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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:CD2AP-CDC5L (FusionGDB2 ID:14486)

Fusion Gene Summary for CD2AP-CDC5L

check button Fusion gene summary
Fusion gene informationFusion gene name: CD2AP-CDC5L
Fusion gene ID: 14486
HgeneTgene
Gene symbol

CD2AP

CDC5L

Gene ID

23607

988

Gene nameCD2 associated proteincell division cycle 5 like
SynonymsCMSCDC5|CDC5-LIKE|CEF1|PCDC5RP|dJ319D22.1
Cytomap

6p12.3

6p21.1

Type of geneprotein-codingprotein-coding
DescriptionCD2-associated proteinCas ligand with multiple Src homology 3 (SH3) domainsadapter protein CMScas ligand with multiple SH3 domainscell division cycle 5-like proteinCDC5 cell division cycle 5-likeCdc5-related proteindJ319D22.1 (CDC5-like protein)pombe cdc5-related protein
Modification date2020032720200313
UniProtAcc.

Q99459

Ensembl transtripts involved in fusion geneENST00000359314, ENST00000486693, 
ENST00000371477, 
Fusion gene scores* DoF score18 X 10 X 12=21608 X 6 X 6=288
# samples 208
** MAII scorelog2(20/2160*10)=-3.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/288*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CD2AP [Title/Abstract] AND CDC5L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCD2AP(47471176)-CDC5L(44413392), # 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
TgeneCDC5L

GO:0000398

mRNA splicing, via spliceosome

28076346

TgeneCDC5L

GO:0045944

positive regulation of transcription by RNA polymerase II

11082045


check buttonFusion gene breakpoints across CD2AP (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across CDC5L (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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-FP-8210-01ACD2APchr6

47471176

+CDC5Lchr6

44413392

+


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Fusion Gene ORF analysis for CD2AP-CDC5L

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
In-frameENST00000359314ENST00000371477CD2APchr6

47471176

+CDC5Lchr6

44413392

+
intron-3CDSENST00000486693ENST00000371477CD2APchr6

47471176

+CDC5Lchr6

44413392

+

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)
ENST00000359314CD2APchr647471176+ENST00000371477CDC5Lchr644413392+4654621456938160

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
ENST00000359314ENST00000371477CD2APchr647471176+CDC5Lchr644413392+0.0018219430.9981781

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Fusion Genomic Features for CD2AP-CDC5L


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)
CD2APchr647471176+CDC5Lchr644413391+1.39E-060.99999857
CD2APchr647471176+CDC5Lchr644413391+1.39E-060.99999857

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.

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 CD2AP-CDC5L


check button Go to

FGviewer for the breakpoints of chr6:47471176-chr6:44413392

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.CDC5L

Q99459

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: DNA-binding protein involved in cell cycle control. May act as a transcription activator. Plays role in pre-mRNA splicing as core component of precatalytic, catalytic and postcatalytic spliceosomal complexes (PubMed:11991638, PubMed:20176811, PubMed:28502770, PubMed:28076346, PubMed:29361316, PubMed:29360106, PubMed:29301961, PubMed:30728453, PubMed:30705154). Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing. The PRP19-CDC5L complex may also play a role in the response to DNA damage (DDR) (PubMed:20176811). {ECO:0000269|PubMed:10570151, ECO:0000269|PubMed:11082045, ECO:0000269|PubMed:11101529, ECO:0000269|PubMed:11544257, ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:12927788, ECO:0000269|PubMed:18583928, ECO:0000269|PubMed:20176811, ECO:0000269|PubMed:24332808, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770, ECO:0000269|PubMed:29301961, ECO:0000269|PubMed:29360106, ECO:0000269|PubMed:29361316, ECO:0000269|PubMed:30705154, ECO:0000269|PubMed:30728453, ECO:0000269|PubMed:9038199, ECO:0000269|PubMed:9468527, ECO:0000269|PubMed:9632794}.

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
TgeneCDC5Lchr6:47471176chr6:44413392ENST000003714771316764_802697.0803.0Coiled coilOntology_term=ECO:0000255

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCD2APchr6:47471176chr6:44413392ENST00000359314+218577_63855.0640.0Coiled coilOntology_term=ECO:0000255
HgeneCD2APchr6:47471176chr6:44413392ENST00000359314+218336_42255.0640.0Compositional biasNote=Pro-rich
HgeneCD2APchr6:47471176chr6:44413392ENST00000359314+218108_16755.0640.0DomainSH3 2
HgeneCD2APchr6:47471176chr6:44413392ENST00000359314+2181_5955.0640.0DomainSH3 1%3B truncated
HgeneCD2APchr6:47471176chr6:44413392ENST00000359314+218269_33055.0640.0DomainSH3 3
HgeneCD2APchr6:47471176chr6:44413392ENST00000359314+218336_35255.0640.0MotifSH3-binding
HgeneCD2APchr6:47471176chr6:44413392ENST00000359314+218378_39755.0640.0MotifSH3-binding
HgeneCD2APchr6:47471176chr6:44413392ENST00000359314+218410_42255.0640.0MotifSH3-binding
TgeneCDC5Lchr6:47471176chr6:44413392ENST000003714771316142_245697.0803.0Coiled coilOntology_term=ECO:0000255
TgeneCDC5Lchr6:47471176chr6:44413392ENST000003714771316676_701697.0803.0Coiled coilOntology_term=ECO:0000255
TgeneCDC5Lchr6:47471176chr6:44413392ENST00000371477131631_54697.0803.0DNA bindingH-T-H motif
TgeneCDC5Lchr6:47471176chr6:44413392ENST00000371477131682_104697.0803.0DNA bindingH-T-H motif
TgeneCDC5Lchr6:47471176chr6:44413392ENST0000037147713161_56697.0803.0DomainHTH myb-type 1
TgeneCDC5Lchr6:47471176chr6:44413392ENST00000371477131657_108697.0803.0DomainHTH myb-type 2
TgeneCDC5Lchr6:47471176chr6:44413392ENST000003714771316165_271697.0803.0MotifNuclear localization signal


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Fusion Gene Sequence for CD2AP-CDC5L


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.
>In-frame_ENST00000359314_ENST00000371477_TCGA-FP-8210-01A_CD2AP_chr6_47471176_+_CDC5L_chr6_44413392_length(transcript)=4654nt_BP=621nt
CTCTGTCTGGGTCCCCACCTTAGTCTACGGTGTCGCCTTTTCTAACTGCGAGTGCTAAGGAAGAGGCGAGGGGCGGGCTCCGAGGCTAGG
CGGGCGCTCGGGGTTGGAGCCGAGGGTCTGGGCAAACCGGTGGGTCCCTCCCCACTGCGGGAGCGGCCAGGGTGGGAAAACCGCGGTCGG
GCGGGCGGGGTAGGGCCCTCCCGCCGCCGTGGCTCCTGGGGAGGCCAGGGGTGAGGAGCTGTCGCCGCCTTTGCCTCTGCCTCGAGGGCC
GCGCTGAAGAGACTGGTAGGAGAGCGCCGCGGGCGGATGGAGGCGACTCTTCGCCCCGCCTGAGCTCAGGAGGGGCTAGCGCGGAGCGCG
GGTCCCGCCTCCAGCCGCGGGAGCGGCCGCGCGAGCCACCACTGGAGGAGGAGGAGGAGGAGCGGACGTCGGCTTCTCCCCGCGGGAGCC
CCCAGCATGGTTGACTATATTGTGGAGTATGACTATGATGCTGTACATGATGATGAATTAACTATTCGAGTTGGAGAAATCATCAGGAAT
GTGAAAAAGCTACAGGAGGAAGGGTGGCTGGAAGGAGAACTAAATGGGAGAAGAGGAATGTTCCCTGACAATTTCGTTAAGATAAACAGG
GGTCACATGACGACAGAAGCCAAGAGGGCTGCAAAGATGGAAAAGAAGATGAAAATTTTGCTTGGGGGTTACCAGTCTCGTGCTATGGGG
CTCATGAAACAGTTGAATGACTTATGGGACCAAATTGAACAGGCTCACTTGGAGTTACGCACTTTTGAAGAACTCAAGAAACATGAAGAT
TCTGCTATTCCCCGGAGGCTAGAGTGTCTAAAAGAAGACGTTCAGCGACAACAAGAAAGAGAAAAGGAACTTCAACATAGATATGCTGAT
TTGCTGCTGGAGAAAGAGACTTTAAAGTCAAAATTCTGAAGTACAGTTTATATTCTGTCACAGGATTAATTAATTGCCGGTTTTCATACT
CTAGAAGGCTGAAACTGATGTTTATCTTCATTGACAAATTTACCCACCATCTGTGGTTTTTCAGTTGTTTATTTTAAATGATATCGATCT
TACACATTCTGTGTATAAAGACCTTAACTCCACAGGACGGACATTTTAGAGTTTAAATTATTAAGGCTATCATTCTTTTAGTAATGTCAT
ATTTGCAAACTTTTTTAGTTTTGGCCTTTAATTTAAAAAGCCTAATTTTAAAGTGCTGCCTGTGAGTAACTCTTGAATAAAAACAAAATA
TAAAAAATTGAGAATGTAGCCTTTTGTTTGAAGTAATTAGATACTTAAGAGTGCCTGCAAACCAGCAGCTATGTACTCTGTGTCATATTT
AATGAGTAACTCTTGGGTAATCAAAATGGTGATGCAGTATCTTAAACACTTAAGAGGCAGTTCTTTGTGGCTTTGTTAGTTTCAGCAAAG
AGTGGTCATTTCTGTATACACTGACAAGTTAGATTAACTTTTTAGTACCTCAAATTTTTTTTTTGTTAATATCACTTTAAAGAAGGTCTC
TTGTCTGCCAGCTACTTAAATAATTTATGGGTCAGGGCTTAAAAGATTTAACTTCCTTGCCCCATTATTTTCTTATAAGTATTTTTTGAC
AAAGGCATTTTAAAAGTTAATTTCAAGAAGGCCATCAAACTTAAAGCTCTATGTTTAGCCTAAGAAGTCAGTTACATCAGTGTAGAATTT
GGGGAATGGATAGAGGTGGAGATATTTAATTTTATATAATTCATATAAATTGATTTAGTTACAGTATCAGTTGGCTACAAGCTCATTATA
GACTAGCAATGTTTTGACATCACCAAAAACGTTTGCCCAGTCTTAGAATACTAGGGACTATAGGAAGGGAAGGGATTCATTCATTCATTC
GATATTGAATGTATACCCTGTGCCAGAGTCTTAGAGAGAGAACAACAAACAAAATAGGCCTAGTTCTTGTTTAGTAGAGCTTATAGTCTT
TTGAGAATGACAGACAATTAAAATCCAAATGTTTATTTGGTGATTCTTATGTGTCAGACACTTAAGTGTTGGGAGATAAGCAGTTATTAA
GACAGAGTTCTTGCTCTCATGGAGGTGACATTAGTGGGGAGGAGATACTAAGTATGTCCAGGGAAAGTATCAGACCATGAGTTTTAGATT
CTGTGGAGGAAATTAAAGTAGGGTGATTATGAGATAGTGAATGAGTGGCTATTTTAGACTGGACGATCAAAGAGACCTCTTGGAAGGCAG
CTATGCTCACCACTATACCACTGCACTGTGCCGCACCGTACCACTATAAGCTGCACGGCCAAAGAGACCTCTTAAAGAAGTAACATTTAA
GATAACATGTGATTGACATTTTAGAATGGGCTATCCTTGTGAGATTCAAGGAAAGAACATCCTAGGTGGAGTGAATAGCAAACATAAAGC
CTCTTTTGTATGTTTGAGGAACAAAAAGGACAATGCAGCTAGAGTGTCAAGAATGGCATTTCTGTATATAAGACCTCGTTGTATAGAGCC
ACATAAATAAGGCTATAATAAGGAATTTGGATCTTACTTTAAATATGATAAGAATCGATGAGAAGATCTAAGCAAAGGAATGACATGATC
AGATTTGGTTTTAGAAACATCACTATCTCCTTAGTGTGTAAAATCTCACCAGGCTGGAGATAGGGAAGCCAGTCCAATTAGGAGCCTGAT
GCAGTGATCCAGACAAAAAAATAATAGTGATTCTAACTAGAGTCCAGGTAATAGTAGTGGAGATATGTGGAGAGACATGATAGGTATATA
CTTAATAGTCTTATCAGACGATAAATTGATATTTTCCTGGTGTGTAGTCACTTAATTCAAATACTTTTTTCAGTAAGTTCTGGGTTTTCT
AGGAAAAACTTCAGTATCATCAGTGAATAATGATAGTGTTTCTTCTGATAGTTTTATTTCACTTTTATTGCATGTTTTGTTATCTGAAAT
GTTTAGGACAATGTTAACAATAATGATGTTAGACATTTTTTTTTCTTATTTTAATGGGAATGTCCATAGTTTTAAGTTTGCTGTTGGGAG
TTAGATAGTCTTTATCTGAAAGACAGTGTCTCTCTTTTAGTTTTTAAAGAGTTTGAATTAGAAATGGCTCTGGAACTTTAAACAGTATAC
CATTTGGGCATCTATTAAAGCATTCATATAATTGTTCTCATTTGATGTTTTGATGAGGTATATTAATAGATTTTCCCACATTAAATCATC
TTTGCACTCCTGGAATCAGGTAGATTAATTTTTAAAAGAAATTTTAAAGGATTTATAGTTTATTTGCACTTTTTGTAGACTTGAATTATA
TGGATTTAAAAGTTGATCTAATATTAATAAAGGCTCACTTTGTTTTCAAAATTTGAAGTAATTCACATACTTATAGCCTAAAAAAATCGG
CAGGAATTACAAAATTTCAAAACTGGCACATTGTAAACTGCATATGCATTTGCCAGGTAGTGGTGCCACTTGAAATGGTGAACAGACACA
CTGTTATCCTTTGTCAGTATCCTGTAAAGCCCAGGATTCTTTACCAGCACCATACAGCGATTTTGGTGACTATTTTAACATTCACACTGA
GGCCAGGGGTGGTGAGTCATGCCTGTAATCCTAGCACTTTGGGAGGCCAAGGTGGGAGGATCATTTGAGCTCAGGAGTTCAAGATTAGCC
TGGGTAACATAGTGAGACCCTGTCTCTATTAAAAAATAATAATAAAAATAACATTCACATTGGTATTGTTCACTAAGGTATTGGTTGTTA
AGGCATTCATTAAGGTATTGTTAAAACTTGTGTTAAGCATGTTAAAGTCTCAGTAACTTTGGGATAGAAATAAAATGTGATAAAAAGCTG
AAAGAAACCACCACAAGGGAGAGTCCTTTTTGAAATATTAGAGACATAATGCTGTCTAATAAAAAACGACATCAAAGAAAAACTACACTA
CAGTGACTGCAGACTTAATGTTGGCCAACCATGCATCCTCCCTAGAAATGCATTTGAATTTGATTTACTAATCTTTTATTTAGGAAATTT
ACATTTTTACATTAGTGAGATTGGTCTTTTGGGCTATTGTACTTTTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTCTCACCCAGGCT
GGAGTGCAGTAGTGCAATCTTGGCCCACTGCAACCTCTGCCTCCTGGGCTCGAGTGATTCTCTGCCTCAGCCTTCCAAGTAGCTGGGACT
ACAGGCATGTGCCACCGCACCTGGCTAATTTTTGTGTTTTTAGTAGAGATGGGGTTTTGCTATGTTGGCCAGGCTGGTCTTGAATTCCTG
ACCTCAGGTGATCCACCTACCTCGGCCTCCCAAAGTGCTAGAATTACAGGTGTGAGCCACCATGCCCAGCCTGGTTATTGTATTTTGATA
TTGGGATTTTGCTAGCTCTCTAAAGTAAATAGGATAACTGTATATCTTTTTCTGTGCATTAAGCAGTTATAACATGGGAATGATTTGTTC
ATGAAAGGTTGAAAGTCTGTACTTACAGAACTTTTGAGTTCACAGTGCTTTCTGGAAATAATTTCTTTATAACTGTCAGTTTCTTTTGTG

>In-frame_ENST00000359314_ENST00000371477_TCGA-FP-8210-01A_CD2AP_chr6_47471176_+_CDC5L_chr6_44413392_length(amino acids)=160AA_start in transcript=456_stop in transcript=938
MVDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKINRGHMTTEAKRAAKMEKKMKILLGGYQSRAMGLM

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Fusion Gene PPI Analysis for CD2AP-CDC5L


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
TgeneCDC5Lchr6:47471176chr6:44413392ENST000003714771316706_800697.0803.0PLRG1


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
HgeneCD2APchr6:47471176chr6:44413392ENST00000359314+2181_17555.0640.0ANLN and localization to the midbody
TgeneCDC5Lchr6:47471176chr6:44413392ENST000003714771316501_659697.0803.0DAPK3
TgeneCDC5Lchr6:47471176chr6:44413392ENST000003714771316260_606697.0803.0PPP1R8


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 CD2AP-CDC5L


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 CD2AP-CDC5L


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCD2APC0002395Alzheimer's Disease3CTD_human
HgeneCD2APC0011265Presenile dementia3CTD_human
HgeneCD2APC0276496Familial Alzheimer Disease (FAD)3CTD_human
HgeneCD2APC0494463Alzheimer Disease, Late Onset3CTD_human
HgeneCD2APC0546126Acute Confusional Senile Dementia3CTD_human
HgeneCD2APC0750900Alzheimer's Disease, Focal Onset3CTD_human
HgeneCD2APC0750901Alzheimer Disease, Early Onset3CTD_human
HgeneCD2APC1842982FOCAL SEGMENTAL GLOMERULOSCLEROSIS 3, SUSCEPTIBILITY TO2GENOMICS_ENGLAND
HgeneCD2APC1868672NEPHROTIC SYNDROME, STEROID-RESISTANT, AUTOSOMAL RECESSIVE1ORPHANET