PMS2 p.Pro470Phe
c.1408_1409delinsTT · rs1583320391 · VCV819134
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 2 | phastCons 0.6 |
| Regional constraint | o/e 1.09 | unconstrained · MANE · 22 kb · p 0.015 · regional, not allelic |
| Region caveats | ||
| Repeat context | seg dup | · reads may not map uniquely · confidence, not pathogenicity |
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
- PMS2
- Protein
- p.Pro470Phe
- Coding
- c.1408_1409delinsTT
- MANE Select
- NM_000535
- dbSNP
- rs1583320391
- Type
- Indel
- Location
- chr7:5987356 (GRCh38)
- Gene constraint
- LOEUF 0.898 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.37 · 9 PDB
- Residue 470
- the 'disordered' region; a UniProt-annotated variant site (in lynch4; benign; no effect on protein abundance; no effect on subcellular localization; normal dna mismatch repair activity)
Similar variants
- PMS2 p.Pro470delinsValPheTer Pathogenic ★ same residue
- PMS2 p.Pro470Leu Uncertain significance ★★ ⚠ same residue
- PMS2 p.Pro470= Benign/Likely benign ★★ same residue
- PMS2 p.Pro470delinsCysLeuLeuAlaLeuGlnValProSerLeuThrLysAlaSerTer Pathogenic ★ same residue
- PMS2 c.24-12_107delinsAAAT Pathogenic ★★★ same condition
- PMS2 c.164-9_178delinsGATCC Likely pathogenic ★★ same condition
- PMS2 c.538-65_589delinsGCAACATCCAATTGGT Likely pathogenic ★★ same condition
- PMS2 p.? 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/pms2-p-pro470phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown