ABI1
abl interactor 1
Basic information
Region (hg38): 10:26746593-26861087
Previous symbols: [ "SSH3BP1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (34 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABI1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001012750.3. 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 | 2 | |||||
| missense | 30 | 31 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 30 | 2 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ABI1 | protein_coding | protein_coding | ENST00000376142 | 12 | 114495 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.639 | 0.361 | 125696 | 0 | 4 | 125700 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.09 | 182 | 281 | 0.648 | 0.0000138 | 3268 |
| Missense in Polyphen | 49 | 97.349 | 0.50334 | 1215 | ||
| Synonymous | -0.195 | 101 | 98.5 | 1.03 | 0.00000481 | 1055 |
| Loss of Function | 3.72 | 5 | 25.1 | 0.199 | 0.00000135 | 291 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.000207 | 0.000198 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000395 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May act in negative regulation of cell growth and transformation by interacting with nonreceptor tyrosine kinases ABL1 and/or ABL2. May play a role in regulation of EGF-induced Erk pathway activation. Involved in cytoskeletal reorganization and EGFR signaling. Together with EPS8 participates in transduction of signals from Ras to Rac. In vitro, a trimeric complex of ABI1, EPS8 and SOS1 exhibits Rac specific guanine nucleotide exchange factor (GEF) activity and ABI1 seems to act as an adapter in the complex. Regulates ABL1/c-Abl-mediated phosphorylation of ENAH. Recruits WASF1 to lamellipodia and there seems to regulate WASF1 protein level. In brain, seems to regulate the dendritic outgrowth and branching as well as to determine the shape and number of synaptic contacts of developing neurons. {ECO:0000269|PubMed:11003655, ECO:0000269|PubMed:18328268}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving ABI1 is a cause of acute leukemias. Translocation t(10;11)(p11.2;q23) with KMT2A/MLL1. ABI1 isoform 2 was found to be present in acute leukemia KMT2A/MLL1-ABI1 fusion transcript. {ECO:0000269|PubMed:9694699}.;
- Pathway
- EGF-EGFR Signaling Pathway;Signal Transduction;VEGFA-VEGFR2 Pathway;Fcgamma receptor (FCGR) dependent phagocytosis;Innate Immune System;Immune System;RHO GTPases Activate WASPs and WAVEs;RHO GTPase Effectors;Signaling by Rho GTPases;EGFR1;Regulation of RAC1 activity;ErbB1 downstream signaling;Regulation of actin dynamics for phagocytic cup formation;Signaling by VEGF;Signaling by Receptor Tyrosine Kinases;Stabilization and expansion of the E-cadherin adherens junction;RAC1 signaling pathway;Alpha4 beta1 integrin signaling events;PDGFR-beta signaling pathway;E-cadherin signaling in the nascent adherens junction
(Consensus)
Recessive Scores
- pRec
- 0.297
Intolerance Scores
- loftool
- 0.0520
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.69
Haploinsufficiency Scores
- pHI
- 0.524
- hipred
- Y
- hipred_score
- 0.745
- ghis
- 0.662
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.707
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Abi1
- 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); immune system phenotype; embryo phenotype; growth/size/body region phenotype; 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); 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); craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- somitogenesis;transmembrane receptor protein tyrosine kinase signaling pathway;actin polymerization or depolymerization;negative regulation of cell population proliferation;viral process;peptidyl-tyrosine phosphorylation;megakaryocyte development;Fc-gamma receptor signaling pathway involved in phagocytosis;vascular endothelial growth factor receptor signaling pathway;dendrite morphogenesis;positive regulation of protein tyrosine kinase activity;lamellipodium morphogenesis
- Cellular component
- nucleus;endoplasmic reticulum;cytosol;cytoskeleton;postsynaptic density;lamellipodium;cell junction;growth cone;SCAR complex;filopodium tip;postsynaptic membrane;extracellular exosome
- Molecular function
- protein binding;cytoskeletal protein binding;SH3 domain binding;protein tyrosine kinase activator activity;cadherin binding