date]).

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