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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:ABL1-PALM2-AKAP2 (FusionGDB2 ID:HG25TG445815)

Fusion Gene Summary for ABL1-PALM2-AKAP2

check button Fusion gene summary
Fusion gene informationFusion gene name: ABL1-PALM2-AKAP2
Fusion gene ID: hg25tg445815
HgeneTgene
Gene symbol

ABL1

PALM2-AKAP2

Gene ID

25

445815

Gene nameABL proto-oncogene 1, non-receptor tyrosine kinasePALM2 and AKAP2 fusion
SynonymsABL|BCR-ABL|CHDSKM|JTK7|bcr/abl|c-ABL|c-ABL1|p150|v-ablAKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PALM2-AKAP2|PRKA2
Cytomap('ABL1')('PALM2-AKAP2')

9q34.12

9q31.3

Type of geneprotein-codingprotein-coding
Descriptiontyrosine-protein kinase ABL1ABL protooncogene 1 nonreceptor tyrosine kinaseAbelson tyrosine-protein kinase 1bcr/c-abl oncogene proteinc-abl oncogene 1, receptor tyrosine kinaseproto-oncogene c-Ablproto-oncogene tyrosine-protein kinase ABL1truncatedA-kinase anchor protein 2PALM2-AKAP2 proteinparalemmin-2A kinase (PRKA) anchor protein 2A-kinase anchoring protein 2PALM2-AKAP2 fusionPALM2-AKAP2 readthroughparalemmin 2protein kinase A anchoring protein 2protein kinase A2
Modification date2020032720200313
UniProtAcc

P00519

.
Ensembl transtripts involved in fusion geneENST00000318560, 
Fusion gene scores* DoF score21 X 55 X 13=1501518 X 17 X 5=1530
# samples 6819
** MAII scorelog2(68/15015*10)=-4.46472591830681
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(19/1530*10)=-3.00946032924907
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ABL1 [Title/Abstract] AND PALM2-AKAP2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointABL1(133694977)-PALM2-AKAP2(112812941), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneABL1

GO:0006974

cellular response to DNA damage stimulus

15657060

HgeneABL1

GO:0006975

DNA damage induced protein phosphorylation

18280240

HgeneABL1

GO:0018108

peptidyl-tyrosine phosphorylation

7590236|9144171|10713049|11121037

HgeneABL1

GO:0038083

peptidyl-tyrosine autophosphorylation

10518561

HgeneABL1

GO:0042770

signal transduction in response to DNA damage

9037071|15657060

HgeneABL1

GO:0043065

positive regulation of apoptotic process

9037071

HgeneABL1

GO:0046777

protein autophosphorylation

10713049

HgeneABL1

GO:0050731

positive regulation of peptidyl-tyrosine phosphorylation

15657060

HgeneABL1

GO:0051353

positive regulation of oxidoreductase activity

12893824

HgeneABL1

GO:0051444

negative regulation of ubiquitin-protein transferase activity

20823226

HgeneABL1

GO:0070301

cellular response to hydrogen peroxide

10713049

HgeneABL1

GO:0071103

DNA conformation change

9558345

HgeneABL1

GO:0071901

negative regulation of protein serine/threonine kinase activity

11121037

HgeneABL1

GO:1990051

activation of protein kinase C activity

10713049

HgeneABL1

GO:2001020

regulation of response to DNA damage stimulus

9461559



check button Fusion gene information
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand


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Fusion Gene ORF analysis for ABL1-PALM2-AKAP2

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for ABL1-PALM2-AKAP2


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for ABL1-PALM2-AKAP2


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:133694977/:112812941)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
ABL1

P00519

.
FUNCTION: Non-receptor tyrosine-protein kinase that plays a role in many key processes linked to cell growth and survival such as cytoskeleton remodeling in response to extracellular stimuli, cell motility and adhesion, receptor endocytosis, autophagy, DNA damage response and apoptosis. Coordinates actin remodeling through tyrosine phosphorylation of proteins controlling cytoskeleton dynamics like WASF3 (involved in branch formation); ANXA1 (involved in membrane anchoring); DBN1, DBNL, CTTN, RAPH1 and ENAH (involved in signaling); or MAPT and PXN (microtubule-binding proteins). Phosphorylation of WASF3 is critical for the stimulation of lamellipodia formation and cell migration. Involved in the regulation of cell adhesion and motility through phosphorylation of key regulators of these processes such as BCAR1, CRK, CRKL, DOK1, EFS or NEDD9. Phosphorylates multiple receptor tyrosine kinases and more particularly promotes endocytosis of EGFR, facilitates the formation of neuromuscular synapses through MUSK, inhibits PDGFRB-mediated chemotaxis and modulates the endocytosis of activated B-cell receptor complexes. Other substrates which are involved in endocytosis regulation are the caveolin (CAV1) and RIN1. Moreover, ABL1 regulates the CBL family of ubiquitin ligases that drive receptor down-regulation and actin remodeling. Phosphorylation of CBL leads to increased EGFR stability. Involved in late-stage autophagy by regulating positively the trafficking and function of lysosomal components. ABL1 targets to mitochondria in response to oxidative stress and thereby mediates mitochondrial dysfunction and cell death. In response to oxidative stress, phosphorylates serine/threonine kinase PRKD2 at 'Tyr-717' (PubMed:28428613). ABL1 is also translocated in the nucleus where it has DNA-binding activity and is involved in DNA-damage response and apoptosis. Many substrates are known mediators of DNA repair: DDB1, DDB2, ERCC3, ERCC6, RAD9A, RAD51, RAD52 or WRN. Activates the proapoptotic pathway when the DNA damage is too severe to be repaired. Phosphorylates TP73, a primary regulator for this type of damage-induced apoptosis. Phosphorylates the caspase CASP9 on 'Tyr-153' and regulates its processing in the apoptotic response to DNA damage. Phosphorylates PSMA7 that leads to an inhibition of proteasomal activity and cell cycle transition blocks. ABL1 acts also as a regulator of multiple pathological signaling cascades during infection. Several known tyrosine-phosphorylated microbial proteins have been identified as ABL1 substrates. This is the case of A36R of Vaccinia virus, Tir (translocated intimin receptor) of pathogenic E.coli and possibly Citrobacter, CagA (cytotoxin-associated gene A) of H.pylori, or AnkA (ankyrin repeat-containing protein A) of A.phagocytophilum. Pathogens can highjack ABL1 kinase signaling to reorganize the host actin cytoskeleton for multiple purposes, like facilitating intracellular movement and host cell exit. Finally, functions as its own regulator through autocatalytic activity as well as through phosphorylation of its inhibitor, ABI1. Regulates T-cell differentiation in a TBX21-dependent manner. Phosphorylates TBX21 on tyrosine residues leading to an enhancement of its transcriptional activator activity (By similarity). {ECO:0000250|UniProtKB:P00520, ECO:0000269|PubMed:10391250, ECO:0000269|PubMed:11971963, ECO:0000269|PubMed:12379650, ECO:0000269|PubMed:12531427, ECO:0000269|PubMed:12672821, ECO:0000269|PubMed:15031292, ECO:0000269|PubMed:15556646, ECO:0000269|PubMed:15657060, ECO:0000269|PubMed:15886098, ECO:0000269|PubMed:16424036, ECO:0000269|PubMed:16678104, ECO:0000269|PubMed:16943190, ECO:0000269|PubMed:17306540, ECO:0000269|PubMed:17623672, ECO:0000269|PubMed:18328268, ECO:0000269|PubMed:18945674, ECO:0000269|PubMed:19891780, ECO:0000269|PubMed:20357770, ECO:0000269|PubMed:20417104, ECO:0000269|PubMed:28428613, ECO:0000269|PubMed:9037071, ECO:0000269|PubMed:9144171, ECO:0000269|PubMed:9461559}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for ABL1-PALM2-AKAP2


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for ABL1-PALM2-AKAP2


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for ABL1-PALM2-AKAP2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneABL1P00519DB00619ImatinibInhibitorSmall moleculeApproved
HgeneABL1P00519DB00619ImatinibInhibitorSmall moleculeApproved
HgeneABL1P00519DB00619ImatinibInhibitorSmall moleculeApproved
HgeneABL1P00519DB06616BosutinibInhibitorSmall moleculeApproved
HgeneABL1P00519DB06616BosutinibInhibitorSmall moleculeApproved
HgeneABL1P00519DB06616BosutinibInhibitorSmall moleculeApproved
HgeneABL1P00519DB08896RegorafenibInhibitorSmall moleculeApproved
HgeneABL1P00519DB08896RegorafenibInhibitorSmall moleculeApproved
HgeneABL1P00519DB08896RegorafenibInhibitorSmall moleculeApproved
HgeneABL1P00519DB01254DasatinibMultitargetSmall moleculeApproved|Investigational
HgeneABL1P00519DB01254DasatinibMultitargetSmall moleculeApproved|Investigational
HgeneABL1P00519DB01254DasatinibMultitargetSmall moleculeApproved|Investigational
HgeneABL1P00519DB04868NilotinibInhibitorSmall moleculeApproved|Investigational
HgeneABL1P00519DB04868NilotinibInhibitorSmall moleculeApproved|Investigational
HgeneABL1P00519DB04868NilotinibInhibitorSmall moleculeApproved|Investigational
HgeneABL1P00519DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
HgeneABL1P00519DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
HgeneABL1P00519DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
HgeneABL1P00519DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
HgeneABL1P00519DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
HgeneABL1P00519DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
HgeneABL1P00519DB12267BrigatinibInhibitorSmall moleculeApproved|Investigational
HgeneABL1P00519DB12267BrigatinibInhibitorSmall moleculeApproved|Investigational
HgeneABL1P00519DB12267BrigatinibInhibitorSmall moleculeApproved|Investigational

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Related Diseases for ABL1-PALM2-AKAP2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneABL1C0023473Myeloid Leukemia, Chronic3CGI;CTD_human;ORPHANET
HgeneABL1C0023452Childhood Acute Lymphoblastic Leukemia2CTD_human
HgeneABL1C0023453L2 Acute Lymphoblastic Leukemia2CTD_human
HgeneABL1C1961102Precursor Cell Lymphoblastic Leukemia Lymphoma2CGI;CTD_human
HgeneABL1C0001418Adenocarcinoma1CTD_human
HgeneABL1C0003706Arachnodactyly1GENOMICS_ENGLAND
HgeneABL1C0005941Bone Diseases, Developmental1CTD_human
HgeneABL1C0006142Malignant neoplasm of breast1CTD_human
HgeneABL1C0006413Burkitt Lymphoma1ORPHANET
HgeneABL1C0014859Esophageal Neoplasms1CTD_human
HgeneABL1C0015544Failure to Thrive1CTD_human
HgeneABL1C0018798Congenital Heart Defects1CTD_human
HgeneABL1C0023903Liver neoplasms1CTD_human
HgeneABL1C0027659Neoplasms, Experimental1CTD_human
HgeneABL1C0032927Precancerous Conditions1CTD_human
HgeneABL1C0039075Syndactyly1GENOMICS_ENGLAND
HgeneABL1C0151491Congenital musculoskeletal anomalies1CTD_human
HgeneABL1C0205641Adenocarcinoma, Basal Cell1CTD_human
HgeneABL1C0205642Adenocarcinoma, Oxyphilic1CTD_human
HgeneABL1C0205643Carcinoma, Cribriform1CTD_human
HgeneABL1C0205644Carcinoma, Granular Cell1CTD_human
HgeneABL1C0205645Adenocarcinoma, Tubular1CTD_human
HgeneABL1C0265610Clinodactyly of fingers1GENOMICS_ENGLAND
HgeneABL1C0282313Condition, Preneoplastic1CTD_human
HgeneABL1C0345904Malignant neoplasm of liver1CTD_human
HgeneABL1C0546837Malignant neoplasm of esophagus1CTD_human
HgeneABL1C0596263Carcinogenesis1CTD_human
HgeneABL1C0678222Breast Carcinoma1CTD_human
HgeneABL1C1257931Mammary Neoplasms, Human1CTD_human
HgeneABL1C1292769Precursor B-cell lymphoblastic leukemia1ORPHANET
HgeneABL1C1458155Mammary Neoplasms1CTD_human
HgeneABL1C1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1CGI;ORPHANET
HgeneABL1C4539857CONGENITAL HEART DEFECTS AND SKELETAL MALFORMATIONS SYNDROME1GENOMICS_ENGLAND;UNIPROT
HgeneABL1C4551485Clinodactyly1GENOMICS_ENGLAND
HgeneABL1C4704874Mammary Carcinoma, Human1CTD_human