Is PTEN p.Val54del (c.157GTA[1]) pathogenic?

PTEN p.Val54del (c.157GTA[1]) is classified Conflicting classifications of pathogenicity in PTEN (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-11-25). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with PTEN p.Val54del (c.157GTA[1])?

PTEN p.Val54del (c.157GTA[1]) is associated with hereditary neoplastic syndrome, PTEN hamartoma tumor syndrome (ClinVar).

How common is PTEN p.Val54del (c.157GTA[1]) in the general population?

PTEN p.Val54del (c.157GTA[1]) is absent from gnomAD (gnomAD).

PTEN p.Val54del

c.157GTA[1] · rs1554893831 · VCV480382

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 · substitutions only
Constraint at this position
Conservation	phyloP 1.8	GERP -0.14, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PTEN
Protein: p.Val54del
Coding: c.157GTA[1]
MANE Select: NM_000314
dbSNP: rs1554893831
Type: Microsatellite
Location: chr10:87894102 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI 0.05 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 83.76 · 12 PDB
Residue 54: an α-helix; the phosphatase tensin-type domain

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: PTEN hamartoma tumor syndrome

Similar variants

PTEN p.Val54= Benign/Likely benign ★★ same residue
PTEN p.Val54delinsGlyThrIleLeuMetMetTer Pathogenic ★ same residue
PTEN p.Val54Gly Uncertain significance ★ ⚠ same residue
PTEN p.Val54Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
PTEN p.Asp52del Likely pathogenic ★★★ same condition
PTEN p.Ile33del Likely pathogenic ★★★ same condition
PTEN p.Tyr178del Likely pathogenic ★★★ same condition
PTEN p.Met199del Uncertain significance ★★★ 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-val54del (accessed [today's date]).

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