NPR3 p.Ser269=
c.807C>T · VCV4805966
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.37 | GERP 0.74, phastCons 0.98 |
| Overall | ||
| CADD | 10.85 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Overall
0.00131%
2/152,282 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- NPR3
- Protein
- p.Ser269=
- Coding
- c.807C>T
- MANE Select
- NM_001077350 · reported on NM_001204375
- Type
- single nucleotide variant
- Location
- chr5:32724735 (GRCh38)
- Structure
- AlphaFold pLDDT 66.63 · 10 PDB
- Residue 269
- an α-helix
Similar variants
- NPR3 p.Ala274Val Uncertain significance ★★ same type
- NPR3 p.Arg530Gln Uncertain significance ★★ ⚠ same type
- NPR3 p.Asp306Asn Uncertain significance ★★ ⚠ same type
- NPR3 p.Glu480Gly Uncertain significance ★★ ⚠ same type
- NPR3 p.Gly453Asp Uncertain significance ★★ ⚠ same type
- NPR3 p.His373Arg Uncertain significance ★★ ⚠ same type
- NPR3 p.Thr428Ser Uncertain significance ★★ ⚠ same type
- NPR3 p.Val369Ala Uncertain significance ★★ ⚠ 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/npr3-p-ser269 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown