PTEN p.Asp19Phe
c.55_56delinsTT · rs1589596354 · VCV825786
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
1
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 12 | GERP 1.8, phastCons 1 |
| Regional constraint | o/e 0.27 | constrained · MANE · 69 kb · p 6.5e-17 · regional, not allelic |
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.Asp19Phe
- Coding
- c.55_56delinsTT
- MANE Select
- NM_000314
- dbSNP
- rs1589596354
- Type
- Indel
- Location
- chr10:87864524 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI 0.05 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.76 · 12 PDB
- Residue 19
- a turn; the phosphatase tensin-type domain; a UniProt-annotated variant site (in malignant melanoma; somatic mutation)
Similar variants
- PTEN p.Asp19Gly Uncertain significance ★★ ⚠ same residue
- PTEN p.Asp326_Lys330delinsAlaTer Pathogenic/Likely pathogenic ★★ same condition
- PTEN p.Met35_Gly36delinsIleArg Pathogenic/Likely pathogenic ★★ same condition
- PTEN p.Asp19Asn Uncertain significance ★★ ⚠ same residue
- PTEN p.Val53Asp Uncertain significance ★★ same condition
- PTEN p.Asp19= Benign/Likely benign ★★ same residue
- PTEN c.210-2_210-1delinsT Likely pathogenic ★ same condition
- PTEN p.Asp19fs 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-asp19phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown