VIPR2

protein-coding

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

Gene summary

This gene encodes a receptor for vasoactive intestinal peptide, a small neuropeptide. Vasoactive intestinal peptide is involved in smooth muscle relaxation, exocrine and endocrine secretion, and water and ion flux in lung and intestinal epithelia. Its actions are effected through integral membrane receptors associated with a guanine nucleotide binding protein which activates adenylate cyclase. [provided by RefSeq, Aug 2011]

MANE transcript

NM_003382.5

Inheritance

—

ClinVar variants

U:53B:9

Top phenotype

Myoepithelial tumor

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr7:159,028,175-159,144,867

External References & Databases

Ensembl (ENSG00000106018)

Transcript & Mutation Effects

hg38 • Region Span ~116.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to VIPR2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 54

not providedTotal: 8

Myoepithelial tumorTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003382.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	2 clinvar	5
missense			52 clinvar	3 clinvar	1 clinvar	56
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	53	6	3	62

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003382.5	RefSeq	NP_003373.2	13	MANE Select
ENST00000262178.7	Ensembl	ENSP00000262178.2	13	MANE Select
NM_001304522.2	RefSeq	NP_001291451.1	11	Standard
NM_001308259.1	RefSeq	NP_001295188.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

signal transduction
cell surface receptor signaling pathway
G protein-coupled receptor signaling pathway
activation of adenylate cyclase activity
cell-cell signaling

Molecular Function

G protein-coupled receptor activity
vasoactive intestinal polypeptide receptor activity
G protein-coupled peptide receptor activity
peptide hormone binding

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262178
Coding exons: 13
Length: 116784
Individuals with no LoFs: 125682
Homozygous LoFs: 0
Heterozygous LoFs: 66
Defined: 125748
p: 0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.283	230	242	0.949	0.0000136	2821
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00017	0.00016	rare
Finnish	0.000052	0.000046	rare
European (Non-Finnish)	0.00026	0.00026	rare
South Asian	0.00039	0.00039	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.167

Intolerance Scores

LoFtool: 0.867
RVIS EVS: -0.62
RVIS percentile EVS: 17.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.256

Gene Damage Prediction

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