NPS

neuropeptide S, the group of Neuropeptides

Basic information

Region (hg38): 10:127549309-127553540

Links

ENSG00000214285 ∙ NCBI:594857 ∙ OMIM:609513 ∙ HGNC:33940 ∙ Uniprot:P0C0P6 ∙ 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 NPS gene.

Variants pathogenicity by type

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

Variants in NPS

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

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

Position	Type	Phenotype	Significance	ClinVar
10-127552508-A-C		not specified	Uncertain significance (Aug 01, 2022)
10-127552584-G-A		not specified	Uncertain significance (Mar 01, 2023)
10-127552599-C-A		not specified	Uncertain significance (Feb 15, 2023)
10-127552625-A-G			Benign (May 17, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPS	protein_coding	protein_coding	ENST00000398023	3	3323

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000141	0.250	124761	0	15	124776	0.0000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.531	53	43.2	1.23	0.00000196	569
Missense in Polyphen		17	11.459	1.4836		142
Synonymous	-0.976	22	16.9	1.30	8.05e-7	178
Loss of Function	-0.688	5	3.59	1.39	1.50e-7	48

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000223	0.000223
Ashkenazi Jewish	0.00	0.00
East Asian	0.000279	0.000278
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.000279	0.000278
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Modulates arousal and anxiety. May play an important anorexigenic role (By similarity). Binds to its receptor NPSR1 with nanomolar affinity to increase intracellular calcium concentrations (PubMed:15312648, PubMed:16790440). {ECO:0000250, ECO:0000269|PubMed:15312648, 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: 0.0143

Intolerance Scores

• loftool: 0.746
• rvis_EVS: 0.88
• rvis_percentile_EVS: 88.96

Haploinsufficiency Scores

• pHI: 0.00487
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00385

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nps

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;visual learning;positive regulation of circadian sleep/wake cycle, wakefulness;positive regulation of synaptic transmission, GABAergic;positive regulation of action potential;positive regulation of synaptic transmission, glutamatergic
• Cellular component: extracellular region