NPY4R

neuropeptide Y receptor Y4, the group of Neuropeptide Y receptors

Basic information

Region (hg38): 10:46461099-46465958

Previous symbols: [ "PPYR1" ]

Links

ENSG00000204174 ∙ NCBI:5540 ∙ OMIM:601790 ∙ HGNC:9329 ∙ Uniprot:P50391 ∙ 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 NPY4R gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPY4R 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			3		2	5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					5	5
Total	0	0	3	0	9

Variants in NPY4R

This is a list of pathogenic ClinVar variants found in the NPY4R region.

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

Position	Type	Phenotype	Significance	ClinVar
10-46461589-T-T			Benign (May 14, 2018)
10-46461612-G-T		not specified	Uncertain significance (May 01, 2024)
10-46461654-T-A		not specified	Uncertain significance (Nov 09, 2021)
10-46461688-A-A			Benign (May 14, 2018)
10-46461700-C-T		not specified	Uncertain significance (Oct 04, 2024)
10-46461739-A-A			Benign (May 14, 2018)
10-46461746-A-G		not specified	Uncertain significance (Aug 13, 2021)
10-46461765-G-C		not specified	Uncertain significance (Aug 12, 2024)
10-46461812-G-A		not specified	Uncertain significance (Dec 04, 2024)
10-46461918-A-G			Benign (May 14, 2018)
10-46461918-A-A			Benign (May 14, 2018)
10-46461945-A-A			Benign (May 14, 2018)
10-46462052-A-C		not specified	Uncertain significance (Jun 02, 2024)
10-46462166-T-C		not specified	Uncertain significance (Dec 10, 2024)
10-46462251-T-C		not specified	Uncertain significance (May 30, 2023)
10-46462271-C-T		not specified	Uncertain significance (Nov 14, 2024)
10-46462341-C-A			Benign (May 14, 2018)
10-46462402-C-G			Benign (Aug 15, 2017)
10-46462504-G-A			Benign (May 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPY4R	protein_coding	protein_coding	ENST00000374312	1	4787

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.21e-7	0.173	125697	0	49	125746	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.139	164	169	0.970	0.00000897	2243
Missense in Polyphen		49	59.307	0.82621		833
Synonymous	-1.80	94	74.3	1.27	0.00000436	691
Loss of Function	-0.172	9	8.46	1.06	4.60e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000707	0.000707
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000193	0.000193
Middle Eastern	0.000707	0.000707
South Asian	0.000163	0.000163
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 PP, PP (2-36) and [Ile-31, Gln-34] PP > [Pro-34] PYY > PYY and [Leu-31, Pro-34] NPY > NPY > PYY (3-36) and NPY (2-36) > PP (13- 36) > PP (31-36) > NPY free acid.
• 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);regulation of eif2;akap95 role in mitosis and chromosome dynamics;GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.68

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.219

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Npy4r
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; normal phenotype; skeleton phenotype; growth/size/body region 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); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;neuropeptide signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;membrane
• Molecular function: pancreatic polypeptide receptor activity;G protein-coupled receptor activity;peptide hormone binding