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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:ZMYM2-IFT88 (FusionGDB2 ID:100650)

Fusion Gene Summary for ZMYM2-IFT88

check button Fusion gene summary
Fusion gene informationFusion gene name: ZMYM2-IFT88
Fusion gene ID: 100650
HgeneTgene
Gene symbol

ZMYM2

IFT88

Gene ID

7750

8100

Gene namezinc finger MYM-type containing 2intraflagellar transport 88
SynonymsFIM|MYM|RAMP|SCLL|ZNF198D13S1056E|DAF19|TG737|TTC10|hTg737
Cytomap

13q12.11

13q12.11

Type of geneprotein-codingprotein-coding
Descriptionzinc finger MYM-type protein 2fused in myeloproliferative disorders proteinrearranged in an atypical myeloproliferative disorderzinc finger protein 198zinc finger, MYM-type 2intraflagellar transport protein 88 homologTPR repeat protein 10intraflagellar transport 88 homologpolaris homologprobe hTg737 (polycystic kidney disease, autosomal recessive)recessive polycystic kidney disease protein Tg737 homologtesticular tissue
Modification date2020031320200313
UniProtAcc.

Q13099

Ensembl transtripts involved in fusion geneENST00000382869, ENST00000382881, 
ENST00000382874, ENST00000382871, 
ENST00000382883, ENST00000494061, 
ENST00000382778, ENST00000351808, 
ENST00000319980, ENST00000537103, 
ENST00000461115, 
Fusion gene scores* DoF score19 X 16 X 11=334410 X 13 X 7=910
# samples 2112
** MAII scorelog2(21/3344*10)=-3.99311361441476
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/910*10)=-2.92283213947754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ZMYM2 [Title/Abstract] AND IFT88 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointZMYM2(20656270)-IFT88(21212471), # samples:1
Anticipated loss of major functional domain due to fusion event.ZMYM2-IFT88 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
ZMYM2-IFT88 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ZMYM2-IFT88 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
ZMYM2-IFT88 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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

check buttonFusion gene breakpoints across ZMYM2 (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 IFT88 (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
ChimerDB4BLCATCGA-E7-A677-01AZMYM2chr13

20656270

+IFT88chr13

21212471

+


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Fusion Gene ORF analysis for ZMYM2-IFT88

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
Frame-shiftENST00000382869ENST00000382778ZMYM2chr13

20656270

+IFT88chr13

21212471

+
Frame-shiftENST00000382869ENST00000351808ZMYM2chr13

20656270

+IFT88chr13

21212471

+
Frame-shiftENST00000382869ENST00000319980ZMYM2chr13

20656270

+IFT88chr13

21212471

+
Frame-shiftENST00000382869ENST00000537103ZMYM2chr13

20656270

+IFT88chr13

21212471

+
5CDS-intronENST00000382869ENST00000461115ZMYM2chr13

20656270

+IFT88chr13

21212471

+
intron-3CDSENST00000382881ENST00000382778ZMYM2chr13

20656270

+IFT88chr13

21212471

+
intron-3CDSENST00000382881ENST00000351808ZMYM2chr13

20656270

+IFT88chr13

21212471

+
intron-3CDSENST00000382881ENST00000319980ZMYM2chr13

20656270

+IFT88chr13

21212471

+
intron-3CDSENST00000382881ENST00000537103ZMYM2chr13

20656270

+IFT88chr13

21212471

+
intron-intronENST00000382881ENST00000461115ZMYM2chr13

20656270

+IFT88chr13

21212471

+
Frame-shiftENST00000382874ENST00000382778ZMYM2chr13

20656270

+IFT88chr13

21212471

+
Frame-shiftENST00000382874ENST00000351808ZMYM2chr13

20656270

+IFT88chr13

21212471

+
Frame-shiftENST00000382874ENST00000319980ZMYM2chr13

20656270

+IFT88chr13

21212471

+
Frame-shiftENST00000382874ENST00000537103ZMYM2chr13

20656270

+IFT88chr13

21212471

+
5CDS-intronENST00000382874ENST00000461115ZMYM2chr13

20656270

+IFT88chr13

21212471

+
Frame-shiftENST00000382871ENST00000382778ZMYM2chr13

20656270

+IFT88chr13

21212471

+
Frame-shiftENST00000382871ENST00000351808ZMYM2chr13

20656270

+IFT88chr13

21212471

+
Frame-shiftENST00000382871ENST00000319980ZMYM2chr13

20656270

+IFT88chr13

21212471

+
Frame-shiftENST00000382871ENST00000537103ZMYM2chr13

20656270

+IFT88chr13

21212471

+
5CDS-intronENST00000382871ENST00000461115ZMYM2chr13

20656270

+IFT88chr13

21212471

+
intron-3CDSENST00000382883ENST00000382778ZMYM2chr13

20656270

+IFT88chr13

21212471

+
intron-3CDSENST00000382883ENST00000351808ZMYM2chr13

20656270

+IFT88chr13

21212471

+
intron-3CDSENST00000382883ENST00000319980ZMYM2chr13

20656270

+IFT88chr13

21212471

+
intron-3CDSENST00000382883ENST00000537103ZMYM2chr13

20656270

+IFT88chr13

21212471

+
intron-intronENST00000382883ENST00000461115ZMYM2chr13

20656270

+IFT88chr13

21212471

+
3UTR-3CDSENST00000494061ENST00000382778ZMYM2chr13

20656270

+IFT88chr13

21212471

+
3UTR-3CDSENST00000494061ENST00000351808ZMYM2chr13

20656270

+IFT88chr13

21212471

+
3UTR-3CDSENST00000494061ENST00000319980ZMYM2chr13

20656270

+IFT88chr13

21212471

+
3UTR-3CDSENST00000494061ENST00000537103ZMYM2chr13

20656270

+IFT88chr13

21212471

+
3UTR-intronENST00000494061ENST00000461115ZMYM2chr13

20656270

+IFT88chr13

21212471

+

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)

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

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Fusion Genomic Features for ZMYM2-IFT88


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)
ZMYM2chr1320656270+IFT88chr1321212470+0.0265781660.9734219
ZMYM2chr1320656270+IFT88chr1321212470+0.0265781660.9734219

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 ZMYM2-IFT88


check button Go to

FGviewer for the breakpoints of :-:

.
- 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
.IFT88

Q13099

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: Involved in primary cilium biogenesis. Also involved in autophagy since it is required for trafficking of ATG16L and the expansion of the autophagic compartment. {ECO:0000250|UniProtKB:Q61371}.

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

- 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 ZMYM2-IFT88


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.

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Fusion Gene PPI Analysis for ZMYM2-IFT88


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 ZMYM2-IFT88


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 ZMYM2-IFT88


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneZMYM2C0020796Profound Mental Retardation1CTD_human
HgeneZMYM2C0025363Mental Retardation, Psychosocial1CTD_human
HgeneZMYM2C0027022Myeloproliferative disease1CTD_human
HgeneZMYM2C0917816Mental deficiency1CTD_human
HgeneZMYM2C3714756Intellectual Disability1CTD_human
TgeneIFT88C0085548Autosomal Recessive Polycystic Kidney Disease2CTD_human
TgeneIFT88C0023903Liver neoplasms1CTD_human
TgeneIFT88C0032927Precancerous Conditions1CTD_human
TgeneIFT88C0035334Retinitis Pigmentosa1ORPHANET
TgeneIFT88C0152427Polydactyly1CTD_human
TgeneIFT88C0238198Gastrointestinal Stromal Tumors1CTD_human
TgeneIFT88C0282313Condition, Preneoplastic1CTD_human
TgeneIFT88C0345904Malignant neoplasm of liver1CTD_human
TgeneIFT88C3179349Gastrointestinal Stromal Sarcoma1CTD_human