ARHGDIB
protein-codingRho GDP dissociation inhibitor beta, the group of Receptor ligands|Minor histocompatibility antigens
Gene summary
Members of the Rho (or ARH) protein family (see MIM 165390) and other Ras-related small GTP-binding proteins (see MIM 179520) are involved in diverse cellular events, including cell signaling, proliferation, cytoskeletal organization, and secretion. The GTP-binding proteins are active only in the GTP-bound state. At least 3 classes of proteins tightly regulate cycling between the GTP-bound and GDP-bound states: GTPase-activating proteins (GAPs), guanine nucleotide-releasing factors (GRFs), and GDP-dissociation inhibitors (GDIs). The GDIs, including ARHGDIB, decrease the rate of GDP dissociation from Ras-like GTPases (summary by Scherle et al., 1993 [PubMed 8356058]).[supplied by OMIM, Dec 2010]
- RAP1GN1
- GDIA2
- GDID4
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~19.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ARHGDIB variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001175.7. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 24 | 24 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 27 | 0 | 0 | 27 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001166.3 | 5 | MANE Select | |
| Ensembl | ENSP00000228945.4 | 5 | MANE Select | |
| RefSeq | NP_001308349.1 | 5 | Standard | |
| RefSeq | NP_001308350.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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
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
Molecular Function
- GTPase activity
- Rho GDP-dissociation inhibitor activity
- GTPase activator activity
- protein binding
- Rac GTPase binding
Cellular Component
- cytoplasm
- cytosol
- cytoskeleton
- membrane
- cytoplasmic vesicle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000228945
- Coding exons
- 5
- Length
- 19712
- Individuals with no LoFs
- 125733
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 13
- Defined
- 125747
- p
- 0.0000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0438 | 111 | 112 | 0.988 | 0.00000601 | 1322 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00011 | 0.000097 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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}.;
Recessive Scores
- pRec
- 0.157
Intolerance Scores
- LoFtool
- 0.350
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 49.76
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.987
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |