PKD2 p.Phe472fs
c.1412dup · VCV4531953
Pathogenic
Multiple submitters
Classification
Pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
polycystic kidney disease 2
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-escape possible for C-terminal truncations |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PKD2
- Protein
- p.Phe472fs
- Coding
- c.1412dup
- MANE Select
- NM_000297
- Type
- Duplication
- Location
- chr4:88046731 (GRCh38)
- Structure
- AlphaFold pLDDT 69.85 · 4 PDB
- Residue 472
- the ph domain
Disease context
polycystic kidney disease 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Autosomal dominant polycystic kidney disease (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adolescent, Adult, Childhood
- Prevalence
- 1-5 / 10 000 (Europe)
Similar variants
- PKD2 p.Asn412fs Pathogenic/Likely pathogenic ★★ same condition
- PKD2 p.Asn720fs Pathogenic ★★ same condition
- PKD2 p.Gln557fs Pathogenic ★★ same condition
- PKD2 p.Glu727fs Pathogenic/Likely pathogenic ★★ same condition
- PKD2 p.Gly240fs Pathogenic ★★ same condition
- PKD2 p.Val262fs Pathogenic/Likely pathogenic ★★ same condition
- PKD2 p.Val318fs Pathogenic/Likely pathogenic ★★ same condition
- PKD2 c.709+4dup Uncertain significance ★★ 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/pkd2-p-phe472fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown