NPR3 p.Ser317=
c.951G>A · rs765541392 · VCV2170859
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00659%, sas)
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 3 | GERP -0.65, phastCons 1 |
| Overall | ||
| CADD | 12.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00659%
South Asian · 6/91,074 alleles
Filtering AF
0.00286%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00195%
Overall
0.00211%
34/1,613,752 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00659% | 15,179 |
| Finnishnot grpmax-eligible | 0.00312% | 32,005 |
| European (non-Finnish) | 0.00212% | 47,192 |
| African / African-American | 0.00133% | 74,912 |
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.Ser317=
- Coding
- c.951G>A
- MANE Select
- NM_001077350 · reported on NM_001204375
- dbSNP
- rs765541392
- Type
- single nucleotide variant
- Location
- chr5:32738922 (GRCh38)
- Structure
- AlphaFold pLDDT 66.63 · 10 PDB
- Residue 317
- 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-ser317 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown