NPY2R

neuropeptide Y receptor Y2, the group of Neuropeptide Y receptors

Basic information

Region (hg38): 4:155208635-155217078

Links

ENSG00000185149 ∙ NCBI:4887 ∙ OMIM:162642 ∙ HGNC:7957 ∙ Uniprot:P49146 ∙ 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 NPY2R gene.

• Inborn genetic diseases (10 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPY2R 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	3	5
missense			10	2	1	13
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	4	4

Variants in NPY2R

This is a list of pathogenic ClinVar variants found in the NPY2R region.

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

Position	Type	Phenotype	Significance	ClinVar
4-155214003-T-C			Likely benign (Jul 10, 2018)
4-155214016-C-A		not specified	Uncertain significance (Feb 12, 2024)
4-155214054-G-C		not specified	Uncertain significance (Mar 23, 2022)
4-155214098-C-T			Benign (Aug 21, 2018)
4-155214136-T-C		not specified	Uncertain significance (Jan 17, 2023)
4-155214267-T-C		not specified	Uncertain significance (Oct 22, 2021)
4-155214305-G-A			Likely benign (Jun 05, 2018)
4-155214382-G-A		not specified	Uncertain significance (Aug 31, 2022)
4-155214433-G-A		not specified	Uncertain significance (Jun 27, 2022)
4-155214453-G-A			Benign (Mar 01, 2018)
4-155214489-G-A		not specified	Uncertain significance (Aug 28, 2023)
4-155214537-A-T		not specified	Uncertain significance (Dec 06, 2022)
4-155214578-C-A		not specified	Uncertain significance (Jul 20, 2021)
4-155214593-C-G			Benign (Mar 29, 2018)
4-155214850-A-G		not specified	Uncertain significance (Jan 30, 2024)
4-155214917-C-T			Benign (Jun 08, 2018)
4-155214973-G-A			Likely benign (Jul 04, 2018)
4-155215046-T-G		not specified	Uncertain significance (Feb 03, 2023)
4-155215049-C-A			Likely benign (Jul 16, 2018)
4-155215050-C-A		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPY2R	protein_coding	protein_coding	ENST00000329476	1	8450

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0355	0.932	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.812	178	211	0.843	0.0000112	2496
Missense in Polyphen		51	80.009	0.63743		961
Synonymous	-1.28	101	85.9	1.18	0.00000471	786
Loss of Function	1.85	4	10.5	0.383	6.16e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for neuropeptide Y and peptide YY. The rank order of affinity of this receptor for pancreatic polypeptides is PYY > NPY > PYY (3-36) > NPY (2-36) > [Ile-31, Gln-34] PP > [Leu- 31, Pro-34] NPY > PP, [Pro-34] PYY and NPY free acid.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);Sympathetic Nerve Pathway (Neuroeffector Junction);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: 0.158

Intolerance Scores

• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.59

Haploinsufficiency Scores

• pHI: 0.284
• hipred: Y
• hipred_score: 0.604
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.170

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Npy2r
• Phenotype: growth/size/body region phenotype; taste/olfaction phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; skeleton phenotype; renal/urinary system phenotype; liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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; reproductive system 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); digestive/alimentary 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: behavioral fear response;positive regulation of peptide secretion;outflow tract morphogenesis;cardiac left ventricle morphogenesis;G protein-coupled receptor signaling pathway;adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;neuropeptide signaling pathway;nitric oxide mediated signal transduction;aging;locomotory behavior;positive regulation of cell-substrate adhesion;positive regulation of dopamine secretion;negative regulation of cAMP-mediated signaling;positive regulation of smooth muscle contraction;positive regulation of circadian sleep/wake cycle, non-REM sleep;secretion;negative regulation of secretion;regulation of sensory perception of pain;negative regulation of synaptic transmission, glutamatergic;negative regulation of excitatory postsynaptic potential;negative regulation of feeding behavior
• Cellular component: plasma membrane;integral component of plasma membrane;non-motile cilium
• Molecular function: peptide YY receptor activity;neuropeptide Y receptor activity;calcium channel regulator activity;protein binding;signaling receptor activity