NPY

neuropeptide Y, the group of Neuropeptides

Basic information

Region (hg38): 7:24284187-24291862

Links

ENSG00000122585 ∙ NCBI:4852 ∙ OMIM:162640 ∙ HGNC:7955 ∙ Uniprot:P01303 ∙ 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 NPY gene.

• not provided (8 variants)
• Inborn genetic diseases (4 variants)
• NEUROPEPTIDE Y POLYMORPHISM (1 variants)

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				1	3	4
missense			4	1	1	6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	4	3	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: gnomAD

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: dbNSFP

• 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