VIPR1

protein-coding

vasoactive intestinal peptide receptor 1, 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. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

MANE transcript

NM_004624.4

Inheritance

—

ClinVar variants

U:83B:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.31

Max pathogenic AF

—

Genomic locus

chr3:42,489,299-42,537,573

External References & Databases

Ensembl (ENSG00000114812)

Transcript & Mutation Effects

hg38 • Region Span ~48.3 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 VIPR1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 83

not providedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004624.4. 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			1 clinvar	2 clinvar	5 clinvar	8
missense			80 clinvar	6 clinvar	3 clinvar	89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	83	8	8	99

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 84 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004624.4	RefSeq	NP_004615.2	13	MANE Select
ENST00000325123.5	Ensembl	ENSP00000327246.4	13	MANE Select
NM_001251882.2	RefSeq	NP_001238811.1	12	Standard
NM_001251883.2	RefSeq	NP_001238812.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neuroactive ligand-receptor interaction - Homo sapiens (human)
GPCRs, Class B Secretin-like
Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways
Signaling by GPCR
Signal Transduction

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

Molecular Function

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

Cellular Component

plasma membrane
integral component of plasma membrane
receptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325123
Coding exons: 13
Length: 48269
Individuals with no LoFs: 125656
Homozygous LoFs: 0
Heterozygous LoFs: 90
Defined: 125746
p: 0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0658	259	262	0.989	0.0000156	2939
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0016	0.0016	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00035	0.00034	rare
South Asian	0.00023	0.00023	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.241

Intolerance Scores

LoFtool: 0.788
RVIS EVS: -0.44
RVIS percentile EVS: 24.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.770

Gene Damage Prediction

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