NPSR1

neuropeptide S receptor 1, the group of Neuropeptide S receptor

Basic information

Region (hg38): 7:34658217-34878332

Previous symbols: [ "GPR154" ]

Links

ENSG00000187258 ∙ NCBI:387129 ∙ OMIM:608595 ∙ HGNC:23631 ∙ Uniprot:Q6W5P4 ∙ 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 NPSR1 gene.

• Inborn genetic diseases (5 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPSR1 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				1	1	2
missense			5		1	6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	5	1	2

Variants in NPSR1

This is a list of pathogenic ClinVar variants found in the NPSR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-34658444-A-G		not specified	Uncertain significance (Mar 29, 2022)
7-34658485-G-A		not specified	Uncertain significance (May 18, 2022)
7-34684545-C-G			Benign (Jun 30, 2017)
7-34778501-A-T		Asthma-related traits, susceptibility to, 2	risk factor (Apr 09, 2004)
7-34778523-C-T			Likely benign (May 01, 2022)
7-34778526-G-A			Benign (Feb 08, 2018)
7-34811812-A-G			Benign (Feb 08, 2018)
7-34827574-G-A		not specified	Uncertain significance (Oct 29, 2021)
7-34844932-T-C		not specified	Uncertain significance (Jan 27, 2022)
7-34848488-A-G		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPSR1	protein_coding	protein_coding	ENST00000359791	9	220094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.05e-9	0.429	125137	0	611	125748	0.00243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.376	224	209	1.07	0.0000110	2444
Missense in Polyphen		80	68.71	1.1643		871
Synonymous	0.0743	80	80.8	0.989	0.00000457	739
Loss of Function	0.989	16	20.9	0.766	0.00000123	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0283	0.0287
Ashkenazi Jewish	0.00	0.00
East Asian	0.000872	0.000870
Finnish	0.00240	0.00241
European (Non-Finnish)	0.000335	0.000334
Middle Eastern	0.000872	0.000870
South Asian	0.000262	0.000261
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: G-protein coupled receptor for neuropeptide S (NPS) (PubMed:16790440). Promotes mobilization of intracellular Ca(2+) stores (PubMed:16790440). Inhibits cell growth in response to NPS binding (PubMed:15947423). Involved in pathogenesis of asthma and other IgE-mediated diseases. {ECO:0000269|PubMed:15312648, ECO:0000269|PubMed:15947423, ECO:0000269|PubMed:16790440}.
• Pathway: Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.193

Intolerance Scores

• loftool: 0.895
• rvis_EVS: 1.34
• rvis_percentile_EVS: 94.25

Haploinsufficiency Scores

• pHI: 0.234
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.152

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Npsr1
• Phenotype: respiratory system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;positive regulation of release of sequestered calcium ion into cytosol
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane
• Molecular function: vasopressin receptor activity;neuropeptide receptor activity