VTI1B
vesicle transport through interaction with t-SNAREs 1B, the group of SNAREs
Basic information
Region (hg38): 14:67647085-67674820
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (41 variants)
- not_provided (3 variants)
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. These statistics are base on transcript: NM_000006370.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 41 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 41 | 0 | 1 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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