NPR2

Chr 9ARAD

natriuretic peptide receptor 2

Also known as: AMDM, ANPRB, ANPb, ECDM, GC-B, GCB, GUC2B, GUCY2B

This gene encodes natriuretic peptide receptor B, which serves as the primary receptor for C-type natriuretic peptide and exhibits guanylyl cyclase activity upon ligand binding to regulate skeletal growth. Mutations cause acromesomelic dysplasia Maroteaux type, epiphyseal chondrodysplasia Miura type, and short stature with nonspecific skeletal abnormalities through both autosomal recessive and autosomal dominant inheritance patterns. The gene shows very low intolerance to loss-of-function variants (pLI 0.00004, LOEUF 0.495), indicating tolerance to protein-truncating mutations.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismAR/ADLOEUF 0.493 OMIM phenotypes
Clinical SummaryNPR2
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.33) despite low pLI — interpret in context.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint
0.49LOEUF
pLI 0.000
Z-score 4.54
OE 0.33 (0.230.49)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
2.96Z-score
OE missense 0.66 (0.610.72)
398 obs / 602.3 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.33 (0.230.49)
00.351.4
Missense OE0.66 (0.610.72)
00.61.4
Synonymous OE0.96
01.21.6
LoF obs/exp: 18 / 54.0Missense obs/exp: 398 / 602.3Syn Z: 0.46
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveNPR2-related acromesomelic dysplasia Maroteaux typeLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.74top 25%
GOF
0.82top 10%
LOF
0.2581th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Literature Evidence

DNOur in vitro findings indicate that NPR2 mutations have a dominant negative effect, and their dominant-negative mechanisms vary corresponding to the molecular pathogenesis of the mutations.PMID:24471569
GOFA similar phenotype was described in a family with an activating NPR2 mutation within the guanylyl cyclase domain.PMID:24057292
LOFWith these data, we were able to rigorously verify that NPR2 functional haploinsufficiency contributes to short stature.PMID:25703509

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

NPR2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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