Is PTEN p.Tyr16= (c.48T>C) pathogenic?

PTEN p.Tyr16= (c.48T>C) is classified Benign/Likely benign in PTEN (ClinVar, Multiple submitters, 6 submitters; last evaluated 2025-07-29). Very rare (popmax 0.00167%, amr); Associated with hereditary neoplastic syndrome.

What condition is associated with PTEN p.Tyr16= (c.48T>C)?

PTEN p.Tyr16= (c.48T>C) is associated with hereditary neoplastic syndrome, Cowden syndrome 1, PTEN hamartoma tumor syndrome (ClinVar).

How common is PTEN p.Tyr16= (c.48T>C) in the general population?

PTEN p.Tyr16= (c.48T>C) is very rare (popmax 0.00167%, amr) (gnomAD).

PTEN p.Tyr16=

c.48T>C · rs587782187 · VCV215732

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

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 -0.77	GERP -3.6, phastCons 0.016
Overall
CADD	8.915	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,030 alleles

Filtering AF 0.0005% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000366%

Overall 0.000821% 12/1,461,850 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	60,030
European (non-Finnish)	0.000932%	107,274

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.Tyr16=
Coding: c.48T>C
MANE Select: NM_000314
dbSNP: rs587782187
Type: single nucleotide variant
Location: chr10:87864517 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI 0.05 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 83.76 · 12 PDB
Residue 16: the phosphatase tensin-type domain; a UniProt-annotated variant site (loss of phosphatase activity towards ins(1,3,4,5)p4; retains the ability to bind phospholipid membranes)

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.Tyr16His Uncertain significance ★★★ ⚠ same residue
PTEN p.Tyr16Asp Pathogenic/Likely pathogenic ★★ same residue
PTEN p.Tyr16Ter Pathogenic ★★ same residue
PTEN p.Tyr16Cys Uncertain significance ★★ ⚠ same residue
PTEN p.Tyr16Asn Uncertain significance ★ ⚠ same residue
PTEN p.Tyr16Ser Uncertain significance ★ ⚠ same residue
PTEN p.Tyr16fs Pathogenic ★★ same residue
PTEN p.Tyr16_Gln17delinsTer Pathogenic ★ same residue

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-tyr16 (accessed [today's date]).

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