NPY5R

neuropeptide Y receptor Y5, the group of Neuropeptide Y receptors

Basic information

Region (hg38): 4:163343891-163351934

Links

ENSG00000164129 ∙ NCBI:4889 ∙ OMIM:602001 ∙ HGNC:7958 ∙ Uniprot:Q15761 ∙ 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 NPY5R gene.

• Inborn genetic diseases (10 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPY5R 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				2		2
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	3	0

Variants in NPY5R

This is a list of pathogenic ClinVar variants found in the NPY5R region.

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

Position	Type	Phenotype	Significance	ClinVar
4-163350313-G-C		not specified	Uncertain significance (Jan 30, 2024)
4-163350438-C-T			Likely benign (May 25, 2018)
4-163350469-C-G		not specified	Uncertain significance (May 11, 2022)
4-163350482-G-A		not specified	Uncertain significance (Aug 10, 2021)
4-163350617-A-G		not specified	Uncertain significance (Oct 26, 2022)
4-163350687-C-T			Likely benign (Jun 23, 2018)
4-163350724-T-G		not specified	Uncertain significance (Jun 27, 2023)
4-163350727-A-T		not specified	Uncertain significance (Sep 14, 2023)
4-163350728-C-G		not specified	Uncertain significance (Nov 18, 2022)
4-163351022-A-C		not specified	Uncertain significance (Oct 20, 2023)
4-163351058-C-A		not specified	Uncertain significance (Oct 10, 2023)
4-163351120-A-C		not specified	Uncertain significance (Jul 13, 2021)
4-163351189-G-A			Likely benign (Dec 31, 2019)
4-163351223-G-T		not specified	Uncertain significance (Nov 02, 2023)
4-163351279-T-C		not specified	Uncertain significance (Dec 08, 2023)
4-163351287-G-T		not specified	Uncertain significance (Feb 15, 2023)
4-163351334-G-A		not specified	Uncertain significance (Mar 06, 2023)
4-163351547-A-G		not specified	Uncertain significance (Dec 19, 2023)
4-163351574-C-G		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPY5R	protein_coding	protein_coding	ENST00000515560	1	7996

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00637	0.919	125731	0	12	125743	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.734	195	226	0.863	0.0000108	2938
Missense in Polyphen		65	83.643	0.77712		1156
Synonymous	0.434	77	82.0	0.939	0.00000396	868
Loss of Function	1.53	5	10.3	0.485	5.02e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for neuropeptide Y and peptide YY. The activity of this receptor is mediated by G proteins that inhibit adenylate cyclase activity. Seems to be associated with food intake. Could be involved in feeding disorders.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);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: 0.137

Intolerance Scores

• loftool: 0.443
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.237
• hipred: Y
• hipred_score: 0.604
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.268

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Npy5r
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype

Gene ontology

• Biological process: positive regulation of acute inflammatory response;negative regulation of acute inflammatory response to antigenic stimulus;outflow tract morphogenesis;cardiac left ventricle morphogenesis;G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;chemical synaptic transmission;aging;negative regulation of glutamate secretion;negative regulation of synaptic transmission, GABAergic;eating behavior;negative regulation of apoptotic process;positive regulation of smooth muscle cell proliferation;generation of ovulation cycle rhythm;positive regulation of ERK1 and ERK2 cascade
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane;membrane;neuron projection
• Molecular function: peptide YY receptor activity;pancreatic polypeptide receptor activity;neuropeptide Y receptor activity