NPPB

natriuretic peptide B, the group of Neuropeptides

Basic information

Region (hg38): 1:11857464-11858945

Links

ENSG00000120937 ∙ NCBI:4879 ∙ OMIM:600295 ∙ HGNC:7940 ∙ Uniprot:P16860 ∙ 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 NPPB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPPB 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					2	2
missense			15		3	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	15	0	6

Variants in NPPB

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

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

Position	Type	Phenotype	Significance	ClinVar
1-11857662-C-T		not specified	Uncertain significance (Dec 15, 2023)
1-11858204-G-T			Benign (Feb 08, 2018)
1-11858222-C-T		not specified	Uncertain significance (Mar 01, 2024)
1-11858228-C-A		not specified	Uncertain significance (Feb 14, 2025)
1-11858280-G-C		not specified	Uncertain significance (Dec 09, 2024)
1-11858285-A-G		not specified	Uncertain significance (Dec 18, 2023)
1-11858307-G-A		not specified	Uncertain significance (Dec 06, 2023)
1-11858322-C-A			Benign (Jul 17, 2018)
1-11858331-G-A		not specified	Uncertain significance (Nov 10, 2024)
1-11858334-G-A		not specified	Uncertain significance (Dec 19, 2022)
1-11858339-C-T		not specified	Uncertain significance (Jan 09, 2025)
1-11858345-C-G		not specified	Uncertain significance (May 20, 2024)
1-11858345-C-T		not specified	Uncertain significance (Apr 07, 2023)
1-11858364-G-A		not specified	Uncertain significance (Nov 17, 2023)
1-11858365-G-A			Benign (Dec 31, 2019)
1-11858378-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-11858387-C-T			Benign (Jun 27, 2018)
1-11858395-C-G		not specified	Uncertain significance (Mar 28, 2024)
1-11858414-G-A		not specified	Uncertain significance (Jan 10, 2023)
1-11858452-C-A		not specified	Uncertain significance (Dec 07, 2023)
1-11858760-C-A			Benign (May 29, 2018)
1-11858780-A-G			Benign (Jun 14, 2018)
1-11858809-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-11858821-T-C		not specified	Uncertain significance (Mar 05, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPPB	protein_coding	protein_coding	ENST00000376468	3	1468

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000988	0.199	125712	0	32	125744	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.152	88	84.1	1.05	0.00000523	840
Missense in Polyphen		20	19.255	1.0387		218
Synonymous	0.101	34	34.8	0.978	0.00000184	302
Loss of Function	-0.414	7	5.91	1.18	3.50e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000370	0.000368
Ashkenazi Jewish	0.000963	0.000893
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000130	0.000123
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cardiac hormone which may function as a paracrine antifibrotic factor in the heart. Also plays a key role in cardiovascular homeostasis through natriuresis, diuresis, vasorelaxation, and inhibition of renin and aldosterone secretion. Specifically binds and stimulates the cGMP production of the NPR1 receptor. Binds the clearance receptor NPR3. {ECO:0000269|PubMed:1672777}.
• Pathway: cGMP-PKG signaling pathway - Homo sapiens (human);MicroRNAs in cardiomyocyte hypertrophy;NO-cGMP-PKG mediated Neuroprotection;alk in cardiac myocytes (Consensus)

Intolerance Scores

• loftool: 0.700
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.58

Haploinsufficiency Scores

• pHI: 0.0599
• hipred: N
• hipred_score: 0.182

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.557

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nppb
• Phenotype: muscle 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)

Gene ontology

• Biological process: negative regulation of systemic arterial blood pressure;cGMP biosynthetic process;protein folding;cell surface receptor signaling pathway;receptor guanylyl cyclase signaling pathway;neuropeptide signaling pathway;body fluid secretion;regulation of blood pressure;regulation of signaling receptor activity;negative regulation of angiogenesis;cGMP-mediated signaling;negative regulation of cell growth;positive regulation of urine volume;positive regulation of renal sodium excretion;regulation of vascular permeability;regulation of blood vessel diameter
• Cellular component: extracellular region;extracellular space;nucleus;cytoplasm;protein-containing complex
• Molecular function: signaling receptor binding;hormone activity;protein binding;diuretic hormone activity;hormone receptor binding