ABR
ABR activator of RhoGEF and GTPase, the group of Dbl family Rho GEFs|Pleckstrin homology domain containing|MicroRNA protein coding host genes|C2 domain containing
Basic information
Region (hg38): 17:1003519-1229738
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (81 variants)
- not_provided (3 variants)
- ABR-related_disorder (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABR gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021962.5. 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 | 3 | |||||
| missense | 80 | 82 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 80 | 4 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ABR | protein_coding | protein_coding | ENST00000302538 | 23 | 225558 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.627 | 0.373 | 125732 | 0 | 16 | 125748 | 0.0000636 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.89 | 269 | 518 | 0.519 | 0.0000315 | 5631 |
| Missense in Polyphen | 84 | 187.35 | 0.44836 | 1947 | ||
| Synonymous | -0.521 | 239 | 229 | 1.04 | 0.0000158 | 1631 |
| Loss of Function | 5.00 | 10 | 47.0 | 0.213 | 0.00000226 | 559 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000616 | 0.0000615 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000464 | 0.0000462 |
| European (Non-Finnish) | 0.0000913 | 0.0000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: GTPase-activating protein for RAC and CDC42. Promotes the exchange of RAC or CDC42-bound GDP by GTP, thereby activating them.;
- Pathway
- Signaling by GPCR;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;Regulation of RAC1 activity;NRAGE signals death through JNK;Death Receptor Signalling;p75 NTR receptor-mediated signalling;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
- 0.319
- rvis_EVS
- -1.04
- rvis_percentile_EVS
- 7.8
Haploinsufficiency Scores
- pHI
- 0.593
- hipred
- Y
- hipred_score
- 0.774
- ghis
- 0.541
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.528
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Abr
- Phenotype
- cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); hearing/vestibular/ear 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); normal phenotype;
Gene ontology
- Biological process
- negative regulation of cellular extravasation;G protein-coupled receptor signaling pathway;small GTPase mediated signal transduction;brain development;actin cytoskeleton organization;response to lipopolysaccharide;regulation of Rho protein signal transduction;inner ear morphogenesis;positive regulation of apoptotic process;regulation of vascular permeability;negative regulation of neutrophil degranulation;positive regulation of GTPase activity;negative regulation of inflammatory response;positive regulation of phagocytosis;modulation of chemical synaptic transmission;neuromuscular process controlling balance;regulation of small GTPase mediated signal transduction;negative regulation of blood vessel remodeling
- Cellular component
- cytosol;plasma membrane;membrane;Schaffer collateral - CA1 synapse;glutamatergic synapse
- Molecular function
- guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;GTPase activator activity