NPR2 p.Ser127=
c.381T>C · VCV4903120
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00266%, afr)
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 -0.053 | GERP -3.5, phastCons 0.88 |
| Overall | ||
| CADD | 10.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00266%
African / African-American · 2/75,054 alleles
Filtering AF
0.000442%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000124%
2/1,614,184 alleles · very rare
exomes 2/1,461,882 · genomes 0/152,302 · joint denominator
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
- NPR2
- Protein
- p.Ser127=
- Coding
- c.381T>C
- MANE Select
- NM_003995
- Type
- single nucleotide variant
- Location
- chr9:35792789 (GRCh38)
- Gene constraint
- LOEUF 0.517 · pLI 0.45 (gnomAD)
- Structure
- AlphaFold pLDDT 84.00
Similar variants
- NPR2 c.1436+1G>T Likely pathogenic ★★ same type
- NPR2 c.1887+2T>A Pathogenic/Likely pathogenic ★★ same type
- NPR2 p.Arg299Ter Pathogenic ★★ same type
- NPR2 p.Arg363Ter Pathogenic ★★ same type
- NPR2 p.Arg388Gln Pathogenic ★★ same type
- NPR2 p.Arg479Ter Pathogenic/Likely pathogenic ★★ same type
- NPR2 p.Arg741Ter Pathogenic/Likely pathogenic ★★ same type
- NPR2 p.Arg749Trp Pathogenic/Likely 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/npr2-p-ser127 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown