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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene Breakpoints

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Tumorigenic MoA (Mechanism of Action) Scenarios of Fusion Geness

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Fusion Genomic Features

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Fusion Gene ORF Annotations

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Fusion Protein Retained/Non-Retained Functional Features

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Fusion Transcript Sequences

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Fusion Protein Sequences

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Personalized Fusion Protein Sequences

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Fusion Gene Expressed Samples

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Related Drugs

Fusion gene:TPX2_BCL2L1 (FusionGDB2 ID:HG22974TG598)

Fusion Gene Summary for TPX2_BCL2L1

check button Fusion gene summary
Fusion gene informationFusion gene name: TPX2_BCL2L1
Fusion gene ID: hg22974tg598
HgeneTgene
Gene symbol

TPX2

BCL2L1

Gene ID

22974

598

Gene nameTPX2 microtubule nucleation factorBCL2 like 1
SynonymsC20orf1|C20orf2|DIL-2|DIL2|FLS353|GD:C20orf1|HCA519|HCTP4|REPP86|p100BCL-XL/S|BCL2L|BCLX|Bcl-X|PPP1R52
Cytomap

20q11.21

20q11.21

Type of geneprotein-codingprotein-coding
Descriptiontargeting protein for Xklp2TPX2, microtubule-associated protein homologTPX2, microtubule-associated, homologdifferentially expressed in cancerous and non-cancerous lung cells 2differentially expressed in cancerous and noncancerous lung cells 2differebcl-2-like protein 1apoptosis regulator Bcl-Xprotein phosphatase 1, regulatory subunit 52
Modification date2024041120240411
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000300403, ENST00000340513, 
ENST00000300403, ENST00000340513, 
Fusion gene scores* DoF score* DoF score (Degree of Frequency) = # partners X # break points X # disease types
20 X 18 X 25=9000		* DoF score (Degree of Frequency) = # partners X # break points X # disease types
11 X 13 X 22=3146
# samples 7832
** MAII score** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)
log2(78/9000*10)=-3.52837897235479
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)
log2(32/3146*10)=-3.29737486052832
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TPX2 [Title/Abstract] AND BCL2L1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTPX2(30327424)-BCL2L1(30310133), # samples:3


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Fusion Gene Breakpoints for TPX2_BCL2L1


check button RNA-seq based exon junction arranged fusion gene breakpoints from 8 resources (TCGA, CCLE, cBioPortal, GenBank, ChimerDB, ChimerKB, ChildHoodFusions, and GTEx). For the expressed sample information, go to Fusion Gene Sample section.
HgeneHchrHbpTgeneTchrTbp
TPX2chr2030327424BCL2L1chr2030310133
TPX2chr2030327424BCL2L1chr2030310151
TPX2chr2030327150BCL2L1chr2030310133
TPX2chr2030330450BCL2L1chr2030253889


check button DNA-seq based exon junction arranged fusion gene breakpoints from dbVar. For the expressed sample information, go to Fusion Gene Sample section.
HgeneHchrHbpTgeneTchrTbpSV type


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Tumorigenic MoA (Mechanism of Action) Scenarios of Fusion Genes for TPX2_BCL2L1


check button To generate these tumorigenic scenario annotations, we implemented a deduction-first, retrieval-later computational framework. The pipeline first applies rule-guided reasoning across ten core mechanistic categories (M1–M10) derived from fusion gene biology to infer candidate mechanisms, tumorigenic scenarios, targeting points, and targeting backgrounds. To ensure empirical accountability, a governed Python workflow retrieves literature candidates via NCBI E-utilities and Europe PMC using tiered searches. Using JSON Schema-constrained LLM evidence judges (GPT-5.6 Luna and Terra), retrieved articles are evaluated for specificity and confidence without de novo PMID generation. This produces two distinct versions: a strict version restricted to high- or medium-confidence fusion-specific evidence, and an extended version incorporating broader gene-, pathway-, and contextual evidence.
* We have 10 tumorigenic mechanism categories of fusion genes as shown below.
Constitutively Active Kinases, Catalytic Domain Dysregulation, & Transmembrane Ligand FusionsAberrant Chimeric Transcription Factor / Fusion Transcription Factor ActivityEpigenetic Reprogramming / Histone Modifier DysregulationChromatin Remodeling DysregulationCondensate-Driven Transcriptional Rewiring / LLPPromoter / Enhancer HijackingDominant-Negative AntagonismCell Cycle / Checkpoint Bypass / RNA Processing DysregulationSubcellular Mislocalization / Spatial DysregulationNuclear Body / Sub-organellar Architecture Disruption & Differentiation Blockade

* Strict version: Restricted to high- or medium-confidence fusion-specific evidence.
Fusion Gene NameMechanism CategoryMechanism PubMedTumorigenic ScenariosTumorigenic Scenario PubMedTargeting PointsTargeting PubMedMechanism BackgroundMechanism Background PubMed

* Extended version: Includes all strict-level fusion evidence plus broader gene-, pathway-, and low-confidence contextual evidence.
Fusion Gene NameMechanism CategoryMechanism PubMedTumorigenic ScenariosTumorigenic Scenario PubMedTargeting PointsTargeting PubMedMechanism BackgroundMechanism Background PubMed

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

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneTPX2

GO:0007020

microtubule nucleation

26414402

HgeneTPX2

GO:0007026

negative regulation of microtubule depolymerization

26414402

HgeneTPX2

GO:0032147

activation of protein kinase activity

14580337|19801554

HgeneTPX2

GO:0090307

mitotic spindle assembly

26165940|37728657

TgeneBCL2L1

GO:0001836

release of cytochrome c from mitochondria

9843949

TgeneBCL2L1

GO:0034097

response to cytokine

9184696

TgeneBCL2L1

GO:0043066

negative regulation of apoptotic process

7650367

TgeneBCL2L1

GO:0043066

negative regulation of apoptotic process

9388232

TgeneBCL2L1

GO:0046902

regulation of mitochondrial membrane permeability

9843949

TgeneBCL2L1

GO:0051607

defense response to virus

17428862

TgeneBCL2L1

GO:0051881

regulation of mitochondrial membrane potential

9843949

TgeneBCL2L1

GO:1900118

negative regulation of execution phase of apoptosis

20673843

TgeneBCL2L1

GO:1902042

negative regulation of extrinsic apoptotic signaling pathway via death domain receptors

26582200

TgeneBCL2L1

GO:1902230

negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage

16608847

TgeneBCL2L1

GO:1902236

negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway

29507230

TgeneBCL2L1

GO:1903077

negative regulation of protein localization to plasma membrane

21041309

TgeneBCL2L1

GO:2001243

negative regulation of intrinsic apoptotic signaling pathway

12011449


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Fusion Genomic Features for TPX2_BCL2L1


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) of In-frame fusion genes. 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)
TPX2chr2030327424+BCL2L1chr2030310133-2.14e-061.00e+00
TPX2chr2030327424+BCL2L1chr2030310151-7.35e-051.00e+00
TPX2chr2030330450+BCL2L1chr2030253889-1.87e-071.00e+00


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) of 5UTR-3CSD fusion genes (N-truncated cases).
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

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) of 5CDS-3UTR fusion genes (C-truncated cases).
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of six genomic regulatory feature tracks across a ±5 kb window centered on the fusion breakpoints. We input the breakpoint sequences into AlphaGenome and obtained predicted genome tracks at single-base-pair resolution for each modality by running a single forward pass over the reference sequence. Specifically, for each breakpoint, AlphaGenome processed and returned predicted track data across diverse modalities, which were then averaged across all tracks within each output type and visualized across the ±5 kb window. The left panel shows the 5'-gene breakpoint ±5 kb area, and the right panel shows the 3'-gene breakpoint area, with tracks grouped by category: chromatin accessibility (DNase-seq, ATAC-seq), active transcription (RNA-seq, CAGE), and chromatin binding (ChIP-Histone, ChIP-TF).
genomic feature

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Fusion Gene ORF Annotations for TPX2_BCL2L1

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
5UTR-3CDSENST00000300403ENST00000307677TPX2chr20

30330450

+BCL2L1chr20

30253889

-
5UTR-3CDSENST00000300403ENST00000376055TPX2chr20

30330450

+BCL2L1chr20

30253889

-
5UTR-3CDSENST00000300403ENST00000376062TPX2chr20

30330450

+BCL2L1chr20

30253889

-
5UTR-3CDSENST00000300403ENST00000420653TPX2chr20

30330450

+BCL2L1chr20

30253889

-
5UTR-3CDSENST00000340513ENST00000307677TPX2chr20

30330450

+BCL2L1chr20

30253889

-
5UTR-3CDSENST00000340513ENST00000376055TPX2chr20

30330450

+BCL2L1chr20

30253889

-
5UTR-3CDSENST00000340513ENST00000376062TPX2chr20

30330450

+BCL2L1chr20

30253889

-
5UTR-3CDSENST00000340513ENST00000420653TPX2chr20

30330450

+BCL2L1chr20

30253889

-
5UTR-5UTRENST00000300403ENST00000307677TPX2chr20

30327424

+BCL2L1chr20

30310133

-
5UTR-5UTRENST00000300403ENST00000307677TPX2chr20

30327424

+BCL2L1chr20

30310151

-
5UTR-5UTRENST00000300403ENST00000376055TPX2chr20

30327424

+BCL2L1chr20

30310133

-
5UTR-5UTRENST00000300403ENST00000376055TPX2chr20

30327424

+BCL2L1chr20

30310151

-
5UTR-5UTRENST00000300403ENST00000376062TPX2chr20

30327424

+BCL2L1chr20

30310133

-
5UTR-5UTRENST00000300403ENST00000376062TPX2chr20

30327424

+BCL2L1chr20

30310151

-
5UTR-5UTRENST00000300403ENST00000420653TPX2chr20

30327424

+BCL2L1chr20

30310133

-
5UTR-5UTRENST00000340513ENST00000307677TPX2chr20

30327424

+BCL2L1chr20

30310133

-
5UTR-5UTRENST00000340513ENST00000307677TPX2chr20

30327424

+BCL2L1chr20

30310151

-
5UTR-5UTRENST00000340513ENST00000376055TPX2chr20

30327424

+BCL2L1chr20

30310133

-
5UTR-5UTRENST00000340513ENST00000376055TPX2chr20

30327424

+BCL2L1chr20

30310151

-
5UTR-5UTRENST00000340513ENST00000376062TPX2chr20

30327424

+BCL2L1chr20

30310133

-
5UTR-5UTRENST00000340513ENST00000376062TPX2chr20

30327424

+BCL2L1chr20

30310151

-
5UTR-5UTRENST00000340513ENST00000420653TPX2chr20

30327424

+BCL2L1chr20

30310133

-

check buttonORFfinder Result Based On The Fusion Transcript Sequences of the In-frame Fusion Genes.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)		Seq length
(peptide)

check buttonORFfinder Result Based On The Fusion Transcript Sequences of the 5UTR-3CDS Fusion Genes for N-Truncated Protein Search.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)		Seq length
(peptide)

check buttonORFfinder Result Based On The Fusion Transcript Sequences of the 5CDS-3UTR Fusion Genes for C-Truncated Protein Search.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)		Seq length
(peptide)

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.
HenstTenstHgeneHchrHbpTgeneTchrTbpNo-coding scoreCoding score

check buttonDeepORF Prediction of The Coding Potential Based on The Fusion Transcript Sequence of 5UTR-3CDS Fusion Genes (Potential N-Truncated Proteins).
HenstTenstHgeneHchrHbpTgeneTchrTbpNo-coding scoreCoding score

check buttonDeepORF Prediction of The Coding Potential Based on The Fusion Transcript Sequence of 5CDS-3UTR Fusion Genes (Potential C-Truncated Proteins).
HenstTenstHgeneHchrHbpTgeneTchrTbpNo-coding scoreCoding score

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Fusion Protein Retained/Non-Retained Functional Features for TPX2_BCL2L1

check buttonProtein Level Annotation from FGviewer
* Retention 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.
fgviewer annotation
- In-frame and retained protein feature among the 13 regional features (visualization across fusion protein length).
No matching images found for ${hg}_${tg}.

- In-frame and retained protein feature among the 13 regional features (texts).
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


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


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


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Fusion Transcript Sequence for TPX2_BCL2L1

check button In-frame Fusion Transcript Sequences.

check button N-Truncated Transcript (5UTR-3CDS) Sequences

check button C-Truncated Transcript (5CDS-3UTR) Sequences

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Fusion Protein Sequence for TPX2_BCL2L1

check button In-frame Fusion Protein Sequences.

check button N-Truncated Protein (5UTR-3CDS) Sequences

check button C-Truncated Protein (5CDS-3UTR) Sequences

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Personalized Fusion Protein Sequence for TPX2_BCL2L1


check button TCGA Kinase/DNA-binding Domain Mutated Fusion Protein Sequences
NumGene GroupDomain LociFusion Protein IDFusion Gene NamePartnerMutated Residue in WT ProteinSeq. LengthMutated Residue in Fusion Protein

check button CCLE Kinase/DNA-binding Domain Mutated Fusion Protein Sequences

NumGene GroupDomain LociFusion Protein IDFusion Gene NamePartnerMutated Residue in WT ProteinSeq. LengthMutated Residue in Fusion Protein

check button TCGA All Mutated Fusion Protein Sequences


Fusion Protein IDSample IDMutated PartnerAAchange in WTSeq. LengthAAchange in Fusion

check button CCLE All Mutated Fusion Protein Sequences


Fusion Protein IDSample IDMutated PartnerAAchange in WTSeq. LengthAAchange in Fusion

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Fusion Gene Exprssed Samples for TPX2_BCL2L1


check buttonRNA-seq based fusion gene expressed samples.
SourceStudyDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
CCLEDiffuse Type Stomach AdenocarcinomaMKN45TPX2

chr20

30327424+BCL2L1

chr20

30310133

-
CCLEDiffuse Type Stomach AdenocarcinomaMKN45TPX2

chr20

30327424+BCL2L1

chr20

30310151

-
CCLEDiffuse Type Stomach AdenocarcinomaMKN45TPX2

chr20

30327150+BCL2L1

chr20

30310133

-
ChimerDBCESCTCGA-LP-A7HU-01ATPX2

chr20

30330450+BCL2L1

chr20

30253889

-
ChimerDBSTADTCGA-CD-A486-01ATPX2

chr20

30327424+BCL2L1

chr20

30310133

-
cBioPortalCCLE_BROAD_2019MIXED8505C_THYROIDTPX2

chr20

30330450BCL2L1

chr20

30253889

cBioPortalCCLE_BROAD_2019MIXEDMKN45_STOMACHTPX2

chr20

30327424BCL2L1

chr20

30310133

cBioPortalCCLE_BROAD_2019MIXEDMKN45_STOMACHTPX2

chr20

30327424BCL2L1

chr20

30310151


check buttonDNA-seq based fusion gene expressed samples.
SourceStudyDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrandSV type


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Related Drugs for TPX2_BCL2L1


check button PubMed Abstract Search With ['A-B' AND 'drug'], ['A::B' AND 'drug']
* For more details on the Studied, Reported, Approved Drugs targeting this fusion gene, Go to FusionPub.
PMIDFusion Gene NameDrugStudy Title

check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status