VTI1B

vesicle transport through interaction with t-SNAREs 1B, the group of SNAREs

Basic information

Region (hg38): 14:67647085-67674820

Links

ENSG00000100568 ∙ NCBI:10490 ∙ OMIM:603207 ∙ HGNC:17793 ∙ Uniprot:Q9UEU0 ∙ 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 VTI1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VTI1B 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	1
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8	1	1	10
Total	0	0	23	1	2

Variants in VTI1B

This is a list of pathogenic ClinVar variants found in the VTI1B region.

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

Position	Type	Phenotype	Significance	ClinVar
14-67648051-C-A		not specified	Uncertain significance (Jan 10, 2022)
14-67650779-G-A			Benign/Likely benign (Oct 01, 2022)
14-67650811-T-C		not specified	Uncertain significance (May 22, 2023)
14-67650829-A-G		not specified	Uncertain significance (Jun 12, 2023)
14-67650843-G-A		not specified	Uncertain significance (Mar 24, 2023)
14-67650873-C-T		not specified	Uncertain significance (Aug 02, 2021)
14-67650888-G-A		not specified	Uncertain significance (Aug 02, 2021)
14-67650907-G-A		not specified	Uncertain significance (Feb 12, 2024)
14-67650909-G-T		not specified	Uncertain significance (Jan 30, 2024)
14-67651432-C-T		not specified	Uncertain significance (Nov 21, 2023)
14-67651435-G-A		not specified	Uncertain significance (Nov 12, 2021)
14-67651480-C-A		not specified	Uncertain significance (May 26, 2022)
14-67653468-T-C		not specified	Uncertain significance (Jan 17, 2024)
14-67656423-T-G		not specified	Uncertain significance (Jun 03, 2024)
14-67656465-A-G		not specified	Uncertain significance (Mar 07, 2024)
14-67656466-T-C		not specified	Uncertain significance (Jan 11, 2023)
14-67656514-G-T		not specified	Uncertain significance (Jan 24, 2024)
14-67656565-T-C		not specified	Uncertain significance (Apr 27, 2022)
14-67656583-G-T		not specified	Uncertain significance (Nov 12, 2021)
14-67656586-G-A		not specified	Uncertain significance (Jul 26, 2021)
14-67659795-G-A		not specified	Uncertain significance (Sep 22, 2023)
14-67659819-C-T		not specified	Uncertain significance (Dec 18, 2023)
14-67659832-C-T		not specified	Uncertain significance (Jun 09, 2022)
14-67659843-C-T		not specified	Uncertain significance (Mar 30, 2024)
14-67659871-G-T		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VTI1B	protein_coding	protein_coding	ENST00000554659	6	27757

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.108	0.886	125728	0	19	125747	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.427	122	136	0.897	0.00000798	1487
Missense in Polyphen		16	26.76	0.5979		314
Synonymous	1.01	38	46.8	0.812	0.00000212	457
Loss of Function	2.41	4	13.6	0.295	9.12e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000968	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: V-SNARE that mediates vesicle transport pathways through interactions with t-SNAREs on the target membrane. These interactions are proposed to mediate aspects of the specificity of vesicle trafficking and to promote fusion of the lipid bilayers. May be concerned with increased secretion of cytokines associated with cellular senescence. {ECO:0000269|PubMed:23217709}.
• Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.400
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.464
• hipred: Y
• hipred_score: 0.726
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.652

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vti1b
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); liver/biliary system phenotype; growth/size/body region 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); cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: platelet degranulation;protein targeting to vacuole;endoplasmic reticulum to Golgi vesicle-mediated transport;intra-Golgi vesicle-mediated transport;Golgi to vacuole transport;vesicle docking involved in exocytosis;cell population proliferation;vesicle-mediated transport;retrograde transport, endosome to Golgi;vesicle fusion with Golgi apparatus;membrane fusion;autophagosome maturation;regulation of protein localization to plasma membrane
• Cellular component: extracellular region;lysosomal membrane;endoplasmic reticulum membrane;Golgi apparatus;cytosol;synaptic vesicle;ER to Golgi transport vesicle membrane;integral component of membrane;platelet alpha granule lumen;SNARE complex;early endosome membrane;late endosome membrane;vesicle;neuronal cell body;intracellular membrane-bounded organelle;perinuclear region of cytoplasm;recycling endosome;recycling endosome membrane
• Molecular function: SNARE binding;SNAP receptor activity;protein binding;chloride channel inhibitor activity