Is PTEN p.Ala39= (c.117A>G) pathogenic?

PTEN p.Ala39= (c.117A>G) is classified Benign/Likely benign in PTEN (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-02-11). Very rare (popmax 0.00017%, nfe); Associated with Cowden syndrome 1.

What condition is associated with PTEN p.Ala39= (c.117A>G)?

PTEN p.Ala39= (c.117A>G) is associated with Cowden syndrome 1, hereditary neoplastic syndrome, PTEN hamartoma tumor syndrome (ClinVar).

How common is PTEN p.Ala39= (c.117A>G) in the general population?

PTEN p.Ala39= (c.117A>G) is very rare (popmax 0.00017%, nfe) (gnomAD).

PTEN p.Ala39=

c.117A>G · rs1223327870 · VCV1741672

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00017%, nfe)

Conditions

Cowden syndrome 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.49	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 6.9	GERP 1.2, phastCons 1
Overall
CADD	21.9	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00017% European (non-Finnish) · 2/1,179,256 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000137% 2/1,460,628 alleles · very rare

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: PTEN
Protein: p.Ala39=
Coding: c.117A>G
MANE Select: NM_000314
dbSNP: rs1223327870
Type: single nucleotide variant
Location: chr10:87894062 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI 0.05 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 83.76 · 12 PDB
Residue 39: a β-strand; the phosphatase tensin-type domain

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

Disease context

Cowden syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome PTEN hamartoma tumor syndrome

Similar variants

PTEN p.Ala39Thr Likely pathogenic ★★★ same residue
PTEN p.Ala39Val Likely pathogenic ★★★ same residue
PTEN p.Ala39Pro Likely pathogenic ★ same residue
PTEN p.Ala39Glu Uncertain significance ★ ⚠ same residue
PTEN p.Ala39Ser Uncertain significance ★ same residue
PTEN c.1026+1G>A Pathogenic ★★★ same condition
PTEN c.1027-1852A>G Likely pathogenic ★★★ same condition
PTEN c.1027-1G>A 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-ala39 (accessed [today's date]).

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