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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:B2M-CDK2AP1 (FusionGDB2 ID:8622)

Fusion Gene Summary for B2M-CDK2AP1

check button Fusion gene summary
Fusion gene informationFusion gene name: B2M-CDK2AP1
Fusion gene ID: 8622
HgeneTgene
Gene symbol

B2M

CDK2AP1

Gene ID

567

8099

Gene namebeta-2-microglobulincyclin dependent kinase 2 associated protein 1
SynonymsIMD43DOC1|DORC1|ST19|doc-1|p12DOC-1
Cytomap

15q21.1

12q24.31

Type of geneprotein-codingprotein-coding
Descriptionbeta-2-microglobulinbeta chain of MHC class I moleculesbeta-2-microglobincyclin-dependent kinase 2-associated protein 1CDK2-associated protein 1Deleted in oral cancer-1deleted in oral cancer 1putative oral cancer suppressor
Modification date2020032920200313
UniProtAcc

P61769

O14519

Ensembl transtripts involved in fusion geneENST00000544417, ENST00000558401, 
ENST00000559916, ENST00000559220, 
ENST00000535979, ENST00000538446, 
ENST00000542174, ENST00000544658, 
ENST00000261692, 
Fusion gene scores* DoF score32 X 24 X 12=92169 X 5 X 5=225
# samples 439
** MAII scorelog2(43/9216*10)=-4.42173215185285
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/225*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: B2M [Title/Abstract] AND CDK2AP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointB2M(45003811)-CDK2AP1(123751829), # 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
HgeneB2M

GO:0002726

positive regulation of T cell cytokine production

24643698

HgeneB2M

GO:0007611

learning or memory

26147761

HgeneB2M

GO:0050680

negative regulation of epithelial cell proliferation

28213472

HgeneB2M

GO:0050768

negative regulation of neurogenesis

26147761

HgeneB2M

GO:0090647

modulation of age-related behavioral decline

26147761

HgeneB2M

GO:1900121

negative regulation of receptor binding

9465039

HgeneB2M

GO:1990000

amyloid fibril formation

28468825

HgeneB2M

GO:2000774

positive regulation of cellular senescence

28213472

HgeneB2M

GO:2000978

negative regulation of forebrain neuron differentiation

26147761

TgeneCDK2AP1

GO:0001934

positive regulation of protein phosphorylation

9506968


check buttonFusion gene breakpoints across B2M (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across CDK2AP1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChimerDB4STADTCGA-BR-A4PD-01AB2Mchr15

45003811

+CDK2AP1chr12

123751829

-


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Fusion Gene ORF analysis for B2M-CDK2AP1

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
5CDS-5UTRENST00000544417ENST00000535979B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
5CDS-5UTRENST00000544417ENST00000538446B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
5CDS-5UTRENST00000544417ENST00000542174B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
5CDS-5UTRENST00000544417ENST00000544658B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
5CDS-5UTRENST00000558401ENST00000535979B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
5CDS-5UTRENST00000558401ENST00000538446B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
5CDS-5UTRENST00000558401ENST00000542174B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
5CDS-5UTRENST00000558401ENST00000544658B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
5CDS-5UTRENST00000559916ENST00000535979B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
5CDS-5UTRENST00000559916ENST00000538446B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
5CDS-5UTRENST00000559916ENST00000542174B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
5CDS-5UTRENST00000559916ENST00000544658B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
In-frameENST00000544417ENST00000261692B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
In-frameENST00000558401ENST00000261692B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
In-frameENST00000559916ENST00000261692B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
intron-3CDSENST00000559220ENST00000261692B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
intron-5UTRENST00000559220ENST00000535979B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
intron-5UTRENST00000559220ENST00000538446B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
intron-5UTRENST00000559220ENST00000542174B2Mchr15

45003811

+CDK2AP1chr12

123751829

-
intron-5UTRENST00000559220ENST00000544658B2Mchr15

45003811

+CDK2AP1chr12

123751829

-

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)
ENST00000558401B2Mchr1545003811+ENST00000261692CDK2AP1chr12123751829-118513731429132
ENST00000559916B2Mchr1545003811+ENST00000261692CDK2AP1chr12123751829-114910134393119
ENST00000544417B2Mchr1545003811+ENST00000261692CDK2AP1chr12123751829-11459730389119

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
ENST00000558401ENST00000261692B2Mchr1545003811+CDK2AP1chr12123751829-0.0165501960.98344976
ENST00000559916ENST00000261692B2Mchr1545003811+CDK2AP1chr12123751829-0.0128164780.9871836
ENST00000544417ENST00000261692B2Mchr1545003811+CDK2AP1chr12123751829-0.0105113750.98948854

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Fusion Genomic Features for B2M-CDK2AP1


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.
genomic feature

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for B2M-CDK2AP1


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/chr15:45003811/chr12:123751829)
- 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
B2M

P61769

CDK2AP1

O14519

FUNCTION: Component of the class I major histocompatibility complex (MHC). Involved in the presentation of peptide antigens to the immune system. Exogenously applied M.tuberculosis EsxA or EsxA-EsxB (or EsxA expressed in host) binds B2M and decreases its export to the cell surface (total protein levels do not change), probably leading to defects in class I antigen presentation (PubMed:25356553). {ECO:0000269|PubMed:25356553}.FUNCTION: specific inhibitor of the cell-cycle kinase CDK2. {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
TgeneCDK2AP1chr15:45003811chr12:123751829ENST00000535979041_60088.0RegionNote=Intrinsically disordered
TgeneCDK2AP1chr15:45003811chr12:123751829ENST00000538446041_60088.0RegionNote=Intrinsically disordered
TgeneCDK2AP1chr15:45003811chr12:123751829ENST00000542174031_60088.0RegionNote=Intrinsically disordered
TgeneCDK2AP1chr15:45003811chr12:123751829ENST00000544658041_60088.0RegionNote=Intrinsically disordered

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneB2Mchr15:45003811chr12:123751829ENST00000558401+1425_11322498.0DomainNote=Ig-like C1-type
HgeneB2Mchr15:45003811chr12:123751829ENST00000559916+1325_11322120.0DomainNote=Ig-like C1-type
TgeneCDK2AP1chr15:45003811chr12:123751829ENST00000261692041_6018116.0RegionNote=Intrinsically disordered


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Fusion Gene Sequence for B2M-CDK2AP1


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.
>8622_8622_1_B2M-CDK2AP1_B2M_chr15_45003811_ENST00000544417_CDK2AP1_chr12_123751829_ENST00000261692_length(transcript)=1145nt_BP=97nt
ATTCCTGAAGCTGACAGCATTCGGGCCGAGATGTCTCGCTCCGTGGCCTTAGCTGTGCTCGCGCTACTCTCTCTTTCTGGCCTGGAGGCT
ATCCAGCCTGGGAGTGTCCACTCGCCTTCCACCAGCATGGCAACGTCTTCACAGTACCGCCAGCTGCTCAGTGACTACGGGCCACCGTCC
CTAGGCTACACCCAGGGAACTGGGAACAGCCAGGTGCCCCAAAGCAAATACGCGGAGCTGCTGGCCATCATTGAAGAGCTGGGGAAGGAG
ATCAGACCCACGTACGCAGGGAGCAAGAGTGCCATGGAGAGGCTGAAGCGCGGCATCATTCACGCTAGAGGACTGGTTCGGGAGTGCTTG
GCAGAAACGGAACGGAATGCCAGATCCTAGCTGCCTTGTTGGTTTTGAAGGATTTCCATCTTTTTACAAGATGAGAAGTTACAGTTCATC
TCCCCTGTTCAGATGAAACCCTTGTTTTCAAAATGGTTACAGTTTCGTTTTTCCTCCCATGGTTCACTTGGCTCTGAACCTACAGTCTCA
AAGATTGAGAAAAGATTTTGCAGTTAATTAGGATTTGCATTTTAAGTAGTTAGGAACTGCCCAGGTTTTTTTTGTTTTTTAAGCATTGAT
TTAAAAGATGCACGGAAAGTTATCTTACAGCAAACTGTAGTTTGCCTCCAAGACACCATTGTCTCCCTTTAATCTTCTCTTTTGTATACA
TTTGTTACCCATGGTGTTCTTTGTTCCTTTTCATAAGCTAATACCACTGTAGGGATTTTGTTTTGAACGCATATTGACAGCACGCTTTAC
TTAGTAGCCGGTTCCCATTTGCCATACAATGTAGGTTCTGCTTAATGTAACTTCTTTTTTGCTTAAGCATTTGCATGACTATTAGTGCTT
CAAAGTCAATTTTTAAAAATGCACAAGTTATAAATACAGAAGAAAGAGCAACCCACCAAACCTAACAAGGACCCCCGAACACTTTCATAC
TAAGACTGTAAGTAGATCTCAGTTCTGCGTTTATTGTAAGTTGATAAAAACATCTGGAAGAAAATGACTAAAACTGTTTGCATCTTTGTA

>8622_8622_1_B2M-CDK2AP1_B2M_chr15_45003811_ENST00000544417_CDK2AP1_chr12_123751829_ENST00000261692_length(amino acids)=119AA_BP=23
MSRSVALAVLALLSLSGLEAIQPGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSKYAELLAIIEELGKEIRPTYAGSKS

--------------------------------------------------------------
>8622_8622_2_B2M-CDK2AP1_B2M_chr15_45003811_ENST00000558401_CDK2AP1_chr12_123751829_ENST00000261692_length(transcript)=1185nt_BP=137nt
GCACGCGTTTAATATAAGTGGAGGCGTCGCGCTGGCGGGCATTCCTGAAGCTGACAGCATTCGGGCCGAGATGTCTCGCTCCGTGGCCTT
AGCTGTGCTCGCGCTACTCTCTCTTTCTGGCCTGGAGGCTATCCAGCCTGGGAGTGTCCACTCGCCTTCCACCAGCATGGCAACGTCTTC
ACAGTACCGCCAGCTGCTCAGTGACTACGGGCCACCGTCCCTAGGCTACACCCAGGGAACTGGGAACAGCCAGGTGCCCCAAAGCAAATA
CGCGGAGCTGCTGGCCATCATTGAAGAGCTGGGGAAGGAGATCAGACCCACGTACGCAGGGAGCAAGAGTGCCATGGAGAGGCTGAAGCG
CGGCATCATTCACGCTAGAGGACTGGTTCGGGAGTGCTTGGCAGAAACGGAACGGAATGCCAGATCCTAGCTGCCTTGTTGGTTTTGAAG
GATTTCCATCTTTTTACAAGATGAGAAGTTACAGTTCATCTCCCCTGTTCAGATGAAACCCTTGTTTTCAAAATGGTTACAGTTTCGTTT
TTCCTCCCATGGTTCACTTGGCTCTGAACCTACAGTCTCAAAGATTGAGAAAAGATTTTGCAGTTAATTAGGATTTGCATTTTAAGTAGT
TAGGAACTGCCCAGGTTTTTTTTGTTTTTTAAGCATTGATTTAAAAGATGCACGGAAAGTTATCTTACAGCAAACTGTAGTTTGCCTCCA
AGACACCATTGTCTCCCTTTAATCTTCTCTTTTGTATACATTTGTTACCCATGGTGTTCTTTGTTCCTTTTCATAAGCTAATACCACTGT
AGGGATTTTGTTTTGAACGCATATTGACAGCACGCTTTACTTAGTAGCCGGTTCCCATTTGCCATACAATGTAGGTTCTGCTTAATGTAA
CTTCTTTTTTGCTTAAGCATTTGCATGACTATTAGTGCTTCAAAGTCAATTTTTAAAAATGCACAAGTTATAAATACAGAAGAAAGAGCA
ACCCACCAAACCTAACAAGGACCCCCGAACACTTTCATACTAAGACTGTAAGTAGATCTCAGTTCTGCGTTTATTGTAAGTTGATAAAAA
CATCTGGAAGAAAATGACTAAAACTGTTTGCATCTTTGTATGTATTTATTACTTGATGTAATAAAGCTTATTTTCATTAACAATTTGTAT

>8622_8622_2_B2M-CDK2AP1_B2M_chr15_45003811_ENST00000558401_CDK2AP1_chr12_123751829_ENST00000261692_length(amino acids)=132AA_BP=36
MAGIPEADSIRAEMSRSVALAVLALLSLSGLEAIQPGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSKYAELLAIIEEL

--------------------------------------------------------------
>8622_8622_3_B2M-CDK2AP1_B2M_chr15_45003811_ENST00000559916_CDK2AP1_chr12_123751829_ENST00000261692_length(transcript)=1149nt_BP=101nt
GGGCATTCCTGAAGCTGACAGCATTCGGGCCGAGATGTCTCGCTCCGTGGCCTTAGCTGTGCTCGCGCTACTCTCTCTTTCTGGCCTGGA
GGCTATCCAGCCTGGGAGTGTCCACTCGCCTTCCACCAGCATGGCAACGTCTTCACAGTACCGCCAGCTGCTCAGTGACTACGGGCCACC
GTCCCTAGGCTACACCCAGGGAACTGGGAACAGCCAGGTGCCCCAAAGCAAATACGCGGAGCTGCTGGCCATCATTGAAGAGCTGGGGAA
GGAGATCAGACCCACGTACGCAGGGAGCAAGAGTGCCATGGAGAGGCTGAAGCGCGGCATCATTCACGCTAGAGGACTGGTTCGGGAGTG
CTTGGCAGAAACGGAACGGAATGCCAGATCCTAGCTGCCTTGTTGGTTTTGAAGGATTTCCATCTTTTTACAAGATGAGAAGTTACAGTT
CATCTCCCCTGTTCAGATGAAACCCTTGTTTTCAAAATGGTTACAGTTTCGTTTTTCCTCCCATGGTTCACTTGGCTCTGAACCTACAGT
CTCAAAGATTGAGAAAAGATTTTGCAGTTAATTAGGATTTGCATTTTAAGTAGTTAGGAACTGCCCAGGTTTTTTTTGTTTTTTAAGCAT
TGATTTAAAAGATGCACGGAAAGTTATCTTACAGCAAACTGTAGTTTGCCTCCAAGACACCATTGTCTCCCTTTAATCTTCTCTTTTGTA
TACATTTGTTACCCATGGTGTTCTTTGTTCCTTTTCATAAGCTAATACCACTGTAGGGATTTTGTTTTGAACGCATATTGACAGCACGCT
TTACTTAGTAGCCGGTTCCCATTTGCCATACAATGTAGGTTCTGCTTAATGTAACTTCTTTTTTGCTTAAGCATTTGCATGACTATTAGT
GCTTCAAAGTCAATTTTTAAAAATGCACAAGTTATAAATACAGAAGAAAGAGCAACCCACCAAACCTAACAAGGACCCCCGAACACTTTC
ATACTAAGACTGTAAGTAGATCTCAGTTCTGCGTTTATTGTAAGTTGATAAAAACATCTGGAAGAAAATGACTAAAACTGTTTGCATCTT

>8622_8622_3_B2M-CDK2AP1_B2M_chr15_45003811_ENST00000559916_CDK2AP1_chr12_123751829_ENST00000261692_length(amino acids)=119AA_BP=23
MSRSVALAVLALLSLSGLEAIQPGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSKYAELLAIIEELGKEIRPTYAGSKS

--------------------------------------------------------------

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Fusion Gene PPI Analysis for B2M-CDK2AP1


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
TgeneCDK2AP1chr15:45003811chr12:123751829ENST000002616920420_2518.333333333333332116.0CDK2AP2
TgeneCDK2AP1chr15:45003811chr12:123751829ENST000005359790420_25088.0CDK2AP2
TgeneCDK2AP1chr15:45003811chr12:123751829ENST000005384460420_25088.0CDK2AP2
TgeneCDK2AP1chr15:45003811chr12:123751829ENST000005421740320_25088.0CDK2AP2
TgeneCDK2AP1chr15:45003811chr12:123751829ENST000005446580420_25088.0CDK2AP2


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 B2M-CDK2AP1


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

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Related Diseases for B2M-CDK2AP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource