PTEN p.Cys124fs
c.370dup · rs2493717485 · VCV1801583
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 5 of 9 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 3.1 | GERP 2.4, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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.Cys124fs
- Coding
- c.370dup
- MANE Select
- NM_000314
- dbSNP
- rs2493717485
- Type
- Duplication
- Location
- chr10:87933128 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI 0.05 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.76 · 12 PDB
- Residue 124
- the phosphatase tensin-type domain; a UniProt-annotated variant site (in mcephas); a UniProt-annotated variant site (in cws1); a UniProt-annotated variant site (in cws1; phosphatase-dead protein with neither lipid nor protein phosphatase activity; loss of phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity); an active site
Similar variants
- PTEN p.Cys124Arg Pathogenic ★★★ same residue
- PTEN p.Cys124Gly Pathogenic ★★ same residue
- PTEN p.Cys124Ser Pathogenic/Likely pathogenic ★★ same residue
- PTEN p.Cys124Trp Pathogenic/Likely pathogenic ★★ same residue
- PTEN p.Cys124Tyr Pathogenic/Likely pathogenic ★★ same residue
- PTEN p.Cys124Phe Pathogenic ★ same residue
- PTEN p.Pro246Leu Pathogenic ★★★ same condition
- PTEN p.Tyr155Cys 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-cys124fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown