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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:GALNTL4-IER3IP1 (FusionGDB2 ID:HG374378TG51124)

Fusion Gene Summary for GALNTL4-IER3IP1

check button Fusion gene summary
Fusion gene informationFusion gene name: GALNTL4-IER3IP1
Fusion gene ID: hg374378tg51124
HgeneTgene
Gene symbol

GALNTL4

IER3IP1

Gene ID

374378

51124

Gene namepolypeptide N-acetylgalactosaminyltransferase 18immediate early response 3 interacting protein 1
SynonymsGALNACT18|GALNT15|GALNTL4|GalNAc-T15|GalNAc-T18HSPC039|MEDS|PRO2309
Cytomap('GALNT18','GALNTL4')('IER3IP1','IER3IP1')

11p15.4

18q21.1

Type of geneprotein-codingprotein-coding
Descriptionpolypeptide N-acetylgalactosaminyltransferase 18GalNAc-transferase 18UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-like protein 4UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15UDP-N-acetyl-alpha-D-galactoimmediate early response 3-interacting protein 1
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000227756, ENST00000526064, 
Fusion gene scores* DoF score12 X 5 X 9=5405 X 3 X 3=45
# samples 135
** MAII scorelog2(13/540*10)=-2.05444778402238
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/45*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: GALNTL4 [Title/Abstract] AND IER3IP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGALNT18(11454168)-IER3IP1(44683908), # samples:2
GALNTL4(11454168)-IER3IP1(44683908), # samples:1
Anticipated loss of major functional domain due to fusion event.GALNT18-IER3IP1 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.
GALNT18-IER3IP1 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.
GALNT18-IER3IP1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
GALNT18-IER3IP1 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
HgeneGALNTL4

GO:0006493

protein O-linked glycosylation

22186971


check buttonFusion gene breakpoints across GALNT18 (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 IER3IP1 (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
* 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-DK-A3IN-01AGALNT18chr11

11454168

-IER3IP1chr18

44683908

-
ChimerDB4BLCATCGA-DK-A3IN-01AGALNTL4chr11

11454168

-IER3IP1chr18

44683908

-


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Fusion Gene ORF analysis for GALNTL4-IER3IP1

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-shiftENST00000227756ENST00000588705GALNT18chr11

11454168

-IER3IP1chr18

44683908

-
In-frameENST00000227756ENST00000256433GALNT18chr11

11454168

-IER3IP1chr18

44683908

-
intron-3CDSENST00000526064ENST00000256433GALNT18chr11

11454168

-IER3IP1chr18

44683908

-
intron-3CDSENST00000526064ENST00000588705GALNT18chr11

11454168

-IER3IP1chr18

44683908

-

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)
ENST00000227756GALNT18chr1111454168-ENST00000256433IER3IP1chr1844683908-230010071991164321

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
ENST00000227756ENST00000256433GALNT18chr1111454168-IER3IP1chr1844683908-0.0014220680.99857795

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Fusion Genomic Features for GALNTL4-IER3IP1


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

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Fusion Protein Features for GALNTL4-IER3IP1


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/:11454168/:44683908)
- 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
..
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}.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
HgeneGALNT18chr11:11454168chr18:44683908ENST00000227756-3111_12198608.0Topological domainCytoplasmic
HgeneGALNT18chr11:11454168chr18:44683908ENST00000227756-31113_35198608.0TransmembraneHelical%3B Signal-anchor for type II membrane protein
TgeneIER3IP1chr11:11454168chr18:44683908ENST000002564330362_823083.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneGALNT18chr11:11454168chr18:44683908ENST00000227756-311469_599198608.0DomainRicin B-type lectin
HgeneGALNT18chr11:11454168chr18:44683908ENST00000227756-311153_267198608.0RegionNote=Catalytic subdomain A
HgeneGALNT18chr11:11454168chr18:44683908ENST00000227756-311324_385198608.0RegionNote=Catalytic subdomain B
HgeneGALNT18chr11:11454168chr18:44683908ENST00000227756-31136_607198608.0Topological domainLumenal
TgeneIER3IP1chr11:11454168chr18:44683908ENST00000256433032_223083.0TransmembraneHelical


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Fusion Gene Sequence for GALNTL4-IER3IP1


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.
>32265_32265_1_GALNT18-IER3IP1_GALNT18_chr11_11454168_ENST00000227756_IER3IP1_chr18_44683908_ENST00000256433_length(transcript)=2300nt_BP=1007nt
GCTGTTCTCCTAGCAGCGCGGGCCGGTCGGACCGCCAAGGCAGCCGGCGCTGGCGATGGGAAGCGGCGTGGCCGCCGACACAGGCAGTGG
CAAAGTTTCCCAGACGTACACATCTGGACGCGCGGCTGCCGGCTACCCGTGACCCCTCTAGGAAGGGTTCAGGGATTTTTAATTTGGAAA
AAAATCCACCTGGTTTCCTTTGTCAAGGTCTCTCCGGGTGGCCAGCGGCAGGAGCTGCAAACTTGGGCACGGCGGCTACACCGGCAGCGG
ACCGGGCTTTGGAGAACCTCGGGACTCAGGTGCTGAGGTGCCCAGCGGCTCCGGACGTGCTACGGGGTGCGAGCGCGGGGGAGTTCGGGG
CGCACGACAAGGAAGGGCCCCCGGGAGCTCTATATGGAGGAAGGAGCCCAGAATGGTGTGCACCAGGAAGACCAAAACTTTGGTGTCCAC
TTGCGTGATCCTGAGCGGCATGACTAACATCATCTGCCTGCTCTACGTGGGCTGGGTCACCAACTACATCGCCAGCGTGTATGTGCGGGG
GCAGGAGCCGGCGCCCGACAAGAAGCTGGAGGAAGACAAAGGGGACACTCTGAAGATTATTGAGCGGCTGGACCACCTGGAGAATGTCAT
CAAGCAGCACATTCAAGAGGCTCCTGCCAAGCCTGAGGAGGCAGAGGCCGAGCCCTTCACAGACTCCTCTCTGTTTGCACACTGGGGCCA
GGAGCTCAGCCCCGAAGGCCGGCGCGTGGCCCTGAAGCAATTCCAGTACTACGGCTACAACGCCTACCTCAGCGACCGCCTGCCCCTGGA
CCGGCCCCTGCCTGACCTCAGACCCAGTGGGTGCCGTAACCTCTCATTTCCTGACAGCCTGCCAGAGGTGAGCATCGTGTTCATCTTCGT
CAATGAAGCGCTTTCAGTGCTGCTGCGCTCCATCCACTCGGCCATGGAACGCACGCCCCCACATCTGCTCAAGGAGATCATTCTGGTGGA
TGACAACAGCAGTAACGTTGGCTGGGGAACAGACCAGGGAATTGGTGGATTTGGAGAAGAGCCGGGAATTAAATCACAGCTAATGAACCT
TATTCGATCTGTAAGAACCGTGATGAGAGTGCCATTGATAATAGTAAACTCAATTGCAATTGTGTTACTTTTATTATTTGGATGAATATC
AGTGGAGAAAATGGAGACTCAGAAGAGGACATGCCAGTAGAAGTTATTACTTTGGTCATTATTGGAATATTTATATCTTAGCTGGCTGAC
CTTGCACTTGTCAAAAATGTAAAGCTGAAAATAAAACCAGGGTTTCTATTTATCTGTTTTTTTTTTTAATGTTGCACTTGTAGTTTCATT
ACAAAAGATCAGATCATGAAAGGCAGTAACTCTCCAGGACTGGAATATCTGATTGCTCAGTGTTAATAGTAGTTCATGCTGTGGTGAGAT
TGTTAAAAGGGTGCAAGACTGTTGCTTCTCTTTTTTTAGATATTTTTCTATCTCTCACTTCTCAGGGATGAAATTCTTTTTCAAAGTTTT
GAAGTTCCTTGCAACTTAGCCATGATGTGAGTGGTTATCCCTAGATAAAATTAAAAGGATTTTTAAAAAGTAATTACTGCACATAAAATG
ATAAATAGGTAATTTGAATAATTTTATTTTAAGCTCCTTGGTTAATTATTTTGTCTATTGTCTCAGCTATAAATTCAAATTTATACATAC
TATTGAGTATTAATATTCTCTGATTTCAGGGAGAATTCTGTCAGTCACATGATGATTATGTTTTTGTTTAACATTCTTTCCATGCACTTG
TTATTTTATTAATTTGCCTGAATGATGAGACCAGACCAGTGTCTACAGATTTTCATTGTCAGAAAAATCTATAAGTCTGCCCTTTTTACA
ATGATGATTTAAAAAAAACAACAGCGTAAATATTAGCCCACAAGAGCAGTCCTAAACAATCACAATTACACTGTACTACCCAAGAAGACT
GTTTATTGTGAAGCATTTACCTTTCAAAAAATCATTACATTTCTATTTCTTGGTGGAGCAGCACATTGTGGAGTGTGATTCTTAATTCTT
CATTGAGTTTGTCAATAGGACATTGATGCTGGATAGGTTGTCTTTTGTTTTTATGTCTCAGACCATCTTGTGAGATTGTTTGCCTATCTC
ATAATACAGTTTTATGCAGAAAGGTTGAAACTATGTAAATGGTTTTTATGGAAATTATCAGTTACAATATTTTAAAGGTGTAGAATGGCA

>32265_32265_1_GALNT18-IER3IP1_GALNT18_chr11_11454168_ENST00000227756_IER3IP1_chr18_44683908_ENST00000256433_length(amino acids)=321AA_BP=269
MSRSLRVASGRSCKLGHGGYTGSGPGFGEPRDSGAEVPSGSGRATGCERGGVRGARQGRAPGSSIWRKEPRMVCTRKTKTLVSTCVILSG
MTNIICLLYVGWVTNYIASVYVRGQEPAPDKKLEEDKGDTLKIIERLDHLENVIKQHIQEAPAKPEEAEAEPFTDSSLFAHWGQELSPEG
RRVALKQFQYYGYNAYLSDRLPLDRPLPDLRPSGCRNLSFPDSLPEVSIVFIFVNEALSVLLRSIHSAMERTPPHLLKEIILVDDNSSNV

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

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Fusion Gene PPI Analysis for GALNTL4-IER3IP1


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 GALNTL4-IER3IP1


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 GALNTL4-IER3IP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC3280240MICROCEPHALY, EPILEPSY, AND DIABETES SYNDROME3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0158981Neonatal diabetes mellitus1GENOMICS_ENGLAND
TgeneC3714756Intellectual Disability1GENOMICS_ENGLAND
TgeneC4229700Microcephaly (-3 to -9 SD)1GENOMICS_ENGLAND