ARHGEF7
Rho guanine nucleotide exchange factor 7, the group of Pleckstrin homology domain containing|Dbl family Rho GEFs
Basic information
Region (hg38): 13:111114559-111305737
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (67 variants)
- not_provided (18 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGEF7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001354046.2. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 11 | 14 | ||||
| missense | 65 | 69 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 65 | 7 | 11 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARHGEF7 | protein_coding | protein_coding | ENST00000375741 | 20 | 191179 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000461 | 125742 | 0 | 6 | 125748 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.57 | 313 | 470 | 0.666 | 0.0000278 | 5214 |
| Missense in Polyphen | 90 | 174.92 | 0.51452 | 1863 | ||
| Synonymous | 0.197 | 186 | 189 | 0.982 | 0.0000120 | 1550 |
| Loss of Function | 5.54 | 3 | 41.5 | 0.0723 | 0.00000184 | 527 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000546 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000363 | 0.0000352 |
| Middle Eastern | 0.0000546 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as a RAC1 guanine nucleotide exchange factor (GEF) and can induce membrane ruffling. Functions in cell migration, attachment and cell spreading. Promotes targeting of RAC1 to focal adhesions (By similarity). May function as a positive regulator of apoptosis. Downstream of NMDA receptors and CaMKK-CaMK1 signaling cascade, promotes the formation of spines and synapses in hippocampal neurons. {ECO:0000250, ECO:0000269|PubMed:18184567, ECO:0000269|PubMed:18716323, ECO:0000269|PubMed:19041750}.;
- Pathway
- Regulation of actin cytoskeleton - Homo sapiens (human);Intracellular Signalling Through Adenosine Receptor A2b and Adenosine;Intracellular Signalling Through Adenosine Receptor A2a and Adenosine;Integrin-mediated Cell Adhesion;Regulation of Actin Cytoskeleton;Developmental Biology;Signaling by GPCR;Signal Transduction;EPH-Ephrin signaling;TCR;Ephrin signaling;Rho GTPase cycle;Aurora A signaling;EGFR downregulation;Signaling by EGFR;Signaling by Rho GTPases;EGFR1;agrin in postsynaptic differentiation;Regulation of RAC1 activity;NRAGE signals death through JNK;Death Receptor Signalling;p75 NTR receptor-mediated signalling;Axon guidance;G alpha (12/13) signalling events;Integrin-linked kinase signaling;Signaling by Receptor Tyrosine Kinases;GPCR downstream signalling;Regulation of CDC42 activity;CDC42 signaling events;Internalization of ErbB1;Signaling events mediated by focal adhesion kinase;Cell death signalling via NRAGE, NRIF and NADE
(Consensus)
Recessive Scores
- pRec
- 0.624
Intolerance Scores
- loftool
- 0.444
- rvis_EVS
- -1.04
- rvis_percentile_EVS
- 7.8
Haploinsufficiency Scores
- pHI
- 0.224
- hipred
- Y
- hipred_score
- 0.745
- ghis
- 0.577
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.894
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Arhgef7
- 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); homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- arhgef7b
- Affected structure
- leukocyte
- Phenotype tag
- abnormal
- Phenotype quality
- accumulation
Gene ontology
- Biological process
- hematopoietic progenitor cell differentiation;Golgi organization;signal transduction;G protein-coupled receptor signaling pathway;nervous system development;positive regulation of fibroblast migration;lamellipodium assembly;positive regulation of protein binding;regulation of Rho protein signal transduction;intracellular signal transduction;negative regulation of epidermal growth factor receptor signaling pathway;positive regulation of apoptotic process;positive regulation of GTPase activity;ephrin receptor signaling pathway;focal adhesion assembly;regulation of small GTPase mediated signal transduction;positive regulation of growth hormone secretion;positive regulation of substrate adhesion-dependent cell spreading;regulation of GTP binding;positive regulation of lamellipodium morphogenesis
- Cellular component
- storage vacuole;ruffle;cytosol;plasma membrane;focal adhesion;cell cortex;lamellipodium;protein-containing complex;neuron projection;neuronal cell body
- Molecular function
- guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;protein binding;protein kinase binding