VIPR2

vasoactive intestinal peptide receptor 2, the group of Vasoactive intestinal peptide family receptors

Basic information

Region (hg38): 7:159028174-159144867

Links

ENSG00000106018 ∙ NCBI:7434 ∙ OMIM:601970 ∙ HGNC:12695 ∙ Uniprot:P41587 ∙ 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 VIPR2 gene.

• Inborn genetic diseases (17 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VIPR2 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			15	3	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	15	5	4

Variants in VIPR2

This is a list of pathogenic ClinVar variants found in the VIPR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-159030656-C-A		not specified	Uncertain significance (May 25, 2022)
7-159030665-C-T		not specified	Uncertain significance (Apr 13, 2022)
7-159030677-A-G		not specified	Uncertain significance (Apr 07, 2022)
7-159030694-G-C		not specified	Uncertain significance (Nov 17, 2023)
7-159030704-A-G			Benign (Aug 28, 2018)
7-159030707-G-A		not specified	Uncertain significance (Aug 08, 2022)
7-159030743-G-T		not specified	Likely benign (Nov 15, 2021)
7-159031940-G-T		not specified	Uncertain significance (Feb 11, 2022)
7-159031954-C-T			Likely benign (Aug 30, 2018)
7-159031958-G-A			Likely benign (Feb 01, 2021)
7-159032034-C-T			Benign/Likely benign (Jan 01, 2024)
7-159032056-T-C		not specified	Uncertain significance (Sep 20, 2023)
7-159034243-T-A		not specified	Uncertain significance (Dec 14, 2023)
7-159034618-C-G		not specified	Uncertain significance (Nov 10, 2022)
7-159034631-G-A		not specified	Uncertain significance (Sep 27, 2022)
7-159035953-C-T		not specified	Uncertain significance (Dec 06, 2021)
7-159035971-G-C		not specified	Uncertain significance (May 23, 2023)
7-159036874-A-G		not specified	Uncertain significance (Aug 16, 2021)
7-159036876-G-C		not specified	Uncertain significance (Feb 22, 2023)
7-159043055-G-A		not specified	Uncertain significance (Mar 24, 2023)
7-159043113-G-A			Benign (Apr 10, 2018)
7-159058488-G-A		not specified	Uncertain significance (Oct 06, 2023)
7-159058509-T-C		not specified	Uncertain significance (Dec 01, 2022)
7-159096904-G-A			Likely benign (Oct 01, 2022)
7-159103785-C-T		not specified	Uncertain significance (Mar 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VIPR2	protein_coding	protein_coding	ENST00000262178	13	116784

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.72e-11	0.570	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.283	230	242	0.949	0.0000136	2821
Missense in Polyphen		88	103.33	0.85167		1214
Synonymous	-0.283	112	108	1.03	0.00000702	860
Loss of Function	1.35	20	27.7	0.723	0.00000156	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000717	0.000716
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000169	0.000163
Finnish	0.0000522	0.0000462
European (Non-Finnish)	0.000264	0.000264
Middle Eastern	0.000169	0.000163
South Asian	0.000392	0.000392
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This is a receptor for VIP as well as PACAP-38 and -27, the activity of this receptor is mediated by G proteins which activate adenylyl cyclase. Can be coupled to phospholipase C. {ECO:0000269|PubMed:8926282}.
• Pathway: cAMP signaling pathway - Homo sapiens (human);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;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.167

Intolerance Scores

• loftool: 0.867
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.31

Haploinsufficiency Scores

• pHI: 0.133
• hipred: N
• hipred_score: 0.318
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.256

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vipr2
• 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); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: signal transduction;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;activation of adenylate cyclase activity;cell-cell signaling;negative regulation of smooth muscle cell proliferation
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity;vasoactive intestinal polypeptide receptor activity;G protein-coupled peptide receptor activity;peptide hormone binding