ARHGEF18

protein-coding

Rho/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

NM_001367823.1

Inheritance

AR, AD

ClinVar variants

P:31U:487B:347

Top phenotype

Retinitis pigmentosa 78

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr19:7,348,937-7,472,485

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~123.5 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosa 78STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0044314

Submitter: PanelApp Australia

retinitis pigmentosa 78LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0044314

Submitter: G2P

retinitis pigmentosa 78STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0044314

Submitter: Labcorp Genetics (formerly Invitae)

retinitis pigmentosaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019200

Submitter: Orphanet

inherited retinal dystrophyMODERATE

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)

Retinitis pigmentosa 78AR

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

Refs: 28132693Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ARHGEF18 variants in ClinVar

8 Conditions Cataloged
not providedTotal: 1032
Inborn genetic diseasesTotal: 223
not specifiedTotal: 178
ARHGEF18-related disorderTotal: 40
Retinitis pigmentosa 78Total: 23
Retinal dystrophyTotal: 10
Optic atrophyTotal: 2
Autosomal recessive retinitis pigmentosaTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
8
clinvar
298
clinvar
5
clinvar
311
missense
1
clinvar
466
clinvar
37
clinvar
7
clinvar
511
nonsense
8
clinvar
4
clinvar
3
clinvar
15
start loss
0
frameshift
3
clinvar
10
clinvar
2
clinvar
15
splice donor/acceptor (+/-2bp)
5
clinvar
8
clinvar
13
Total112048733512865

Highest pathogenic variant AF is 0.000102873826

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001367823.1RefSeqNP_001354752.128MANE Select
ENST00000668164.2EnsemblENSP00000499655.228MANE Select
NM_001130955.2RefSeqNP_001124427.219Standard
NM_001367824.1RefSeqNP_001354753.119Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
arhgef18bDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.255687400.7670.00005167544
Missense (PolyPhen)175249.760.700682556
Synonymous0.6433193340.9550.00002592378
Loss of Function4.651550.80.2960.00000243585

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000710.00062rare
Latino/Admixed American0.000150.00014rare
Ashkenazi Jewish0.000210.00020rare
East Asian0.000110.00011rare
Finnish0.000100.000092rare
European (Non-Finnish)0.000170.00017rare
South Asian0.000130.00013rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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