VTA1
Basic information
Region (hg38): 6:142147162-142224685
Previous symbols: [ "C6orf55" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (36 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the VTA1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016485.5. 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 | 0 | |||||
| missense | 34 | 35 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 34 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VTA1 | protein_coding | protein_coding | ENST00000367630 | 8 | 77460 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000399 | 0.963 | 125726 | 0 | 18 | 125744 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.315 | 181 | 169 | 1.07 | 0.00000846 | 2003 |
| Missense in Polyphen | 61 | 69.357 | 0.87951 | 827 | ||
| Synonymous | -0.832 | 69 | 60.7 | 1.14 | 0.00000313 | 584 |
| Loss of Function | 1.85 | 8 | 16.0 | 0.500 | 7.63e-7 | 204 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000244 | 0.000217 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000112 | 0.000105 |
| Middle Eastern | 0.000244 | 0.000217 |
| South Asian | 0.0000335 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the endosomal multivesicular bodies (MVB) pathway. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. Thought to be a cofactor of VPS4A/B, which catalyzes disassembles membrane-associated ESCRT-III assemblies. Involved in the sorting and down-regulation of EGFR (By similarity). Involved in HIV-1 budding. {ECO:0000250, ECO:0000269|PubMed:15644320}.;
- Pathway
- Endocytosis - Homo sapiens (human);Disease;Vesicle-mediated transport;Membrane Trafficking;Budding and maturation of HIV virion;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;Endosomal Sorting Complex Required For Transport (ESCRT);Infectious disease
(Consensus)
Recessive Scores
- pRec
- 0.142
Intolerance Scores
- loftool
- 0.702
- rvis_EVS
- 0.48
- rvis_percentile_EVS
- 79.25
Haploinsufficiency Scores
- pHI
- 0.386
- hipred
- Y
- hipred_score
- 0.613
- ghis
- 0.512
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.942
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vta1
- Phenotype
Gene ontology
- Biological process
- protein transport;macroautophagy;viral life cycle;multivesicular body assembly;viral budding;multivesicular body sorting pathway;ESCRT III complex disassembly
- Cellular component
- nucleoplasm;cytosol;endosome membrane;intracellular membrane-bounded organelle;extracellular exosome
- Molecular function
- protein binding;protein C-terminus binding