NPPC

natriuretic peptide C, the group of Neuropeptides

Basic information

Region (hg38): 2:231921809-231926396

Links

ENSG00000163273 ∙ NCBI:4880 ∙ OMIM:600296 ∙ HGNC:7941 ∙ Uniprot:P23582 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• short stature with nonspecific skeletal abnormalities (Limited), mode of inheritance: AD

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPPC 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				7	2	9
missense			34	2	2	38
nonsense			2			2
start loss			1			1
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding				3		3
Total	0	0	38	12	4

Variants in NPPC

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

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

Position	Type	Phenotype	Significance	ClinVar
2-231925441-C-T			Uncertain significance (Mar 27, 2022)
2-231925442-T-A			Uncertain significance (Jul 07, 2023)
2-231925444-A-G			Uncertain significance (Mar 25, 2021)
2-231925452-G-T			Benign (Sep 17, 2023)
2-231925458-G-A			Likely benign (Dec 07, 2023)
2-231925464-C-G			Uncertain significance (Jan 14, 2024)
2-231925479-G-A			Likely benign (Jun 05, 2022)
2-231925481-C-A			Uncertain significance (Jan 25, 2023)
2-231925493-C-G			Uncertain significance (Apr 22, 2021)
2-231925493-C-T			Uncertain significance (Jan 31, 2024)
2-231925504-G-T			Likely benign (Jan 04, 2022)
2-231925511-T-C		not specified	Uncertain significance (May 23, 2024)
2-231925512-G-T			Uncertain significance (Jun 23, 2021)
2-231925519-C-G		not specified	Uncertain significance (Mar 01, 2024)
2-231925549-G-T		not specified	Uncertain significance (Apr 22, 2022)
2-231925559-C-T			Uncertain significance (Jun 16, 2023)
2-231925561-C-T			Uncertain significance (Aug 16, 2021)
2-231925566-C-T			Likely benign (Mar 31, 2023)
2-231925570-G-A		not specified	Uncertain significance (Jan 16, 2024)
2-231925577-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-231925580-G-T			Uncertain significance (Dec 06, 2022)
2-231925595-G-T		not specified	Uncertain significance (Jun 17, 2024)
2-231925603-C-T			Uncertain significance (Aug 24, 2022)
2-231925607-C-T			Uncertain significance (Apr 30, 2023)
2-231925612-T-G		not specified	Uncertain significance (Jul 19, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPPC	protein_coding	protein_coding	ENST00000409852	2	4584

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0606	0.734	123355	0	3	123358	0.0000122

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.323	58	65.3	0.888	0.00000297	765
Missense in Polyphen		12	11.941	1.005		106
Synonymous	0.613	27	31.4	0.861	0.00000141	289
Loss of Function	0.820	2	3.70	0.540	1.60e-7	48

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000285	0.0000271
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hormone which plays a role in endochondral ossification through regulation of cartilaginous growth plate chondrocytes proliferation and differentiation. May also be vasoactive and natriuretic. Specifically binds and stimulates the cGMP production of the NPR2 receptor. Binds the clearance receptor NPR3 (By similarity). {ECO:0000250, ECO:0000269|PubMed:1672777}.
• Pathway: Fluid shear stress and atherosclerosis - Homo sapiens (human);Physiological factors;Cardiac conduction;Muscle contraction (Consensus)

Recessive Scores

• pRec: 0.241

Intolerance Scores

• loftool: 0.517
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.274
• hipred: Y
• hipred_score: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nppc
• Phenotype: homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail 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); reproductive system phenotype

Gene ontology

• Biological process: ossification;response to hypoxia;growth plate cartilage chondrocyte differentiation;growth plate cartilage chondrocyte proliferation;cGMP biosynthetic process;protein folding;receptor guanylyl cyclase signaling pathway;negative regulation of cell population proliferation;post-embryonic development;regulation of signaling receptor activity;positive regulation of cGMP-mediated signaling;cGMP-mediated signaling;reproductive process;negative regulation of collagen biosynthetic process;regulation of multicellular organism growth;response to ethanol;positive regulation of osteoblast differentiation;regulation of smooth muscle cell proliferation;negative regulation of meiotic cell cycle;positive regulation of blood vessel diameter;negative regulation of oocyte maturation;regulation of cardiac conduction;negative regulation of DNA biosynthetic process
• Cellular component: extracellular region;extracellular space;secretory granule;protein-containing complex
• Molecular function: signaling receptor binding;hormone activity;hormone receptor binding