ARHGEF1

Rho guanine nucleotide exchange factor 1, the group of Dbl family Rho GEFs

Basic information

Region (hg38): 19:41883173-41930150

Links

ENSG00000076928NCBI:9138OMIM:601855HGNC:681Uniprot:Q92888AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • immunodeficiency 62 (Limited), mode of inheritance: Unknown
  • immunodeficiency 62 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Immunodeficiency 62ARAllergy/Immunology/Infectious; OncologicThe condition can involve early-onset, recurrent, and severe infections and diagnosis may allow preventative measures and early and prompt treatment of infections (for example, with IVIG); Cancer has been described, and awareness of an increased risk may allow early diagnosis and managementAllergy/Immunology/Infectious; Oncologic30521495

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARHGEF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGEF1 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
3
clinvar
170
clinvar
5
clinvar
178
missense
311
clinvar
10
clinvar
2
clinvar
323
nonsense
1
clinvar
1
start loss
1
clinvar
1
frameshift
3
clinvar
3
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
30
42
10
82
non coding
4
clinvar
116
clinvar
11
clinvar
131
Total 0 0 326 296 18

Variants in ARHGEF1

This is a list of pathogenic ClinVar variants found in the ARHGEF1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
19-41884469-T-A Uncertain significance (Jan 08, 2025)1451068
19-41884477-C-T Uncertain significance (Sep 30, 2023)1367771
19-41884481-C-A Benign (Dec 05, 2024)1169555
19-41884481-C-G not specified Uncertain significance (Jan 24, 2024)3129001
19-41884490-G-A Uncertain significance (Oct 29, 2023)2891397
19-41884490-G-C Uncertain significance (Aug 08, 2024)3624827
19-41884504-C-A Likely benign (Aug 31, 2023)2876524
19-41884504-C-T Likely benign (Jul 29, 2022)2020148
19-41884506-G-A Likely benign (Apr 25, 2024)2111859
19-41884509-C-T Likely benign (Mar 31, 2023)2785720
19-41888051-C-G Likely benign (Jun 24, 2024)1636774
19-41888059-T-C ARHGEF1-related disorder Benign (Feb 03, 2025)1165766
19-41888060-C-T Likely benign (Mar 05, 2024)2096045
19-41888066-C-T Likely benign (Dec 09, 2024)1050715
19-41888067-T-C Likely benign (Nov 19, 2023)2697380
19-41888069-C-G Uncertain significance (May 01, 2023)3023433
19-41888073-G-A Likely benign (Jan 02, 2024)1982844
19-41888080-G-C Uncertain significance (Feb 17, 2024)2113428
19-41888082-G-C Uncertain significance (Aug 14, 2023)2896933
19-41888093-T-C Uncertain significance (Jun 12, 2024)3656327
19-41888094-C-T Likely benign (Jan 19, 2025)1649941
19-41888095-G-A Uncertain significance (Feb 17, 2024)1480892
19-41888099-G-A Uncertain significance (Oct 25, 2022)2060852
19-41888099-G-C Uncertain significance (Sep 29, 2024)1465275
19-41888102-G-C Uncertain significance (Sep 09, 2023)2759430

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ARHGEF1protein_codingprotein_codingENST00000337665 2847075
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.7680.2321257280201257480.0000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.834076020.6760.00004165945
Missense in Polyphen118209.80.562431995
Synonymous0.7012352490.9440.00001691902
Loss of Function5.371153.20.2070.00000269583

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002070.000207
Ashkenazi Jewish0.00009940.0000992
East Asian0.00005440.0000544
Finnish0.0001210.0000924
European (Non-Finnish)0.00006280.0000615
Middle Eastern0.00005440.0000544
South Asian0.00006590.0000653
Other0.0001740.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Seems to play a role in the regulation of RhoA GTPase by guanine nucleotide-binding alpha-12 (GNA12) and alpha-13 (GNA13) subunits. Acts as GTPase-activating protein (GAP) for GNA12 and GNA13, and as guanine nucleotide exchange factor (GEF) for RhoA GTPase. Activated G alpha 13/GNA13 stimulates the RhoGEF activity through interaction with the RGS-like domain. This GEF activity is inhibited by binding to activated GNA12. Mediates angiotensin-2- induced RhoA activation. {ECO:0000269|PubMed:20098430, ECO:0000269|PubMed:8810315, ECO:0000269|PubMed:9641915, ECO:0000269|PubMed:9641916}.;
Pathway
Platelet activation - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);G Protein Signaling Pathways;EGF-EGFR Signaling Pathway;Regulation of Actin Cytoskeleton;G13 Signaling Pathway;Signaling by GPCR;Signal Transduction;pkc-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase;rho cell motility signaling pathway;rac1 cell motility signaling pathway;Rho GTPase cycle;Signaling by Rho GTPases;NRAGE signals death through JNK;Thromboxane A2 receptor signaling;Death Receptor Signalling;p75 NTR receptor-mediated signalling;G alpha (12/13) signalling events;GPCR downstream signalling;PAR1-mediated thrombin signaling events;LPA receptor mediated events;Cell death signalling via NRAGE, NRIF and NADE;Regulation of RhoA activity (Consensus)

Recessive Scores

pRec
0.150

Intolerance Scores

loftool
0.217
rvis_EVS
-1.84
rvis_percentile_EVS
2.07

Haploinsufficiency Scores

pHI
0.109
hipred
Y
hipred_score
0.654
ghis
0.611

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.960

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Arhgef1
Phenotype
immune 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; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
G protein-coupled receptor signaling pathway;Rho protein signal transduction;cell population proliferation;regulation of Rho protein signal transduction;positive regulation of apoptotic process;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
Cellular component
cytoplasm;cytosol;plasma membrane
Molecular function
G protein-coupled receptor binding;RNA binding;guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;GTPase activator activity;protein binding