PKD2 p.Thr628fs
c.1883del · VCV4082496
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
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 9.2 | GERP 0.7, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PKD2
- Protein
- p.Thr628fs
- Coding
- c.1883del
- MANE Select
- NM_000297
- Type
- Deletion
- Location
- chr4:88056252 (GRCh38)
- Structure
- AlphaFold pLDDT 69.85 · 4 PDB
- Residue 628
- the protein kinase domain
Similar variants
- PKD2 p.Thr628Ser Uncertain significance ★ ⚠ same residue
- PKD2 c.1094+3_1094+6del Pathogenic/Likely pathogenic ★★ same type
- PKD2 c.1320-2del Pathogenic ★★ same type
- PKD2 c.2020-1_2020del Pathogenic/Likely pathogenic ★★ same type
- PKD2 c.2020-2del Pathogenic/Likely pathogenic ★★ same type
- PKD2 c.596-12_599del Pathogenic ★★ same type
- PKD2 p.Asn737fs Pathogenic ★★ same type
- PKD2 p.Gly833fs Pathogenic ★★ same type
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-thr628fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown