NPSR1
Basic information
Region (hg38): 7:34658218-34878332
Previous symbols: [ "GPR154" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (21 variants)
- not_provided (5 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. These statistics are base on transcript: NM_000207172.2. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | |||||
missense | 21 | 22 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 21 | 1 | 3 |
GnomAD
Source:
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:
- 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
- ghis
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