VIP

vasoactive intestinal peptide, the group of Neuropeptides

Basic information

Region (hg38): 6:152750797-152759765

Links

ENSG00000146469 ∙ NCBI:7432 ∙ OMIM:192320 ∙ HGNC:12693 ∙ Uniprot:P01282 ∙ 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 VIP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VIP 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	2	4
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	14	2	2

Variants in VIP

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

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

Position	Type	Phenotype	Significance	ClinVar
6-152752226-A-T		See cases	Uncertain significance (Jun 12, 2020)
6-152752237-C-G		not specified	Uncertain significance (Apr 25, 2023)
6-152752250-G-C		not specified	Uncertain significance (Jun 03, 2022)
6-152754240-T-C		not specified	Uncertain significance (Mar 11, 2022)
6-152754261-A-G		not specified	Uncertain significance (Dec 22, 2023)
6-152754294-T-A			Benign (Dec 31, 2019)
6-152755262-G-A			Likely benign (Dec 31, 2019)
6-152755292-T-A		not specified	Uncertain significance (Feb 28, 2024)
6-152755309-A-G		not specified	Uncertain significance (Jun 17, 2024)
6-152755349-A-G		not specified	Uncertain significance (Sep 22, 2022)
6-152755369-G-A		not specified	Uncertain significance (May 31, 2023)
6-152756135-A-T		not specified	Uncertain significance (Apr 09, 2022)
6-152756140-C-T			Likely benign (Jan 23, 2018)
6-152756182-A-C			Benign (Dec 31, 2019)
6-152756194-C-T			Likely benign (Dec 11, 2018)
6-152756196-A-G		not specified	Uncertain significance (Aug 16, 2021)
6-152756197-C-T			Benign (Dec 31, 2019)
6-152756239-G-C		not specified	Uncertain significance (Apr 16, 2024)
6-152756246-A-T		not specified	Uncertain significance (Aug 17, 2022)
6-152756255-G-A		not specified	Uncertain significance (Mar 20, 2023)
6-152757097-A-C		not specified	Uncertain significance (Feb 10, 2022)
6-152757113-C-T		not specified	Uncertain significance (Oct 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VIP	protein_coding	protein_coding	ENST00000367244	5	8968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000420	0.662	125619	0	15	125634	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.293	80	87.7	0.912	0.00000430	1108
Missense in Polyphen		26	28.118	0.92468		355
Synonymous	-0.203	32	30.6	1.05	0.00000148	312
Loss of Function	0.746	6	8.32	0.721	3.49e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000325	0.000325
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000111	0.000109
South Asian	0.00	0.00
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: VIP causes vasodilation, lowers arterial blood pressure, stimulates myocardial contractility, increases glycogenolysis and relaxes the smooth muscle of trachea, stomach and gall bladder. {ECO:0000269|PubMed:15013843}.
• Pathway: Gastric acid production;IL-6 signaling pathway;Signaling by GPCR;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;G alpha (s) signalling events;AndrogenReceptor;Glucagon-type ligand receptors;Class B/2 (Secretin family receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;GPCR signaling-G alpha i;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.331

Intolerance Scores

• loftool: 0.667
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.319
• hipred: N
• hipred_score: 0.231
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.895

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: positive regulation of endothelial cell proliferation;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;phospholipase C-activating G protein-coupled receptor signaling pathway;body fluid secretion;learning or memory;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of epinephrine secretion;regulation of protein localization;negative regulation of apoptotic process;negative regulation of potassium ion transport;positive regulation of protein catabolic process;epinephrine secretion;mRNA stabilization;negative regulation of smooth muscle cell proliferation;regulation of sensory perception of pain;positive regulation of penile erection;prolactin secretion;positive regulation of blood vessel diameter
• Cellular component: extracellular region;neuron projection;perikaryon
• Molecular function: hormone activity;neuropeptide hormone activity;protein binding;peptide hormone receptor binding