NPY1R
neuropeptide Y receptor Y1, the group of Neuropeptide Y receptors
Basic information
Region (hg38): 4:163323961-163344832
Previous symbols: [ "NPYR" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (11 variants)
- not provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPY1R 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 | 11 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 1 |
Variants in NPY1R
This is a list of pathogenic ClinVar variants found in the NPY1R region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-163325337-T-G | Benign (Jul 06, 2018) | |||
| 4-163325458-A-G | not specified | Uncertain significance (Jan 19, 2022) | ||
| 4-163325524-A-G | not specified | Uncertain significance (Jan 17, 2024) | ||
| 4-163325568-T-C | not specified | Uncertain significance (Aug 16, 2022) | ||
| 4-163325703-T-C | not specified | Uncertain significance (Aug 16, 2021) | ||
| 4-163325706-T-C | not specified | Likely benign (Jan 04, 2024) | ||
| 4-163325725-T-C | not specified | Uncertain significance (Mar 11, 2024) | ||
| 4-163325749-G-A | not specified | Uncertain significance (Jul 19, 2022) | ||
| 4-163325897-A-G | not specified | Uncertain significance (Jan 18, 2022) | ||
| 4-163325971-T-C | not specified | Uncertain significance (Oct 05, 2022) | ||
| 4-163325983-G-A | not specified | Uncertain significance (Dec 13, 2022) | ||
| 4-163326097-C-T | not specified | Uncertain significance (Aug 09, 2021) | ||
| 4-163326246-C-G | not specified | Uncertain significance (Mar 28, 2023) | ||
| 4-163326319-A-G | not specified | Uncertain significance (Sep 14, 2023) | ||
| 4-163326401-T-A | not specified | Uncertain significance (Nov 09, 2023) | ||
| 4-163326427-A-G | not specified | Uncertain significance (Feb 27, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NPY1R | protein_coding | protein_coding | ENST00000296533 | 2 | 20872 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0426 | 0.932 | 125728 | 0 | 8 | 125736 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.78 | 132 | 203 | 0.649 | 0.00000995 | 2573 |
| Missense in Polyphen | 27 | 68.182 | 0.396 | 909 | ||
| Synonymous | -0.206 | 79 | 76.7 | 1.03 | 0.00000393 | 733 |
| Loss of Function | 1.94 | 4 | 10.9 | 0.366 | 6.26e-7 | 133 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000906 | 0.0000906 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for neuropeptide Y and peptide YY. The rank order of affinity of this receptor for pancreatic polypeptides is NPY > [Pro-34] PYY, PYY and [Leu-31, Pro-34] NPY > NPY (2-36) > [Ile-31, Gln-34] PP and PYY (3-36) > PP > NPY free acid.;
- Pathway
- Regulation of lipolysis in adipocytes - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Sympathetic Nerve Pathway (Neuroeffector Junction);Endothelin Pathways;Peptide GPCRs;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.199
Intolerance Scores
- loftool
- 0.259
- rvis_EVS
- -0.18
- rvis_percentile_EVS
- 39.95
Haploinsufficiency Scores
- pHI
- 0.417
- hipred
- Y
- hipred_score
- 0.735
- ghis
- 0.557
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.641
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Npy1r
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); taste/olfaction phenotype; muscle phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; skeleton phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; normal 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); 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); hematopoietic system phenotype; limbs/digits/tail 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); immune system phenotype;
Gene ontology
- Biological process
- outflow tract morphogenesis;glucose metabolic process;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;locomotory behavior;feeding behavior;regulation of blood pressure;sensory perception of pain;regulation of multicellular organism growth
- Cellular component
- plasma membrane;integral component of plasma membrane
- Molecular function
- peptide YY receptor activity;pancreatic polypeptide receptor activity;neuropeptide Y receptor activity;protein binding