PTEN p.Ser10del
c.30_32del · rs1114167649 · VCV428224
ClinGen expert panel — PTEN VCEP
Uncertain Significance for PTEN hamartoma tumor syndrome. Applied ACMG criteria (verbatim):
PM6 PM2_Supporting PS3_Moderate
Curation rationale (ClinGen, verbatim)
PTEN c.30_32del (p.Ser10del) is currently classified as a variant of uncertain significance for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.2.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PM2_Supporting: Absent in large sequenced populations OR present at extremely low (<0.00001, 0.001%) allele frequency in the gnomAD cohort. (PMID 27535533). PS3_M: Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = -4.623 (≤ -1.11) on a high throughput phosphatase assay (PMID:29706350) PM6: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (internal laboratory contributor(s) SCV000580011.6)
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 1.3 | GERP 1.6, 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.Ser10del
- Coding
- c.30_32del
- MANE Select
- NM_000314
- dbSNP
- rs1114167649
- Type
- Deletion
- Location
- chr10:87864497 (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)
Disease context
PTEN hamartoma tumor syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: hereditary neoplastic syndrome
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.Ser10Arg Uncertain significance ★ ⚠ same residue
- PTEN p.Ser10Asn Uncertain significance ★ ⚠ same residue
- PTEN p.Ser10Gly Uncertain significance ★ ⚠ same residue
- PTEN p.Ser10= Likely benign ★ same residue
- PTEN p.Ser10fs Pathogenic ★ same residue
- PTEN c.209+4_209+7del Pathogenic ★★★ same condition
- PTEN c.210-2_211del 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-ser10del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown