ARHGDIB
Basic information
Region (hg38): 12:14942031-14961728
Previous symbols: [ "RAP1GN1", "GDIA2", "GDID4" ]
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 ARHGDIB 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in ARHGDIB
This is a list of pathogenic ClinVar variants found in the ARHGDIB region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-14942683-G-A | not specified | Uncertain significance (Jan 26, 2022) | ||
| 12-14944778-T-G | not specified | Uncertain significance (Aug 12, 2021) | ||
| 12-14944829-T-C | not specified | Uncertain significance (Dec 02, 2022) | ||
| 12-14947944-G-T | not specified | Uncertain significance (Oct 06, 2023) | ||
| 12-14950538-C-T | not specified | Uncertain significance (Jun 11, 2021) | ||
| 12-14950605-C-A | not specified | Uncertain significance (Nov 17, 2022) | ||
| 12-14950705-T-C | not specified | Uncertain significance (Sep 20, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARHGDIB | protein_coding | protein_coding | ENST00000228945 | 5 | 19712 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000638 | 0.749 | 125733 | 1 | 13 | 125747 | 0.0000557 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0438 | 111 | 112 | 0.988 | 0.00000601 | 1322 |
| Missense in Polyphen | 26 | 33.246 | 0.78204 | 405 | ||
| Synonymous | -2.39 | 68 | 47.1 | 1.44 | 0.00000285 | 371 |
| Loss of Function | 0.954 | 6 | 9.11 | 0.659 | 4.66e-7 | 118 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000106 | 0.0000967 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Regulates the GDP/GTP exchange reaction of the Rho proteins by inhibiting the dissociation of GDP from them, and the subsequent binding of GTP to them (PubMed:8356058, PubMed:7512369). Regulates reorganization of the actin cytoskeleton mediated by Rho family members (PubMed:8262133). {ECO:0000269|PubMed:7512369, ECO:0000269|PubMed:8262133, ECO:0000269|PubMed:8356058}.;
- Pathway
- Neurotrophin signaling pathway - Homo sapiens (human);Vasopressin-regulated water reabsorption - Homo sapiens (human);Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation;G13 Signaling Pathway;Signal Transduction;caspase cascade in apoptosis;hiv-1 nef: negative effector of fas and tnf;TCR;Rho GTPase cycle;Signaling by Rho GTPases;d4gdi signaling pathway;Caspase Cascade in Apoptosis;Regulation of RhoA activity
(Consensus)
Recessive Scores
- pRec
- 0.157
Intolerance Scores
- loftool
- 0.350
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.76
Haploinsufficiency Scores
- pHI
- 0.185
- hipred
- N
- hipred_score
- 0.493
- ghis
- 0.575
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.987
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Arhgdib
- Phenotype
- endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; reproductive system phenotype; 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); hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- negative regulation of cell adhesion;Rho protein signal transduction;multicellular organism development;regulation of Rho protein signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction;cellular response to redox state;negative regulation of trophoblast cell migration;regulation of actin cytoskeleton reorganization
- Cellular component
- cytoplasm;cytosol;cytoskeleton;membrane;cytoplasmic vesicle;extracellular exosome
- Molecular function
- GTPase activity;Rho GDP-dissociation inhibitor activity;GTPase activator activity;protein binding;Rac GTPase binding