ASAP1
Basic information
Region (hg38): 8:130052104-130443674
Previous symbols: [ "DDEF1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (72 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASAP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018482.4. 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 | 3 | |||||
| missense | 70 | 72 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 70 | 4 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ASAP1 | protein_coding | protein_coding | ENST00000357668 | 29 | 391554 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.00000197 | 125737 | 0 | 10 | 125747 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.31 | 375 | 603 | 0.621 | 0.0000313 | 7349 |
| Missense in Polyphen | 126 | 249.28 | 0.50545 | 3123 | ||
| Synonymous | -0.477 | 250 | 241 | 1.04 | 0.0000135 | 2182 |
| Loss of Function | 6.66 | 6 | 63.1 | 0.0950 | 0.00000318 | 770 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000186 | 0.000185 |
| Ashkenazi Jewish | 0.000100 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000464 | 0.0000462 |
| European (Non-Finnish) | 0.0000443 | 0.0000439 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Possesses phosphatidylinositol 4,5-bisphosphate- dependent GTPase-activating protein activity for ARF1 (ADP ribosylation factor 1) and ARF5 and a lesser activity towards ARF6. May coordinate membrane trafficking with cell growth or actin cytoskeleton remodeling by binding to both SRC and PIP2. May function as a signal transduction protein involved in the differentiation of fibroblasts into adipocytes and possibly other cell types (By similarity). Plays a role in ciliogenesis. {ECO:0000250, ECO:0000269|PubMed:20393563}.;
- Pathway
- Fc gamma R-mediated phagocytosis - Homo sapiens (human);Endocytosis - Homo sapiens (human);EGF-EGFR Signaling Pathway;rho cell motility signaling pathway;t cell receptor signaling pathway;rac1 cell motility signaling pathway;adp-ribosylation factor;EGFR1;Arf1 pathway;VxPx cargo-targeting to cilium;Signaling events mediated by focal adhesion kinase;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.177
Intolerance Scores
- loftool
- 0.190
- rvis_EVS
- -1.24
- rvis_percentile_EVS
- 5.46
Haploinsufficiency Scores
- pHI
- 0.416
- hipred
- Y
- hipred_score
- 0.745
- ghis
- 0.563
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.850
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Asap1
- Phenotype
Gene ontology
- Biological process
- positive regulation of GTPase activity;cilium assembly;negative regulation of dendritic spine development;positive regulation of podosome assembly;positive regulation of membrane tubulation
- Cellular component
- podosome;cytosol;cell projection membrane;dendritic spine
- Molecular function
- phosphatidylserine binding;GTPase activator activity;protein binding;phosphatidylinositol-4,5-bisphosphate binding;phosphatidylinositol-3,4,5-trisphosphate binding;cadherin binding;metal ion binding