VIPR1

vasoactive intestinal peptide receptor 1, the group of Vasoactive intestinal peptide family receptors

Basic information

Region (hg38): 3:42489298-42537573

Links

ENSG00000114812 ∙ NCBI:7433 ∙ OMIM:192321 ∙ HGNC:12694 ∙ Uniprot:P32241 ∙ 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 VIPR1 gene.

• not provided (14 variants)
• Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VIPR1 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	5	7
missense			13	2	3	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2		2
Total	0	0	13	6	8

Variants in VIPR1

This is a list of pathogenic ClinVar variants found in the VIPR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-42502740-G-A		not specified	Uncertain significance (Aug 08, 2023)
3-42502788-C-T		not specified	Uncertain significance (Feb 13, 2024)
3-42513759-C-T		not specified	Uncertain significance (Apr 26, 2023)
3-42513800-G-A		not specified	Uncertain significance (Jul 05, 2022)
3-42513831-C-A		not specified	Uncertain significance (Jul 06, 2021)
3-42519262-C-A		not specified	Uncertain significance (Sep 19, 2022)
3-42519271-G-A		not specified	Uncertain significance (Jul 09, 2021)
3-42519298-C-G		not specified	Uncertain significance (Feb 28, 2024)
3-42519304-T-C			Likely benign (Aug 15, 2018)
3-42525889-C-A			Likely benign (Feb 09, 2018)
3-42525927-G-A			Benign (Dec 31, 2019)
3-42525971-A-G			Benign (Dec 14, 2017)
3-42525981-G-A			Benign (Apr 16, 2018)
3-42527384-C-T			Likely benign (May 02, 2018)
3-42527399-A-T		not specified	Uncertain significance (Oct 12, 2021)
3-42527426-G-A		not specified	Uncertain significance (Aug 17, 2022)
3-42527443-C-T			Likely benign (Dec 15, 2017)
3-42527470-C-T			Benign (Jan 09, 2018)
3-42528058-G-A		not specified	Uncertain significance (May 24, 2023)
3-42528101-C-T			Benign (Jun 26, 2018)
3-42530786-G-A		not specified	Uncertain significance (Oct 02, 2023)
3-42530926-G-T		not specified	Uncertain significance (Sep 17, 2021)
3-42531500-A-T		not specified	Uncertain significance (Jan 31, 2024)
3-42531501-C-G		not specified	Uncertain significance (Mar 08, 2024)
3-42531524-G-A		not specified	Uncertain significance (Jan 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VIPR1	protein_coding	protein_coding	ENST00000325123	13	48269

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.44e-27	0.00000732	125656	0	90	125746	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0658	259	262	0.989	0.0000156	2939
Missense in Polyphen		89	95.762	0.92938		1147
Synonymous	0.972	97	110	0.882	0.00000706	882
Loss of Function	-1.50	35	26.6	1.31	0.00000132	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000452	0.000451
Ashkenazi Jewish	0.00	0.00
East Asian	0.00158	0.00158
Finnish	0.00	0.00
European (Non-Finnish)	0.000348	0.000343
Middle Eastern	0.00158	0.00158
South Asian	0.000230	0.000229
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This is a receptor for VIP. The activity of this receptor is mediated by G proteins which activate adenylyl cyclase. The affinity is VIP = PACAP-27 > PACAP-38. {ECO:0000269|PubMed:8926282}.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);GPCRs, Class B Secretin-like;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;Glucagon-type ligand receptors;Class B/2 (Secretin family receptors);GPCR ligand binding;Glucocorticoid receptor regulatory network;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.241

Intolerance Scores

• loftool: 0.788
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.46

Haploinsufficiency Scores

• pHI: 0.446
• hipred: Y
• hipred_score: 0.619
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.770

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vipr1
• Phenotype: digestive/alimentary phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); 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); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;positive regulation of cell population proliferation
• Cellular component: plasma membrane;integral component of plasma membrane;receptor complex
• Molecular function: vasoactive intestinal polypeptide receptor activity;protein binding;G protein-coupled peptide receptor activity;peptide hormone binding