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Center for Computational Systems Medicine level2
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:SMC5-IMMP2L

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SMC5-IMMP2L
FusionPDB ID: 84018
FusionGDB2.0 ID: 84018
HgeneTgene
Gene symbol

SMC5

IMMP2L

Gene ID

23137

83943

Gene namestructural maintenance of chromosomes 5inner mitochondrial membrane peptidase subunit 2
SynonymsSMC5L1IMMP2L-IT1|IMP2|IMP2-LIKE
Cytomap

9q21.12

7q31.1

Type of geneprotein-codingprotein-coding
Descriptionstructural maintenance of chromosomes protein 5SMC protein 5SMC-5SMC5 structural maintenance of chromosomes 5-like 1hSMC5mitochondrial inner membrane protease subunit 2IMP2 inner mitochondrial membrane peptidase-likeIMP2 inner mitochondrial membrane protease-likeinner mitochondrial membrane peptidase 2 like
Modification date2020031320200313
UniProtAcc

SLF2,FAM178A

Q96T52

Ensembl transtripts involved in fusion geneENST idsENST00000361138, ENST00000471372, 
ENST00000450877, ENST00000489381, 
ENST00000331762, ENST00000405709, 
ENST00000415362, ENST00000437687, 
ENST00000447215, ENST00000452895, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score8 X 10 X 4=32029 X 19 X 14=7714
# samples 932
** MAII scorelog2(9/320*10)=-1.83007499855769
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(32/7714*10)=-4.5913353357414
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: SMC5 [Title/Abstract] AND IMMP2L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SMC5(72882891)-IMMP2L(110603621), # samples:4
Anticipated loss of major functional domain due to fusion event.SMC5-IMMP2L seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
SMC5-IMMP2L seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
* 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
HgeneSMC5

GO:0006974

cellular response to DNA damage stimulus

11408570|25931565


check buttonFusion gene breakpoints across SMC5 (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 IMMP2L (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4BRCATCGA-AO-A124-01ASMC5chr9

72882890

+IMMP2Lchr7

110603620

-
ChimerDB4BRCATCGA-AO-A124-01ASMC5chr9

72882891

-IMMP2Lchr7

110603621

-
ChimerDB4BRCATCGA-AO-A124-01ASMC5chr9

72882891

+IMMP2Lchr7

110603621

-
ChimerDB4BRCATCGA-AO-A124SMC5chr9

72882891

+IMMP2Lchr7

110603621

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000361138SMC5chr972882891+ENST00000405709IMMP2Lchr7110603621-127543834726230
ENST00000361138SMC5chr972882891+ENST00000331762IMMP2Lchr7110603621-127543834726230
ENST00000361138SMC5chr972882891+ENST00000452895IMMP2Lchr7110603621-91343834726230
ENST00000361138SMC5chr972882891+ENST00000415362IMMP2Lchr7110603621-72743834726231
ENST00000361138SMC5chr972882891+ENST00000447215IMMP2Lchr7110603621-12874385900197
ENST00000361138SMC5chr972882891+ENST00000437687IMMP2Lchr7110603621-5324385030168
ENST00000361138SMC5chr972882890+ENST00000405709IMMP2Lchr7110603620-127543834726230
ENST00000361138SMC5chr972882890+ENST00000331762IMMP2Lchr7110603620-127543834726230
ENST00000361138SMC5chr972882890+ENST00000452895IMMP2Lchr7110603620-91343834726230
ENST00000361138SMC5chr972882890+ENST00000415362IMMP2Lchr7110603620-72743834726231
ENST00000361138SMC5chr972882890+ENST00000447215IMMP2Lchr7110603620-12874385900197
ENST00000361138SMC5chr972882890+ENST00000437687IMMP2Lchr7110603620-5324385030168

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
ENST00000361138ENST00000405709SMC5chr972882891+IMMP2Lchr7110603621-0.029617880.9703821
ENST00000361138ENST00000331762SMC5chr972882891+IMMP2Lchr7110603621-0.029617880.9703821
ENST00000361138ENST00000452895SMC5chr972882891+IMMP2Lchr7110603621-0.0659701150.9340299
ENST00000361138ENST00000415362SMC5chr972882891+IMMP2Lchr7110603621-0.063802060.93619794
ENST00000361138ENST00000447215SMC5chr972882891+IMMP2Lchr7110603621-0.0121876110.98781246
ENST00000361138ENST00000437687SMC5chr972882891+IMMP2Lchr7110603621-0.0171888360.9828112
ENST00000361138ENST00000405709SMC5chr972882890+IMMP2Lchr7110603620-0.029617880.9703821
ENST00000361138ENST00000331762SMC5chr972882890+IMMP2Lchr7110603620-0.029617880.9703821
ENST00000361138ENST00000452895SMC5chr972882890+IMMP2Lchr7110603620-0.0659701150.9340299
ENST00000361138ENST00000415362SMC5chr972882890+IMMP2Lchr7110603620-0.063802060.93619794
ENST00000361138ENST00000447215SMC5chr972882890+IMMP2Lchr7110603620-0.0121876110.98781246
ENST00000361138ENST00000437687SMC5chr972882890+IMMP2Lchr7110603620-0.0171888360.9828112

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>84018_84018_1_SMC5-IMMP2L_SMC5_chr9_72882890_ENST00000361138_IMMP2L_chr7_110603620_ENST00000331762_length(amino acids)=230AA_BP=135
MWDAEEARMATPSKKTSTPSPQPSKRALPRDPSSEVPSKRKNSAPQLPLLQSSGPFVEGSIVRISMENFLTYDICEVSPGPHLNMIVGAN
GTGKSSIVCAICLGLAGKPAFMGRADKVGFFVKRGCSRGMVEIELSPKNPEQKIIKRVIALEGDIVRTIGHKNRYVKVPRGHIWVEGDHH

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

>84018_84018_2_SMC5-IMMP2L_SMC5_chr9_72882890_ENST00000361138_IMMP2L_chr7_110603620_ENST00000405709_length(amino acids)=230AA_BP=135
MWDAEEARMATPSKKTSTPSPQPSKRALPRDPSSEVPSKRKNSAPQLPLLQSSGPFVEGSIVRISMENFLTYDICEVSPGPHLNMIVGAN
GTGKSSIVCAICLGLAGKPAFMGRADKVGFFVKRGCSRGMVEIELSPKNPEQKIIKRVIALEGDIVRTIGHKNRYVKVPRGHIWVEGDHH

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

>84018_84018_3_SMC5-IMMP2L_SMC5_chr9_72882890_ENST00000361138_IMMP2L_chr7_110603620_ENST00000415362_length(amino acids)=231AA_BP=135
MWDAEEARMATPSKKTSTPSPQPSKRALPRDPSSEVPSKRKNSAPQLPLLQSSGPFVEGSIVRISMENFLTYDICEVSPGPHLNMIVGAN
GTGKSSIVCAICLGLAGKPAFMGRADKVGFFVKRGCSRGMVEIELSPKNPEQKIIKRVIALEGDIVRTIGHKNRYVKVPRGHIWVEGDHH

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

>84018_84018_4_SMC5-IMMP2L_SMC5_chr9_72882890_ENST00000361138_IMMP2L_chr7_110603620_ENST00000437687_length(amino acids)=168AA_BP=1
MTISPSRAITLLMIFCSGFLGDNSISTMPLEHPLFTKNPTLSARPMKAGFPAKPRQMAHTMLDFPVPLAPTIIFKWGPGDTSQISYVRKF

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

>84018_84018_5_SMC5-IMMP2L_SMC5_chr9_72882890_ENST00000361138_IMMP2L_chr7_110603620_ENST00000447215_length(amino acids)=197AA_BP=1
MLQSYHLKLSFLSLIRKFLFHILFSFLPSLTISPSRAITLLMIFCSGFLGDNSISTMPLEHPLFTKNPTLSARPMKAGFPAKPRQMAHTM
LDFPVPLAPTIIFKWGPGDTSQISYVRKFSIEMRTIEPSTKGPDDCNSGSCGAEFFLLLGTSDEGSLGRALLEGWGLGVDVFLLGVAILA

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

>84018_84018_6_SMC5-IMMP2L_SMC5_chr9_72882890_ENST00000361138_IMMP2L_chr7_110603620_ENST00000452895_length(amino acids)=230AA_BP=135
MWDAEEARMATPSKKTSTPSPQPSKRALPRDPSSEVPSKRKNSAPQLPLLQSSGPFVEGSIVRISMENFLTYDICEVSPGPHLNMIVGAN
GTGKSSIVCAICLGLAGKPAFMGRADKVGFFVKRGCSRGMVEIELSPKNPEQKIIKRVIALEGDIVRTIGHKNRYVKVPRGHIWVEGDHH

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

>84018_84018_7_SMC5-IMMP2L_SMC5_chr9_72882891_ENST00000361138_IMMP2L_chr7_110603621_ENST00000331762_length(amino acids)=230AA_BP=135
MWDAEEARMATPSKKTSTPSPQPSKRALPRDPSSEVPSKRKNSAPQLPLLQSSGPFVEGSIVRISMENFLTYDICEVSPGPHLNMIVGAN
GTGKSSIVCAICLGLAGKPAFMGRADKVGFFVKRGCSRGMVEIELSPKNPEQKIIKRVIALEGDIVRTIGHKNRYVKVPRGHIWVEGDHH

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

>84018_84018_8_SMC5-IMMP2L_SMC5_chr9_72882891_ENST00000361138_IMMP2L_chr7_110603621_ENST00000405709_length(amino acids)=230AA_BP=135
MWDAEEARMATPSKKTSTPSPQPSKRALPRDPSSEVPSKRKNSAPQLPLLQSSGPFVEGSIVRISMENFLTYDICEVSPGPHLNMIVGAN
GTGKSSIVCAICLGLAGKPAFMGRADKVGFFVKRGCSRGMVEIELSPKNPEQKIIKRVIALEGDIVRTIGHKNRYVKVPRGHIWVEGDHH

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

>84018_84018_9_SMC5-IMMP2L_SMC5_chr9_72882891_ENST00000361138_IMMP2L_chr7_110603621_ENST00000415362_length(amino acids)=231AA_BP=135
MWDAEEARMATPSKKTSTPSPQPSKRALPRDPSSEVPSKRKNSAPQLPLLQSSGPFVEGSIVRISMENFLTYDICEVSPGPHLNMIVGAN
GTGKSSIVCAICLGLAGKPAFMGRADKVGFFVKRGCSRGMVEIELSPKNPEQKIIKRVIALEGDIVRTIGHKNRYVKVPRGHIWVEGDHH

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

>84018_84018_10_SMC5-IMMP2L_SMC5_chr9_72882891_ENST00000361138_IMMP2L_chr7_110603621_ENST00000437687_length(amino acids)=168AA_BP=1
MTISPSRAITLLMIFCSGFLGDNSISTMPLEHPLFTKNPTLSARPMKAGFPAKPRQMAHTMLDFPVPLAPTIIFKWGPGDTSQISYVRKF

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

>84018_84018_11_SMC5-IMMP2L_SMC5_chr9_72882891_ENST00000361138_IMMP2L_chr7_110603621_ENST00000447215_length(amino acids)=197AA_BP=1
MLQSYHLKLSFLSLIRKFLFHILFSFLPSLTISPSRAITLLMIFCSGFLGDNSISTMPLEHPLFTKNPTLSARPMKAGFPAKPRQMAHTM
LDFPVPLAPTIIFKWGPGDTSQISYVRKFSIEMRTIEPSTKGPDDCNSGSCGAEFFLLLGTSDEGSLGRALLEGWGLGVDVFLLGVAILA

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

>84018_84018_12_SMC5-IMMP2L_SMC5_chr9_72882891_ENST00000361138_IMMP2L_chr7_110603621_ENST00000452895_length(amino acids)=230AA_BP=135
MWDAEEARMATPSKKTSTPSPQPSKRALPRDPSSEVPSKRKNSAPQLPLLQSSGPFVEGSIVRISMENFLTYDICEVSPGPHLNMIVGAN
GTGKSSIVCAICLGLAGKPAFMGRADKVGFFVKRGCSRGMVEIELSPKNPEQKIIKRVIALEGDIVRTIGHKNRYVKVPRGHIWVEGDHH

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

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Fusion Protein Functional Features


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/chr9:72882891/chr7:110603621)
- 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
SMC5

SLF2,FAM178A

IMMP2L

Q96T52

1173FUNCTION: Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO. {ECO:0000269|PubMed:15814844}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSMC5chr9:72882890chr7:110603620ENST00000361138+32580_87126.666666666666671102.0Nucleotide bindingATP
HgeneSMC5chr9:72882891chr7:110603621ENST00000361138+32580_87126.666666666666671102.0Nucleotide bindingATP

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSMC5chr9:72882890chr7:110603620ENST00000361138+325207_445126.666666666666671102.0Coiled coilOntology_term=ECO:0000255
HgeneSMC5chr9:72882890chr7:110603620ENST00000361138+325647_828126.666666666666671102.0Coiled coilOntology_term=ECO:0000255
HgeneSMC5chr9:72882890chr7:110603620ENST00000361138+325888_927126.666666666666671102.0Coiled coilOntology_term=ECO:0000255
HgeneSMC5chr9:72882891chr7:110603621ENST00000361138+325207_445126.666666666666671102.0Coiled coilOntology_term=ECO:0000255
HgeneSMC5chr9:72882891chr7:110603621ENST00000361138+325647_828126.666666666666671102.0Coiled coilOntology_term=ECO:0000255
HgeneSMC5chr9:72882891chr7:110603621ENST00000361138+325888_927126.666666666666671102.0Coiled coilOntology_term=ECO:0000255
HgeneSMC5chr9:72882890chr7:110603620ENST00000361138+325991_1026126.666666666666671102.0Compositional biasNote=Ala/Asp-rich (DA-box)
HgeneSMC5chr9:72882891chr7:110603621ENST00000361138+325991_1026126.666666666666671102.0Compositional biasNote=Ala/Asp-rich (DA-box)
HgeneSMC5chr9:72882890chr7:110603620ENST00000361138+325446_646126.666666666666671102.0RegionNote=Flexible hinge
HgeneSMC5chr9:72882891chr7:110603621ENST00000361138+325446_646126.666666666666671102.0RegionNote=Flexible hinge
TgeneIMMP2Lchr9:72882890chr7:110603620ENST000003317623719_3779.66666666666667176.0TransmembraneHelical
TgeneIMMP2Lchr9:72882890chr7:110603620ENST000004057092619_3779.66666666666667176.0TransmembraneHelical
TgeneIMMP2Lchr9:72882890chr7:110603620ENST000004153621519_3779.66666666666667176.0TransmembraneHelical
TgeneIMMP2Lchr9:72882890chr7:110603620ENST000004376871419_3779.66666666666667111.0TransmembraneHelical
TgeneIMMP2Lchr9:72882890chr7:110603620ENST000004472152519_3779.66666666666667111.0TransmembraneHelical
TgeneIMMP2Lchr9:72882890chr7:110603620ENST000004528953719_3779.66666666666667176.0TransmembraneHelical
TgeneIMMP2Lchr9:72882891chr7:110603621ENST000003317623719_3779.66666666666667176.0TransmembraneHelical
TgeneIMMP2Lchr9:72882891chr7:110603621ENST000004057092619_3779.66666666666667176.0TransmembraneHelical
TgeneIMMP2Lchr9:72882891chr7:110603621ENST000004153621519_3779.66666666666667176.0TransmembraneHelical
TgeneIMMP2Lchr9:72882891chr7:110603621ENST000004376871419_3779.66666666666667111.0TransmembraneHelical
TgeneIMMP2Lchr9:72882891chr7:110603621ENST000004472152519_3779.66666666666667111.0TransmembraneHelical
TgeneIMMP2Lchr9:72882891chr7:110603621ENST000004528953719_3779.66666666666667176.0TransmembraneHelical


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
SMC5_pLDDT.png
all structure
all structure
IMMP2L_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
SMC5
IMMP2L


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to SMC5-IMMP2L


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to SMC5-IMMP2L


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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