NPR2 p.Val652fs
c.1954del · VCV4281629
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Monogenic short statue
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 13 of 22 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 8 | GERP 1.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- NPR2
- Protein
- p.Val652fs
- Coding
- c.1954del
- MANE Select
- NM_003995
- Type
- Deletion
- Location
- chr9:35805576 (GRCh38)
- Gene constraint
- LOEUF 0.517 · pLI 0.45 (gnomAD)
- Structure
- AlphaFold pLDDT 84.00
- Residue 652
- the protein kinase domain
Disease context
Monogenic short statue
Similar variants
- NPR2 p.Ile364fs Pathogenic/Likely pathogenic ★★ same condition
- NPR2 p.Ile837fs Likely pathogenic ★ same condition
- NPR2 p.Val652Met Uncertain significance ★ ⚠ same residue
- NPR2 p.Val652= Likely benign ★ same residue
- NPR2 c.1436+1G>T Likely pathogenic ★★ same condition
- NPR2 p.Arg299Ter Pathogenic ★★ same condition
- NPR2 p.Arg741Ter Pathogenic/Likely pathogenic ★★ same condition
- NPR2 p.Arg989Leu Pathogenic/Likely 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/npr2-p-val652fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown