VTI1A
vesicle transport through interaction with t-SNAREs 1A, the group of SNAREs|MicroRNA protein coding host genes
Basic information
Region (hg38): 10:112446998-112818744
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the VTI1A 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 | 0 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 0 |
Variants in VTI1A
This is a list of pathogenic ClinVar variants found in the VTI1A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-112464583-C-T | not specified | Uncertain significance (Jan 03, 2024) | ||
| 10-112464646-G-A | not specified | Uncertain significance (Aug 17, 2022) | ||
| 10-112527130-T-C | not specified | Uncertain significance (Mar 29, 2022) | ||
| 10-112668232-G-A | not specified | Uncertain significance (Jun 13, 2024) | ||
| 10-112668280-C-T | not specified | Uncertain significance (May 08, 2024) | ||
| 10-112668941-G-A | not specified | Uncertain significance (Apr 18, 2023) | ||
| 10-112668970-T-C | Hereditary breast ovarian cancer syndrome | Uncertain significance (Aug 01, 2020) | ||
| 10-112668990-G-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 10-112815303-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 10-112815304-G-A | not specified | Uncertain significance (May 23, 2024) | ||
| 10-112815337-T-G | not specified | Uncertain significance (Feb 10, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VTI1A | protein_coding | protein_coding | ENST00000393077 | 8 | 371748 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000542 | 0.975 | 125731 | 0 | 17 | 125748 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.160 | 124 | 129 | 0.960 | 0.00000738 | 1416 |
| Missense in Polyphen | 45 | 41.75 | 1.0779 | 454 | ||
| Synonymous | 0.808 | 39 | 46.0 | 0.848 | 0.00000253 | 399 |
| Loss of Function | 1.99 | 8 | 16.8 | 0.477 | 0.00000104 | 162 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000152 | 0.000149 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000272 | 0.000272 |
| Finnish | 0.0000464 | 0.0000462 |
| European (Non-Finnish) | 0.0000354 | 0.0000352 |
| Middle Eastern | 0.000272 | 0.000272 |
| South Asian | 0.0000982 | 0.0000980 |
| 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. Involved in vesicular transport from the late endosomes to the trans-Golgi network. Along with VAMP7, involved in an non- conventional RAB1-dependent traffic route to the cell surface used by KCNIP1 and KCND2. May be involved in increased cytokine secretion associated with cellular senescence. {ECO:0000269|PubMed:18195106, ECO:0000269|PubMed:19138172}.;
- Pathway
- SNARE interactions in vesicular transport - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Intra-Golgi traffic;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.114
Intolerance Scores
- loftool
- 0.517
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- 0.195
- hipred
- Y
- hipred_score
- 0.631
- ghis
- 0.645
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.820
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vti1a
- 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); 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); normal phenotype; reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hearing/vestibular/ear 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); vision/eye phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- protein targeting to vacuole;endoplasmic reticulum to Golgi vesicle-mediated transport;intra-Golgi vesicle-mediated transport;Golgi to vacuole transport;autophagy;retrograde transport, endosome to Golgi;vesicle fusion with Golgi apparatus;voluntary musculoskeletal movement;Golgi ribbon formation
- Cellular component
- Golgi membrane;endosome;autophagosome;endoplasmic reticulum membrane;Golgi apparatus;cytosol;synaptic vesicle;ER to Golgi transport vesicle membrane;integral component of membrane;clathrin-coated vesicle;SNARE complex;late endosome membrane;trans-Golgi network membrane;neuronal cell body;intracellular membrane-bounded organelle;neuron projection terminus;perinuclear region of cytoplasm
- Molecular function
- SNARE binding;SNAP receptor activity;protein binding