PTEN p.Ser170=
c.510T>C · VCV3903638
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Cowden syndrome 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP 0.11, phastCons 1 |
| Overall | ||
| CADD | 10.94 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PTEN
- Protein
- p.Ser170=
- Coding
- c.510T>C
- MANE Select
- NM_000314
- Type
- single nucleotide variant
- Location
- chr10:87952135 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI 0.05 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.76 · 12 PDB
- Residue 170
- an α-helix; the phosphatase tensin-type domain; a UniProt-annotated variant site (in mcephas); a UniProt-annotated variant site (loss of phosphatase activity towards ins(1,3,4,5)p4; retains ability to bind phospholipid membranes); a UniProt-annotated variant site (in cws1; severely reduced protein phosphatase activity; loss of phosphatase activity towards ins(1,3,4,5)p4)
Similar variants
- PTEN p.Ser170Arg Pathogenic ★★ same residue
- PTEN p.Ser170Asn Likely pathogenic ★★ same residue
- PTEN p.Ser170Ile Pathogenic/Likely pathogenic ★★ same residue
- PTEN p.Ser170Gly Uncertain significance ★ ⚠ same residue
- PTEN p.Ser170fs Pathogenic ★★ same residue
- PTEN p.Ser170Thr Likely pathogenic ★ same residue
- PTEN p.Ser170Cys Uncertain significance ★ ⚠ same residue
- PTEN c.1026+1G>A 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-ser170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown