NPR1

natriuretic peptide receptor 1, the group of Transmembrane guanylate cyclases

Basic information

Region (hg38): 1:153678688-153693992

Previous symbols: [ "ANPRA", "NPRA" ]

Links

ENSG00000169418 ∙ NCBI:4881 ∙ OMIM:108960 ∙ HGNC:7943 ∙ Uniprot:P16066 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NPR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPR1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	2	7
missense			51	1	1	53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2		2
Total	0	0	51	8	3

Variants in NPR1

This is a list of pathogenic ClinVar variants found in the NPR1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-153679125-G-T		not specified	Uncertain significance (Mar 21, 2023)
1-153679128-C-A		not specified	Uncertain significance (Dec 27, 2023)
1-153679131-C-G		not specified	Uncertain significance (Dec 07, 2024)
1-153679283-G-A		not specified	Uncertain significance (Jun 28, 2024)
1-153679311-C-A		not specified	Uncertain significance (Nov 21, 2022)
1-153679454-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-153679460-T-C		not specified	Uncertain significance (Nov 20, 2024)
1-153679547-G-T		not specified	Uncertain significance (Jan 18, 2025)
1-153679685-G-A		not specified	Uncertain significance (Mar 30, 2024)
1-153679703-C-A		not specified	Uncertain significance (Oct 03, 2024)
1-153679784-A-G		not specified	Uncertain significance (Oct 19, 2024)
1-153680552-C-G		not specified	Uncertain significance (Aug 09, 2021)
1-153680560-G-A		not specified	Uncertain significance (Jan 08, 2024)
1-153680568-G-C		not specified	Uncertain significance (Feb 28, 2023)
1-153680572-G-A		not specified	Uncertain significance (Dec 11, 2023)
1-153681181-C-T		not specified	Uncertain significance (Feb 22, 2025)
1-153681241-A-G		not specified	Uncertain significance (May 31, 2023)
1-153681259-A-C		not specified	Uncertain significance (Jan 29, 2025)
1-153681271-A-G		not specified	Uncertain significance (Feb 26, 2024)
1-153681274-T-C		not specified	Uncertain significance (Aug 19, 2021)
1-153681815-C-T		not specified	Uncertain significance (Sep 30, 2024)
1-153683452-A-G		not specified	Uncertain significance (Jul 12, 2022)
1-153683460-C-T		not specified	Uncertain significance (Sep 04, 2024)
1-153683471-C-T			Likely benign (Dec 01, 2022)
1-153683503-G-A		not specified	Uncertain significance (Feb 12, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPR1	protein_coding	protein_coding	ENST00000368680	22	15356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000293	1.00	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.82	414	610	0.679	0.0000358	6776
Missense in Polyphen		143	274.68	0.5206		3109
Synonymous	1.29	231	257	0.898	0.0000146	2216
Loss of Function	4.49	16	50.3	0.318	0.00000249	555

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000207
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000127	0.000123
Middle Eastern	0.000163	0.000163
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for the atrial natriuretic peptide NPPA/ANP and the brain natriuretic peptide NPPB/BNP which are potent vasoactive hormones playing a key role in cardiovascular homeostasis. Has guanylate cyclase activity upon binding of the ligand. {ECO:0000269|PubMed:1672777}.
• Pathway: Aldosterone synthesis and secretion - Homo sapiens (human);Regulation of lipolysis in adipocytes - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Thermogenesis - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);Renin secretion - Homo sapiens (human);Purine metabolism - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);WNT-Ncore;Physiological factors;NO-cGMP-PKG mediated Neuroprotection;Purine metabolism;Cardiac conduction;Muscle contraction;Purine nucleotides nucleosides metabolism (Consensus)

Recessive Scores

• pRec: 0.318

Intolerance Scores

• loftool: 0.186
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.31

Haploinsufficiency Scores

• pHI: 0.260
• hipred: Y
• hipred_score: 0.711
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.968

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Npr1
• Phenotype: reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); neoplasm; respiratory system phenotype; immune system phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype

Gene ontology

• Biological process: cGMP biosynthetic process;protein phosphorylation;signal transduction;cell surface receptor signaling pathway;receptor guanylyl cyclase signaling pathway;G protein-coupled receptor signaling pathway;body fluid secretion;regulation of blood pressure;positive regulation of cGMP-mediated signaling;negative regulation of angiogenesis;cGMP-mediated signaling;negative regulation of cell growth;positive regulation of urine volume;positive regulation of renal sodium excretion;dopamine metabolic process;regulation of vascular permeability;negative regulation of smooth muscle cell proliferation;regulation of blood vessel diameter;regulation of cardiac conduction
• Cellular component: plasma membrane;integral component of membrane;receptor complex
• Molecular function: peptide receptor activity;guanylate cyclase activity;protein kinase activity;ATP binding;GTP binding;G protein-coupled peptide receptor activity;natriuretic peptide receptor activity;peptide hormone binding;protein kinase binding;hormone binding