ARAP2
Basic information
Region (hg38): 4:35948221-36244514
Previous symbols: [ "CENTD1" ]
Links
Phenotypes
GenCC
Source:
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 ARAP2 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 | 2 | |||||
missense | 93 | 97 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 93 | 6 | 0 |
Variants in ARAP2
This is a list of pathogenic ClinVar variants found in the ARAP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
4-36067919-C-A | not specified | Uncertain significance (Sep 17, 2021) | ||
4-36068045-C-A | not specified | Uncertain significance (Jan 23, 2023) | ||
4-36068152-G-C | not specified | Uncertain significance (Jan 23, 2024) | ||
4-36068188-C-A | not specified | Uncertain significance (Jan 23, 2023) | ||
4-36068221-C-T | not specified | Uncertain significance (Apr 19, 2023) | ||
4-36068250-C-T | not specified | Uncertain significance (May 26, 2024) | ||
4-36080239-T-C | not specified | Uncertain significance (Jul 17, 2023) | ||
4-36080247-G-A | not specified | Likely benign (Jan 04, 2022) | ||
4-36082257-T-C | not specified | Uncertain significance (Dec 01, 2022) | ||
4-36082273-C-T | not specified | Uncertain significance (Dec 20, 2021) | ||
4-36083378-G-A | not specified | Uncertain significance (Jan 08, 2024) | ||
4-36083401-C-T | not specified | Uncertain significance (May 26, 2022) | ||
4-36091884-C-T | Likely benign (Feb 01, 2023) | |||
4-36091909-C-T | not specified | Uncertain significance (May 06, 2022) | ||
4-36091930-C-T | not specified | Uncertain significance (Sep 06, 2022) | ||
4-36091931-G-A | not specified | Uncertain significance (Nov 09, 2021) | ||
4-36107583-T-C | not specified | Uncertain significance (Aug 13, 2021) | ||
4-36107589-C-T | not specified | Uncertain significance (Apr 01, 2024) | ||
4-36107607-C-T | not specified | Uncertain significance (Jan 20, 2023) | ||
4-36107613-G-C | not specified | Uncertain significance (Nov 17, 2023) | ||
4-36107649-G-A | not specified | Uncertain significance (Mar 30, 2024) | ||
4-36107675-T-C | not specified | Uncertain significance (Mar 15, 2024) | ||
4-36114203-C-G | not specified | Uncertain significance (Mar 01, 2024) | ||
4-36114223-G-T | not specified | Uncertain significance (May 26, 2023) | ||
4-36114251-C-T | not specified | Uncertain significance (Nov 07, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ARAP2 | protein_coding | protein_coding | ENST00000303965 | 32 | 296289 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
8.77e-14 | 1.00 | 125638 | 1 | 109 | 125748 | 0.000437 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.820 | 923 | 856 | 1.08 | 0.0000430 | 11223 |
Missense in Polyphen | 183 | 204.86 | 0.89328 | 2817 | ||
Synonymous | -0.477 | 316 | 305 | 1.03 | 0.0000156 | 3112 |
Loss of Function | 4.99 | 38 | 88.7 | 0.428 | 0.00000475 | 1138 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000803 | 0.000799 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000229 | 0.000217 |
Finnish | 0.000285 | 0.000277 |
European (Non-Finnish) | 0.000598 | 0.000571 |
Middle Eastern | 0.000229 | 0.000217 |
South Asian | 0.000370 | 0.000359 |
Other | 0.000343 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Phosphatidylinositol 3,4,5-trisphosphate-dependent GTPase-activating protein that modulates actin cytoskeleton remodeling by regulating ARF and RHO family members. Is activated by phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) binding. Can be activated by phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4,5)P2) binding, albeit with lower efficiency (By similarity). {ECO:0000250}.;
- Pathway
- Endocytosis - Homo sapiens (human);Signal Transduction;rho cell motility signaling pathway;t cell receptor signaling pathway;rac1 cell motility signaling pathway;Rho GTPase cycle;adp-ribosylation factor;Signaling by Rho GTPases;Arf6 signaling events
(Consensus)
Intolerance Scores
- loftool
- 0.897
- rvis_EVS
- -0.18
- rvis_percentile_EVS
- 40.17
Haploinsufficiency Scores
- pHI
- 0.150
- hipred
- N
- hipred_score
- 0.448
- ghis
- 0.589
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.162
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Arap2
- Phenotype
- immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
- Cellular component
- cytosol
- Molecular function
- GTPase activator activity;phosphatidylinositol-3,4,5-trisphosphate binding;metal ion binding