Is PTEN p.Thr401= (c.1203A>G) pathogenic?

PTEN p.Thr401= (c.1203A>G) is classified Benign/Likely benign in PTEN (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-08-18). Very rare (popmax 0.00803%, afr); Associated with hereditary neoplastic syndrome.

What condition is associated with PTEN p.Thr401= (c.1203A>G)?

PTEN p.Thr401= (c.1203A>G) is associated with hereditary neoplastic syndrome, Cowden syndrome 1, PTEN hamartoma tumor syndrome (ClinVar).

How common is PTEN p.Thr401= (c.1203A>G) in the general population?

PTEN p.Thr401= (c.1203A>G) is very rare (popmax 0.00803%, afr) (gnomAD).

PTEN p.Thr401=

c.1203A>G · rs876659102 · VCV231341

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00803%, afr)

Conditions

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 0.4	GERP -5, phastCons 0.72
Overall
CADD	5.42	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00803% African / African-American · 6/74,720 alleles

Filtering AF 0.00348% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00229%

Overall 0.000372% 6/1,611,248 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.Thr401=
Coding: c.1203A>G
MANE Select: NM_000314
dbSNP: rs876659102
Type: single nucleotide variant
Location: chr10:87965463 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI 0.05 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 83.76 · 12 PDB
Residue 401: a UniProt-annotated variant site (retains ins(1,3,4,5)p4 and ptdins(3,4,5)p3 phosphatase activity; retains ability to bind phospholipid membranes); a β-strand; a modified residue (phosphothreonine); a UniProt-annotated variant site (in mcephas); the 'disordered' region

Full PTEN 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

Also linked: Cowden syndrome 1 PTEN hamartoma tumor syndrome

Similar variants

PTEN p.Thr401Ile Uncertain significance ★★ ⚠ same residue
PTEN p.Thr401Lys Uncertain significance ★★ ⚠ same residue
PTEN p.Thr401Ala Uncertain significance ★ ⚠ same residue
PTEN p.Thr401fs 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
PTEN c.165-1G>A 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-thr401 (accessed [today's date]).

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