Is NPR2 p.Pro975Ala (c.2923C>G) pathogenic?

NPR2 p.Pro975Ala (c.2923C>G) is classified Uncertain significance in NPR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-17). AlphaMissense: likely pathogenic (0.9935); Absent from gnomAD v4.1.

How common is NPR2 p.Pro975Ala (c.2923C>G) in the general population?

NPR2 p.Pro975Ala (c.2923C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about NPR2 p.Pro975Ala (c.2923C>G)?

AlphaMissense predicts likely pathogenic (score 0.9935) — an in-silico prediction, not a clinical call.

NPR2 p.Pro975Ala

c.2923C>G · VCV4885099

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9935 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9935	likely pathogenic
REVEL	0.791	moderately pathogenic-leaning
SaProt	LLR -15.60	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.9, phastCons 1
Overall
CADD	27.8	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: NPR2
Protein: p.Pro975Ala
Coding: c.2923C>G
MANE Select: NM_003995
Type: single nucleotide variant
Location: chr9:35808790 (GRCh38)
Gene constraint: LOEUF 0.517 · pLI 0.45 (gnomAD)
Structure: AlphaFold pLDDT 84.00
Residue 975: the guanylate cyclase domain

Full NPR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

NPR2 p.Pro975Thr Uncertain significance ★★ ⚠ same residue
NPR2 p.Pro975His Uncertain significance ★ ⚠ same residue
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

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-pro975ala (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown