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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:WDR33_LIMS2 (FusionGDB2 ID:HG55339TG55679)

Fusion Gene Summary for WDR33_LIMS2

check button Fusion gene summary
Fusion gene informationFusion gene name: WDR33_LIMS2
Fusion gene ID: hg55339tg55679
HgeneTgene
Gene symbol

WDR33

LIMS2

Gene ID

55339

55679

Gene nameWD repeat domain 33LIM zinc finger domain containing 2
SynonymsNET14|WDC146LGMD2W|MDRCMTT|PINCH-2|PINCH2
Cytomap

2q14.3

2q14.3

Type of geneprotein-codingprotein-coding
Descriptionpre-mRNA 3' end processing protein WDR33WD repeat-containing protein 33WD repeat-containing protein WDC146WD repeat-containing protein of 146 kDaLIM and senescent cell antigen-like-containing domain protein 2ILK-binding proteinLIM and senescent cell antigen-like domains 2LIM-type zinc finger domains 2particularly interesting new Cys-His protein 2
Modification date2024041120240403
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000322313, ENST00000393006, 
ENST00000409658, 
Fusion gene scores* DoF score* DoF score (Degree of Frequency) = # partners X # break points X # disease types
10 X 10 X 8=800		* DoF score (Degree of Frequency) = # partners X # break points X # disease types
3 X 3 X 4=36
# samples 154
** MAII score** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)
log2(15/800*10)=-2.41503749927884
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(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: WDR33 [Title/Abstract] AND LIMS2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointWDR33(128568585)-LIMS2(128415136), # samples:1


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Fusion Gene Breakpoints for WDR33_LIMS2


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
WDR33chr2128568585LIMS2chr2128400647
WDR33chr2128568585LIMS2chr2128415136


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 WDR33_LIMS2


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

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Fusion Genomic Features for WDR33_LIMS2


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)
WDR33chr2128568585-LIMS2chr2128400647-3.28e-071.00e+00
WDR33chr2128568585-LIMS2chr2128415136-4.82e-081.00e+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).

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Fusion Gene ORF Annotations for WDR33_LIMS2

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-5UTRENST00000322313ENST00000324938WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000322313ENST00000355119WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000322313ENST00000355119WDR33chr2

128568585

-LIMS2chr2

128415136

-
5UTR-5UTRENST00000322313ENST00000409254WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000322313ENST00000409286WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000322313ENST00000409455WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000322313ENST00000409455WDR33chr2

128568585

-LIMS2chr2

128415136

-
5UTR-5UTRENST00000322313ENST00000409754WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000322313ENST00000409808WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000322313ENST00000409808WDR33chr2

128568585

-LIMS2chr2

128415136

-
5UTR-5UTRENST00000322313ENST00000410011WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000322313ENST00000410011WDR33chr2

128568585

-LIMS2chr2

128415136

-
5UTR-5UTRENST00000322313ENST00000410038WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000322313ENST00000545738WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000393006ENST00000324938WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000393006ENST00000355119WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000393006ENST00000355119WDR33chr2

128568585

-LIMS2chr2

128415136

-
5UTR-5UTRENST00000393006ENST00000409254WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000393006ENST00000409286WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000393006ENST00000409455WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000393006ENST00000409455WDR33chr2

128568585

-LIMS2chr2

128415136

-
5UTR-5UTRENST00000393006ENST00000409754WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000393006ENST00000409808WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000393006ENST00000409808WDR33chr2

128568585

-LIMS2chr2

128415136

-
5UTR-5UTRENST00000393006ENST00000410011WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000393006ENST00000410011WDR33chr2

128568585

-LIMS2chr2

128415136

-
5UTR-5UTRENST00000393006ENST00000410038WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000393006ENST00000545738WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000409658ENST00000324938WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000409658ENST00000355119WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000409658ENST00000355119WDR33chr2

128568585

-LIMS2chr2

128415136

-
5UTR-5UTRENST00000409658ENST00000409254WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000409658ENST00000409286WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000409658ENST00000409455WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000409658ENST00000409455WDR33chr2

128568585

-LIMS2chr2

128415136

-
5UTR-5UTRENST00000409658ENST00000409754WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000409658ENST00000409808WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000409658ENST00000409808WDR33chr2

128568585

-LIMS2chr2

128415136

-
5UTR-5UTRENST00000409658ENST00000410011WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000409658ENST00000410011WDR33chr2

128568585

-LIMS2chr2

128415136

-
5UTR-5UTRENST00000409658ENST00000410038WDR33chr2

128568585

-LIMS2chr2

128400647

-
5UTR-5UTRENST00000409658ENST00000545738WDR33chr2

128568585

-LIMS2chr2

128400647

-

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 WDR33_LIMS2

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 WDR33_LIMS2

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 WDR33_LIMS2

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 WDR33_LIMS2


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 WDR33_LIMS2


check buttonRNA-seq based fusion gene expressed samples.
SourceStudyDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDBOVTCGA-25-1625WDR33

chr2

128568585-LIMS2

chr2

128400647

-
ChimerDBOVTCGA-25-1625WDR33

chr2

128568585-LIMS2

chr2

128415136

-

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


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Related Drugs for WDR33_LIMS2


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