PTEN p.Pro38Phe
c.112_113delinsTT · VCV4814036
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
Conditions
1
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 · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 1.5, phastCons 1 |
| Regional constraint | o/e 0.27 | constrained · MANE · 69 kb · p 6.5e-17 · regional, not allelic |
Variant & gene context
- Gene
- PTEN
- Protein
- p.Pro38Phe
- Coding
- c.112_113delinsTT
- MANE Select
- NM_000314
- Type
- Indel
- Location
- chr10:87894057 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI 0.05 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.76 · 12 PDB
- Residue 38
- the phosphatase tensin-type domain
Disease context
PTEN hamartoma tumor syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor PTEN hamartoma tumor syndrome (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- All ages
- Prevalence
- 1-9 / 100 000 (Worldwide)
Similar variants
- PTEN p.Pro38His Likely pathogenic ★★★ same residue
- PTEN p.Pro38Leu Pathogenic ★★★ same residue
- PTEN p.Pro38Ser Uncertain significance ★★★ ⚠ same residue
- PTEN p.Pro38= Likely benign ★★★ same residue
- PTEN p.Pro38fs Pathogenic ★ same residue
- PTEN p.Tyr178_Ser179delinsTer Pathogenic ★★★ same condition
- PTEN c.156_164+4delinsCAT Likely pathogenic ★★ same condition
- PTEN p.Leu182_Lys183insTer 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-pro38phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown