VAPA
Basic information
Region (hg38): 18:9914016-9960021
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (31 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the VAPA gene is commonly pathogenic or not. These statistics are base on transcript: NM_000194434.3. 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 | 0 | |||||
| missense | 23 | 24 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 23 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VAPA | protein_coding | protein_coding | ENST00000340541 | 7 | 46020 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.353 | 0.644 | 124766 | 0 | 8 | 124774 | 0.0000321 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.953 | 125 | 159 | 0.787 | 0.00000776 | 1929 |
| Missense in Polyphen | 8 | 25.502 | 0.31371 | 358 | ||
| Synonymous | 0.544 | 53 | 58.3 | 0.909 | 0.00000307 | 555 |
| Loss of Function | 2.60 | 3 | 13.2 | 0.228 | 6.37e-7 | 172 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000223 | 0.000223 |
| Finnish | 0.0000482 | 0.0000464 |
| European (Non-Finnish) | 0.0000322 | 0.0000265 |
| Middle Eastern | 0.000223 | 0.000223 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to OSBPL3, which mediates recruitment of VAPA to plasma membrane sites (PubMed:25447204). The ORP3-VAPA complex stimulates RRAS signaling which in turn attenuates integrin beta-1 (ITGB1) activation at the cell surface (PubMed:25447204). With OSBPL3, may regulate ER morphology (PubMed:16143324). May play a role in vesicle trafficking (PubMed:11511104, PubMed:19289470). {ECO:0000269|PubMed:11511104, ECO:0000269|PubMed:16143324, ECO:0000269|PubMed:19289470, ECO:0000269|PubMed:25447204}.;
- Pathway
- Cholesterol metabolism - Homo sapiens (human);Exercise-induced Circadian Regulation;Neutrophil degranulation;Metabolism of lipids;Innate Immune System;Immune System;Metabolism;Sphingolipid de novo biosynthesis;Sphingolipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.154
Intolerance Scores
- loftool
- 0.691
- rvis_EVS
- 0.42
- rvis_percentile_EVS
- 76.96
Haploinsufficiency Scores
- pHI
- 0.572
- hipred
- Y
- hipred_score
- 0.550
- ghis
- 0.407
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.935
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vapa
- Phenotype
Gene ontology
- Biological process
- endoplasmic reticulum to Golgi vesicle-mediated transport;endoplasmic reticulum organization;cell death;sphingolipid biosynthetic process;neuron projection development;protein folding in endoplasmic reticulum;positive regulation of I-kappaB kinase/NF-kappaB signaling;neutrophil degranulation;positive regulation by host of viral release from host cell;negative regulation by host of viral genome replication;positive regulation by host of viral genome replication;membrane fusion;protein localization to endoplasmic reticulum;COPII-coated vesicle budding
- Cellular component
- Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;bicellular tight junction;microtubule cytoskeleton;integral component of membrane;nuclear membrane;vesicle;azurophil granule membrane;perinuclear region of cytoplasm;endoplasmic reticulum exit site
- Molecular function
- protein binding;microtubule binding;protein domain specific binding;FFAT motif binding;cadherin binding;protein heterodimerization activity