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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:PITPNB-CCDC117 (FusionGDB2 ID:65569)

Fusion Gene Summary for PITPNB-CCDC117

check button Fusion gene summary
Fusion gene informationFusion gene name: PITPNB-CCDC117
Fusion gene ID: 65569
HgeneTgene
Gene symbol

PITPNB

CCDC117

Gene ID

23760

150275

Gene namephosphatidylinositol transfer protein betacoiled-coil domain containing 117
SynonymsPI-TP-beta|PtdInsTP|VIB1BdJ366L4.1
Cytomap

22q12.1

22q12.1

Type of geneprotein-codingprotein-coding
Descriptionphosphatidylinositol transfer protein beta isoformPtdIns transfer protein betaphosphotidylinositol transfer protein, betacoiled-coil domain-containing protein 117
Modification date2020031320200313
UniProtAcc.

Q8IWD4

Ensembl transtripts involved in fusion geneENST00000320996, ENST00000335272, 
ENST00000455418, 
ENST00000443309, 
ENST00000421503, ENST00000249064, 
ENST00000448492, 
Fusion gene scores* DoF score9 X 7 X 5=3153 X 3 X 2=18
# samples 93
** MAII scorelog2(9/315*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PITPNB [Title/Abstract] AND CCDC117 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPITPNB(28306952)-CCDC117(29176934), # samples:1
Anticipated loss of major functional domain due to fusion event.PITPNB-CCDC117 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PITPNB-CCDC117 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted 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
HgenePITPNB

GO:0015914

phospholipid transport

16274224


check buttonFusion gene breakpoints across PITPNB (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 CCDC117 (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
ChiTaRS5.0N/ADB095411PITPNBchr22

28306952

-CCDC117chr22

29176934

+


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Fusion Gene ORF analysis for PITPNB-CCDC117

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-5UTRENST00000320996ENST00000443309PITPNBchr22

28306952

-CCDC117chr22

29176934

+
5CDS-5UTRENST00000335272ENST00000443309PITPNBchr22

28306952

-CCDC117chr22

29176934

+
5CDS-5UTRENST00000455418ENST00000443309PITPNBchr22

28306952

-CCDC117chr22

29176934

+
5CDS-intronENST00000320996ENST00000421503PITPNBchr22

28306952

-CCDC117chr22

29176934

+
5CDS-intronENST00000335272ENST00000421503PITPNBchr22

28306952

-CCDC117chr22

29176934

+
5CDS-intronENST00000455418ENST00000421503PITPNBchr22

28306952

-CCDC117chr22

29176934

+
Frame-shiftENST00000335272ENST00000249064PITPNBchr22

28306952

-CCDC117chr22

29176934

+
Frame-shiftENST00000335272ENST00000448492PITPNBchr22

28306952

-CCDC117chr22

29176934

+
Frame-shiftENST00000455418ENST00000249064PITPNBchr22

28306952

-CCDC117chr22

29176934

+
Frame-shiftENST00000455418ENST00000448492PITPNBchr22

28306952

-CCDC117chr22

29176934

+
In-frameENST00000320996ENST00000249064PITPNBchr22

28306952

-CCDC117chr22

29176934

+
In-frameENST00000320996ENST00000448492PITPNBchr22

28306952

-CCDC117chr22

29176934

+

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)
ENST00000320996PITPNBchr2228306952-ENST00000249064CCDC117chr2229176934+383126164861265
ENST00000320996PITPNBchr2228306952-ENST00000448492CCDC117chr2229176934+98926164861265

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
ENST00000320996ENST00000249064PITPNBchr2228306952-CCDC117chr2229176934+0.0003092750.9996908
ENST00000320996ENST00000448492PITPNBchr2228306952-CCDC117chr2229176934+0.0015380990.99846196

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Fusion Genomic Features for PITPNB-CCDC117


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)
PITPNBchr2228306951-CCDC117chr2229176935+2.98E-060.999997
PITPNBchr2228306951-CCDC117chr2229176935+2.98E-060.999997

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.
genomic feature of top 1%

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Fusion Protein Features for PITPNB-CCDC117


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/chr22:28306952/chr22:29176934)
- 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
.CCDC117

Q8IWD4

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
TgeneCCDC117chr22:28306952chr22:29176934ENST0000024906415141_16879280.0Coiled coilOntology_term=ECO:0000255

- 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 PITPNB-CCDC117


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.
>65569_65569_1_PITPNB-CCDC117_PITPNB_chr22_28306952_ENST00000320996_CCDC117_chr22_29176934_ENST00000249064_length(transcript)=3831nt_BP=261nt
TGAGAGGCGGTAGCGGCGGCGGCGGCGGTGGTATCGGCGGCAGCTGTGAGGGGGTTCCGGGAAGATGGTGCTGATCAAGGAATTCCGTGT
GGTTTTGCCATGTTCTGTTCAGGAGTATCAGGTTGGGCAGCTTTACTCTGTTGCAGAAGCTAGTAAGAATGAGACTGGTGGTGGAGAAGG
AATTGAAGTCTTAAAGAATGAACCTTATGAGAAGGATGGAGAAAAGGGACAGTATACGCACAAAATTTATCACCTAAAGAGTTGTCCAGT
AAGAAAGAAAAGGATAACTGAAGCAGAGCTCTGTGCTGGTCCTAATGACTGGATTCTTTGTGCACATCAGGATGTAGAGGGGCATGGAGT
AAATCCCAGTGTTAGTGGCCTTTCCATACCTGGGATATTAGATGTTATTTGTGAAGAAATGGATCAGACAACTGGAGAACCACAGTGTGA
AGTTGCCCGAAGGAAGCTTCAGGAGATTGAGGACAGGATAATTGATGAAGATGAAGAAGTTGAAGCTGACAGAAATGTTAACCATCTCCC
CAGTCTTGTCCTTTCTGATACCATGAAAACAGGTTTGAAGAGGGAATTTGATGAAGTTTTTACAAAGAAAATGATTGAGTCTATGAGCCG
TCCTTCCATGGAGCTTGTTCTCTGGAAACCCCTCCCTGAACTCCTTTCTGATAAGCCAAAGCCATCCTCTAATACTAAGAACTATACAGG
AGAGAGCCAAGCTAAGCATGTAGCTGCTGGCACTGCCTTCCCTCAGAGAACTGAACTGTTTTCGGAACCTCGGCCAACAGGGATGTCTCT
TTATAATAGTTTGGAGACAGCTACTAGCACAGAAGAAGAGATGGAACTCTAGAAACCAATTTCTACACTAAAGTTGTCAAATGTTAGAAG
AATCCTGTGTTCAGTTATGAGACTCTTTGCATAGTATAGGGACTTGAAAGTTTTATGAGACGGGTGTAATAATATCTCCACCTGTGATTT
GGGGGTGGGACTCTTATTTTGGGTAGCCATTTATTGACTTCACCTTTTTGCCAAGGACGTTTGTCTCAAGGGAAAAGCAGTTTTCTGTGG
GGCTTATTAAAGGAATGTTGGTTTACATTGTCTTCAAAGACAAGTATAGAAGCTGTATGTGTAAGGGTGACTTAAATCATATGTCACATT
GTCTAAACTATTCAGACACTTGGAGAATATTCTCCTTGAATTAAAAAAGATGATTAAGAAGGATGCTCCTACAACTGTATCCTGACAGTT
AAGTCACAGCTTAATGTGTAGATATGAGCTGTTTACAGTGGTGACTATATATAATTGGGGAGAAGAAGGGAAGAGAGCAGCAGTAGCTTA
AGCCTGTTGCTAAGAAATTTAATTTCTTAGCAACTTGTAATTTAGTTATCAATTCAATATAGCTCTGTTGATTAAATAGCCGATAGTATT
GTGGCTCTCCTCTTTGACTATGAAAATATAGAGAAAGTTTTTTCTTTAAGGCTTTTTTGCCTTGTGCCACTGTTGCTCCTTGGTTTCCCT
TGCGTAATTGATAAGCCCAGTTATTCAGTAATGTTTACAAATTAATTGACTTTGATAGTTAAAAGATTATGAGGTAACCCATCTGCAATT
TGCCTGTGGGAGAAGCATCCTTTAGTTCATCTTAAGGAAGTGCTTTATCAGCTAAACCCAACATTGATAACTTTGGTAATTTTTTTAAAA
AGTTATACTTGTATTAGCAAGTTTTTTTTTTTTTCCCCCACCGCAACCTCCATCTCCCGGGTTCAAGCAATTCTCCTGCCTCACCCTCCC
AAGTAGCTGGGATTACAGGTGCCCACCTCCACGCCCAGCTAATTTTTGTATTTTTAATAGAGACCGGTTTTGCCATGTTGGCCAGGCTGG
TCTCGAACTCCTGACCTCAGGTGATCTGCCCACCCCAGCCTCCCAAAATGCTGGGATTACAGGCGTGAGCCACGGCACGCAGCCAGCAAG
TTGTTTTTAAATGTTAATATAGAAAACAGTGAAGGATTAGCTGAAAATATATGAGCAGGTGACATTGAGGTTTACTGAAATAGCCAATTT
GACTGGTGCTTAGACTATTGTGCAGTAAACCTAAAAGGTAGTGGAGAATTGCTTCCTGCTAGCAGGAAGCCTTCATCTTCTTGAGTACCC
AAACCAGGCTTCAGGTGTCCTTTGAGGATAGCCAGGTTTGAAATTTTTAGTTTCTCAGGAAGAGCTCTTCTATGTGGCAGGGGCTGATAG
GGCAAAATAAAATGACAATTTCTTTATTGCTACAGAGTATCCTCTATAAGTTATTAAACGAGTGTAATGGTATAATGCCCTTCCATCACA
CAACAGGACACCACCCCAGTTTTGTTTTCTGGGTTTCTTCCCCCTTTGTAGGAATCAGATACCTTTTGTAGAAAAAAATGGCTTATGCCA
CGTAAAGGTGAATTTTTAGAAACCACCTTCTAGGCGTTTTTGGAACCCTTACTGAAATCCCTCCCCTTGTTACAGATGGCGTAGAAGTCA
CAAGTCTGTTAATTGGACTGTTGCTTCTTTGCCTGTTCCTGCTTTCTCTTTCTGTCTGGATAGTCAGGAAAAGATTTAATGTTTAATATT
TAAACAAAATATTTAATGTCTATACAGTAAAATTATTCAAACTTCAAACCAGTATTGAAAGCAGTTGGAAACCAGCTAATAGTTTCTTAA
TCTCAGATTTCGAGATGAATGTAAACTGTATTCTTTTGAAATGTGCAAGTGTTTGATTCATGCCATTTGATAAACTTCTGCCTTGTAGTC
ATTGTTTGATGGGACCAACTTGTAAAGTATGAGCCTTAAATAAATCTCCATGCTGAAAAATGTGTTCTAATGCAACACAAAAACATGAAG
TGACTGCCCAGAGGTAGAGTTAGTGTTTAGGTGGAAAGGGAGATGACAGCTTTCCAAAGAAGGACCTAAAACACACCAAGATTGTCTTCT
ACAGGAATTGCTGGGCAGGTCTCCGACTAAAGGTCTTATGATGAAAAGGAAGAAACAAGCCCCCAACACAAGGCTCTGATACTACTGGTA
AATGTAGGAGAGAATTAAGAATCTGTTAATTAAAATCCAAACAGAGCTTATTTCAGTAGTCAAGTTACCTGACATGATAATTATTTCTGC
AGGATAATTGATGTTTTATGTTCTTTTTTGGACTTTATCTTCTTGCAAAAATTTCTACAAAAATTGTTTTCTTCATCCTTGTGGTGCTTA
TTCATCTGAGCCGTCTCCACAGTCCCAATGCCTCTGCTTTTTGTTTTACTTTTGTAGCATAAGGTTTTTGCTTTTGCTTTGCCTTAAGAG
TTCCCTAGGGAGTTACCAGGGCTTTTCGTTTTGTGTAGCTTTTGCAGCATGGATCAAACATTGGCTTACTGTGCTAATGTGTGAAGAGAA
AAAATTCTCTAAAGCAGGTGAGCTTTAATGAACAAATGTGTATTTTATCTGAGTTTGAGTAGGGTGCGTTGTGGATTTTGTTTTTTGGGT
TTTTTTTTTTTTTTTGTAATTATATGAAGAAAGTCCAGTTCTCATAAATATTGATCACTTAAAAAACTTACTCTTTCTTGAAAAGGTACA
CATGTAAAATTTAGGAAAATAACTAAAGTAGGGGCTGGAACCATAAGAAGAATGTTTATCAGCACGTTCATTTATTATTTTGGATTTGGA
ACTTGGCTTTGTTTTTCAATAGTGACAAGAATGGTTCAGTTCTAGGAATGTTCTGGAAGATGCTGTTAATTTTACTTTAAAATGAGAATC

>65569_65569_1_PITPNB-CCDC117_PITPNB_chr22_28306952_ENST00000320996_CCDC117_chr22_29176934_ENST00000249064_length(amino acids)=265AA_BP=65
MVLIKEFRVVLPCSVQEYQVGQLYSVAEASKNETGGGEGIEVLKNEPYEKDGEKGQYTHKIYHLKSCPVRKKRITEAELCAGPNDWILCA
HQDVEGHGVNPSVSGLSIPGILDVICEEMDQTTGEPQCEVARRKLQEIEDRIIDEDEEVEADRNVNHLPSLVLSDTMKTGLKREFDEVFT

--------------------------------------------------------------
>65569_65569_2_PITPNB-CCDC117_PITPNB_chr22_28306952_ENST00000320996_CCDC117_chr22_29176934_ENST00000448492_length(transcript)=989nt_BP=261nt
TGAGAGGCGGTAGCGGCGGCGGCGGCGGTGGTATCGGCGGCAGCTGTGAGGGGGTTCCGGGAAGATGGTGCTGATCAAGGAATTCCGTGT
GGTTTTGCCATGTTCTGTTCAGGAGTATCAGGTTGGGCAGCTTTACTCTGTTGCAGAAGCTAGTAAGAATGAGACTGGTGGTGGAGAAGG
AATTGAAGTCTTAAAGAATGAACCTTATGAGAAGGATGGAGAAAAGGGACAGTATACGCACAAAATTTATCACCTAAAGAGTTGTCCAGT
AAGAAAGAAAAGGATAACTGAAGCAGAGCTCTGTGCTGGTCCTAATGACTGGATTCTTTGTGCACATCAGGATGTAGAGGGGCATGGAGT
AAATCCCAGTGTTAGTGGCCTTTCCATACCTGGGATATTAGATGTTATTTGTGAAGAAATGGATCAGACAACTGGAGAACCACAGTGTGA
AGTTGCCCGAAGGAAGCTTCAGGAGATTGAGGACAGGATAATTGATGAAGATGAAGAAGTTGAAGCTGACAGAAATGTTAACCATCTCCC
CAGTCTTGTCCTTTCTGATACCATGAAAACAGGTTTGAAGAGGGAATTTGATGAAGTTTTTACAAAGAAAATGATTGAGTCTATGAGCCG
TCCTTCCATGGAGCTTGTTCTCTGGAAACCCCTCCCTGAACTCCTTTCTGATAAGCCAAAGCCATCCTCTAATACTAAGAACTATACAGG
AGAGAGCCAAGCTAAGCATGTAGCTGCTGGCACTGCCTTCCCTCAGAGAACTGAACTGTTTTCGGAACCTCGGCCAACAGGGATGTCTCT
TTATAATAGTTTGGAGACAGCTACTAGCACAGAAGAAGAGATGGAACTCTAGAAACCAATTTCTACACTAAAGTTGTCAAATGTTAGAAG

>65569_65569_2_PITPNB-CCDC117_PITPNB_chr22_28306952_ENST00000320996_CCDC117_chr22_29176934_ENST00000448492_length(amino acids)=265AA_BP=65
MVLIKEFRVVLPCSVQEYQVGQLYSVAEASKNETGGGEGIEVLKNEPYEKDGEKGQYTHKIYHLKSCPVRKKRITEAELCAGPNDWILCA
HQDVEGHGVNPSVSGLSIPGILDVICEEMDQTTGEPQCEVARRKLQEIEDRIIDEDEEVEADRNVNHLPSLVLSDTMKTGLKREFDEVFT

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

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Fusion Gene PPI Analysis for PITPNB-CCDC117


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 PITPNB-CCDC117


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 PITPNB-CCDC117


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