Is PTEN p.Lys66= (c.198G>A) pathogenic?

PTEN p.Lys66= (c.198G>A) is classified Benign/Likely benign in PTEN (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-02-11). Very rare (popmax 8.63e-05%, nfe); Associated with Cowden syndrome 1.

What condition is associated with PTEN p.Lys66= (c.198G>A)?

PTEN p.Lys66= (c.198G>A) is associated with Cowden syndrome 1, hereditary neoplastic syndrome (ClinVar).

How common is PTEN p.Lys66= (c.198G>A) in the general population?

PTEN p.Lys66= (c.198G>A) is very rare (popmax 8.63e-05%, nfe) (gnomAD).

PTEN p.Lys66=

c.198G>A · VCV3427436

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 8.63e-05%, nfe)

Conditions

Cowden syndrome 1

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 12	GERP 2.8, phastCons 1
Overall
CADD	15.27	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.63e-05% European (non-Finnish) · 1/1,158,402 alleles

Overall 6.99e-05% 1/1,430,330 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.Lys66=
Coding: c.198G>A
MANE Select: NM_000314
Type: single nucleotide variant
Location: chr10:87925546 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI 0.05 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 83.76 · 12 PDB
Residue 66: a β-strand; 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

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

Also linked: hereditary neoplastic syndrome

Similar variants

PTEN p.Lys66Arg Uncertain significance ★ ⚠ same residue
PTEN p.Lys66fs Pathogenic ★★ same residue
PTEN p.Lys66Asn Likely pathogenic ★★★ same residue
PTEN p.Lys66Ter Pathogenic/Likely pathogenic ★★ same residue
PTEN p.Lys66Glu Likely pathogenic ★ same residue
PTEN p.Lys66Gln Uncertain significance ★ ⚠ same residue
PTEN p.Lys66Met Uncertain significance ⚠ same residue
PTEN c.1026+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-lys66 (accessed [today's date]).

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