Is PTEN p.Ser10= (c.30C>T) pathogenic?

PTEN p.Ser10= (c.30C>T) is classified Likely benign in PTEN (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-08). Very rare (popmax 8.47e-05%, nfe); Associated with PTEN hamartoma tumor syndrome.

What condition is associated with PTEN p.Ser10= (c.30C>T)?

PTEN p.Ser10= (c.30C>T) is associated with PTEN hamartoma tumor syndrome (ClinVar).

How common is PTEN p.Ser10= (c.30C>T) in the general population?

PTEN p.Ser10= (c.30C>T) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

How is PTEN hamartoma tumor syndrome inherited?

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

PTEN p.Ser10=

c.30C>T · rs1564801689 · VCV2812725

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

PTEN hamartoma tumor 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 4	GERP 1.6, phastCons 1
Overall
CADD	14.87	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,024 alleles

Overall 6.84e-05% 1/1,461,826 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.Ser10=
Coding: c.30C>T
MANE Select: NM_000314
dbSNP: rs1564801689
Type: single nucleotide variant
Location: chr10:87864499 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI 0.05 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 83.76 · 12 PDB
Residue 10: an α-helix; a UniProt-annotated variant site (retains phosphatase activity towards ins(1,3,4,5)p4 and ptdins(3,4,5)p3; retains the ability to bind phospholipid membranes)

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

For PTEN hamartoma tumor syndrome (Orphanet):

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

Similar variants

PTEN p.Ser10Thr Uncertain significance ★★★ ⚠ same residue
PTEN p.Ser10del Uncertain significance ★★★ same residue
PTEN p.Ser10Arg Uncertain significance ★ ⚠ same residue
PTEN p.Ser10Asn Uncertain significance ★ ⚠ same residue
PTEN p.Ser10Gly 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-ser10 (accessed [today's date]).

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