ARHGEF12
Rho guanine nucleotide exchange factor 12, the group of Dbl family Rho GEFs|PDZ domain containing
Basic information
Region (hg38): 11:120336413-120489937
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (125 variants)
- not_provided (8 variants)
- Glaucoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGEF12 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015313.3. 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 | 5 | |||||
| missense | 122 | 127 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 123 | 7 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARHGEF12 | protein_coding | protein_coding | ENST00000397843 | 41 | 152859 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 1.00e-8 | 124776 | 0 | 20 | 124796 | 0.0000801 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.25 | 572 | 836 | 0.684 | 0.0000456 | 10095 |
| Missense in Polyphen | 94 | 221.36 | 0.42464 | 2610 | ||
| Synonymous | 1.50 | 258 | 291 | 0.888 | 0.0000149 | 2916 |
| Loss of Function | 8.08 | 10 | 94.9 | 0.105 | 0.00000517 | 1131 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000246 | 0.000246 |
| Ashkenazi Jewish | 0.000100 | 0.0000993 |
| East Asian | 0.000223 | 0.000223 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000625 | 0.0000618 |
| Middle Eastern | 0.000223 | 0.000223 |
| South Asian | 0.0000654 | 0.0000654 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May play a role in the regulation of RhoA GTPase by guanine nucleotide-binding alpha-12 (GNA12) and alpha-13 (GNA13). Acts as guanine nucleotide exchange factor (GEF) for RhoA GTPase and may act as GTPase-activating protein (GAP) for GNA12 and GNA13. {ECO:0000269|PubMed:11094164}.;
- Pathway
- Platelet activation - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Axon guidance - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Developmental Biology;Signaling by GPCR;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;Sema4D induced cell migration and growth-cone collapse;Sema4D in semaphorin signaling;NRAGE signals death through JNK;Semaphorin interactions;Death Receptor Signalling;p75 NTR receptor-mediated signalling;Axon guidance;G alpha (12/13) signalling events;GPCR downstream signalling;Cell death signalling via NRAGE, NRIF and NADE;Regulation of RhoA activity
(Consensus)
Intolerance Scores
- loftool
- 0.241
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 30.94
Haploinsufficiency Scores
- pHI
- 0.471
- hipred
- Y
- hipred_score
- 0.822
- ghis
- 0.541
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Arhgef12
- Phenotype
- immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); hematopoietic 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); embryo phenotype; cellular phenotype; muscle phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- G protein-coupled receptor signaling pathway;Rho protein signal transduction;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;membrane;extracellular exosome
- Molecular function
- G protein-coupled receptor binding;guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;GTPase activator activity;protein binding