NPY
neuropeptide Y, the group of Neuropeptides
Basic information
Region (hg38): 7:24284188-24291862
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPY 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 | 5 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 2 | |||||
| Total | 0 | 0 | 6 | 5 | 4 |
Variants in NPY
This is a list of pathogenic ClinVar variants found in the NPY region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-24285257-G-C | not specified | Uncertain significance (Apr 17, 2023) | ||
| 7-24285260-T-C | NEUROPEPTIDE Y POLYMORPHISM | Benign (Jan 22, 2024) | ||
| 7-24285271-G-A | Uncertain significance (Mar 19, 2022) | |||
| 7-24285274-C-A | not specified | Uncertain significance (Jun 06, 2023) | ||
| 7-24285324-G-A | Benign (Jan 25, 2024) | |||
| 7-24285373-A-C | not specified | Likely benign (Aug 10, 2021) | ||
| 7-24285390-G-A | Benign (Jan 31, 2024) | |||
| 7-24285392-C-A | not specified | Uncertain significance (Sep 15, 2021) | ||
| 7-24285415-A-T | not specified | Uncertain significance (Dec 20, 2023) | ||
| 7-24285443-G-A | Likely benign (Oct 01, 2022) | |||
| 7-24289484-C-CT | Benign (Jan 31, 2024) | |||
| 7-24289514-C-T | Benign (Jan 31, 2024) | |||
| 7-24289544-G-A | Likely benign (Jun 11, 2023) | |||
| 7-24291651-T-C | Likely benign (Aug 02, 2023) | |||
| 7-24291680-T-C | not specified | Uncertain significance (Jul 13, 2021) | ||
| 7-24291686-G-A | Likely benign (Feb 11, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NPY | protein_coding | protein_coding | ENST00000407573 | 3 | 7703 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.143 | 0.786 | 124672 | 0 | 4 | 124676 | 0.0000160 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.643 | 42 | 55.5 | 0.757 | 0.00000256 | 595 |
| Missense in Polyphen | 11 | 23.456 | 0.46896 | 242 | ||
| Synonymous | 0.0280 | 25 | 25.2 | 0.993 | 0.00000112 | 210 |
| Loss of Function | 1.47 | 2 | 5.81 | 0.344 | 3.45e-7 | 56 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000125 | 0.000124 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000183 | 0.0000177 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: NPY is implicated in the control of feeding and in secretion of gonadotrophin-release hormone.;
- Pathway
- Regulation of lipolysis in adipocytes - Homo sapiens (human);Adipocytokine signaling pathway - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Alcoholism - Homo sapiens (human);Sympathetic Nerve Pathway (Neuroeffector Junction);Endothelin Pathways;Signaling by GPCR;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;G alpha (i) signalling events;GPCR signaling-G alpha i;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.641
Intolerance Scores
- loftool
- 0.252
- rvis_EVS
- 0.21
- rvis_percentile_EVS
- 67.72
Haploinsufficiency Scores
- pHI
- 0.573
- hipred
- Y
- hipred_score
- 0.559
- ghis
- 0.397
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.110
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Npy
- Phenotype
- normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system 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); digestive/alimentary phenotype; 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); homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- npy
- Affected structure
- feeding behavior
- Phenotype tag
- abnormal
- Phenotype quality
- decreased process quality
Gene ontology
- Biological process
- calcium ion transport;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;neuropeptide signaling pathway;chemical synaptic transmission;feeding behavior;regulation of blood pressure;cell population proliferation;adult feeding behavior;regulation of signaling receptor activity;central nervous system neuron development;cerebral cortex development;neuron projection development;positive regulation of appetite
- Cellular component
- extracellular region;extracellular space;cell;Golgi apparatus
- Molecular function
- G protein-coupled receptor binding;G protein-coupled receptor activity;signaling receptor binding;neuropeptide hormone activity;calcium channel regulator activity;neuropeptide Y receptor binding