ARHGEF18
protein-codingRho/Rac guanine nucleotide exchange factor 18, the group of Pleckstrin homology domain containing|Dbl family Rho GEFs
Gene summary
Rho GTPases are GTP binding proteins that regulate a wide spectrum of cellular functions. These cellular processes include cytoskeletal rearrangements, gene transcription, cell growth and motility. Activation of Rho GTPases is under the direct control of guanine nucleotide exchange factors (GEFs). The protein encoded by this gene is a guanine nucleotide exchange factor and belongs to the Rho GTPase GEF family. Family members share a common feature, a Dbl (DH) homology domain followed by a pleckstrin (PH) homology domain. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Nov 2018]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~123.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0044314
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0044314
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0044314
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0019200
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0019118
Submitter: ClinGen
*ARHGEF18* was first described as a retinitis pigmentosa-associated gene in 2017 (Arno et al. 2017, PMID: 28132693). The specific disease entity, retinitis pigmentosa 78 (MIM#: 617433), is one of at least 90 reported forms of retinopathy referred to as retinitis pigmentosa. Some of the most common patient phenotypes include; reduced visual acuity, nyctalopia, optic disc pallor, cystoid macular edema, and photopsia, often with diagnosis in adulthood. For the purposes of this gene curation, cases were lumped under the more inclusive disease term "ARHGEF18-related retinopathy", to acknowledge the potential for a broader spectrum of disease to emerge in association with variants in this gene. This curation includes five variants: (1 missense, 2 nonsense, 1 In-frame multiple-codon deletion, and 1 disrupting splicing) that have collectively been reported in 3 probands in 1 publication (PMID: 28132693). An additional proband harboring two variants in *ARHGEF18* has been considered for inclusion but not scored (PMID: 37217489). Overall, the mechanism of pathogenicity appears to be biallelic loss of function, as shown in the variant types found in the probands. This gene-disease relationship is also supported by multiple forms of experimental evidence including animal models and rescue experiments in medaka fish (PMID: 23698346) and studies characterizing the biochemical function of ARHGEF18. Expression of ARHGEF18 activates RhoA and Rac1 but not cdc42, while ARHGEF18 deletion stops the activation of RhoA and Rac1, indicating a role as a specific guanine nucleotide exchange factor in the pathway establishing apicobasal polarity (PMID: 23698346). Two medaka fish models were generated by chemical mutagenesis screening for defects of retinal epithelial polarity, and were identified with loss-of-function mutations in the *ArhGEF18* gene (PMID: 23698346). The models exhibited aberrant retinal morphologies and retinal pigmentation as well as profound disruption of retinal lamination and retinal polarity. This was recapitulated by morpholino-based silencing of the *ArhGEF18* gene, and could be rescued by injection of mRNA encoding either medaka or human *ARHGEF18* (PMID: 23698346). The concurrence of both rescue models suggests that ARHGEF18 function is conserved throughout vertebrates. These experiments show that ARHGEF18 controls retinal layer organization, which could be related to its role in contributing to cell polarity. In conclusion, ARHGEF18 has moderate evidence of association with ARHGEF18-related retinopathy. This classification has been clearly demonstrated and confirmed through both experimental and genetic evidence and has been upheld over time without the emergence of contradictory evidence. The publication of additional case reports will be critical for this gene-disease relationship to reach a more definitive classification. This classification was approved by the Retina GCEP on November 7th, 2024 (SOP Version 10).
Clinical Genomic Database (CGD)
Manifestation: Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ARHGEF18 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001367823.1. 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 | 8 | 298 | 5 | 311 | ||
| missense | 1 | 466 | 37 | 7 | 511 | |
| nonsense | 8 | 4 | 3 | 15 | ||
| start loss | 0 | |||||
| frameshift | 3 | 10 | 2 | 15 | ||
| splice donor/acceptor (+/-2bp) | 5 | 8 | 13 | |||
| Total | 11 | 20 | 487 | 335 | 12 | 865 |
Highest pathogenic variant AF is 0.000102873826
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001354752.1 | 28 | MANE Select | |
| Ensembl | ENSP00000499655.2 | 28 | MANE Select | |
| RefSeq | NP_001124427.2 | 19 | Standard | |
| RefSeq | NP_001354753.1 | 19 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| arhgef18b | Danio rerio | Structure: otolith Quality: morphology abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Tight junction - Homo sapiens (human)
- Signaling by GPCR
- Signal Transduction
- Rho GTPase cycle
- Signaling by Rho GTPases
Biological Process
- transforming growth factor beta receptor signaling pathway
- G protein-coupled receptor signaling pathway
- small GTPase mediated signal transduction
- regulation of cell shape
- actin cytoskeleton organization
Molecular Function
- nucleic acid binding
- guanyl-nucleotide exchange factor activity
- Rho guanyl-nucleotide exchange factor activity
- metal ion binding
Cellular Component
- cytosol
- cytoskeleton
- plasma membrane
- apical plasma membrane
- cell junction
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000359920
- Coding exons
- 19
- Length
- 77365
- Individuals with no LoFs
- 125704
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 44
- Defined
- 125748
- p
- 0.000175
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.25 | 568 | 740 | 0.767 | 0.0000516 | 7544 |
| Missense (PolyPhen) | 175 | 249.76 | 0.70068 | 2556 | ||
| Synonymous | 0.643 | 319 | 334 | 0.955 | 0.0000259 | 2378 |
| Loss of Function | 4.65 | 15 | 50.8 | 0.296 | 0.00000243 | 585 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00071 | 0.00062 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0.00021 | 0.00020 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00010 | 0.000092 | rare |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts as guanine nucleotide exchange factor (GEF) for RhoA GTPases. Its activation induces formation of actin stress fibers. Also acts as a GEF for RAC1, inducing production of reactive oxygen species (ROS). Does not act as a GEF for CDC42. The G protein beta-gamma (Gbetagamma) subunits of heterotrimeric G proteins act as activators, explaining the integrated effects of LPA and other G-protein coupled receptor agonists on actin stress fiber formation, cell shape change and ROS production. Required for EPB41L4B-mediated regulation of the circumferential actomyosin belt in epithelial cells (PubMed:22006950). {ECO:0000269|PubMed:11085924, ECO:0000269|PubMed:14512443, ECO:0000269|PubMed:15558029, ECO:0000269|PubMed:22006950, ECO:0000269|PubMed:28132693}.;
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- LoFtool
- 0.409
- RVIS EVS
- 0.66
- RVIS percentile EVS
- 84.19
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.844
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |