PTEN p.Arg15del
c.39_41del · rs1114167625 · VCV428199
ClinGen expert panel — PTEN VCEP
Uncertain Significance for PTEN hamartoma tumor syndrome. Applied ACMG criteria (verbatim):
PM2 PS4_Supporting
Curation rationale (ClinGen, verbatim)
PTEN c.39_41del (p.Arg15del) is currently classified as a variant of uncertain significance for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PM2: Absent in large sequenced populations (PMID 27535533). PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (PMID 30528446)
ClinGen Evidence Repository → · reported verbatim, not re-tallied by Sugi Variant.
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 11 | GERP 1.8, phastCons 1 |
Population frequency
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.Arg15del
- Coding
- c.39_41del
- MANE Select
- NM_000314
- dbSNP
- rs1114167625
- Type
- Deletion
- Location
- chr10:87864508 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI 0.05 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.76 · 12 PDB
- Residue 15
- the phosphatase tensin-type domain; a UniProt-annotated variant site (in cws1; also found in glioma)
Disease context
PTEN hamartoma tumor syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: Cowden syndrome 1hereditary neoplastic syndrome
For PTEN hamartoma tumor syndrome (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- All ages
- Prevalence
- 1-9 / 100 000 (Worldwide)
Similar variants
- PTEN p.Arg15Lys Likely pathogenic ★★★ same residue
- PTEN p.Arg15Thr Likely pathogenic ★★★ same residue
- PTEN p.Arg15fs Pathogenic ★★ same residue
- PTEN p.Arg15Ile Likely pathogenic ★★ same residue
- PTEN p.Arg15Ser Pathogenic/Likely pathogenic ★★ same residue
- PTEN p.Arg15Ter Pathogenic ★★ same residue
- PTEN p.Arg15Gly Likely pathogenic ★ same residue
- PTEN p.Arg15_Tyr16delinsSerHis Uncertain significance ★ 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-arg15del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown