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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:SERGEF-KCNC1 (FusionGDB2 ID:80634)

Fusion Gene Summary for SERGEF-KCNC1

check button Fusion gene summary
Fusion gene informationFusion gene name: SERGEF-KCNC1
Fusion gene ID: 80634
HgeneTgene
Gene symbol

SERGEF

KCNC1

Gene ID

26297

3746

Gene namesecretion regulating guanine nucleotide exchange factorpotassium voltage-gated channel subfamily C member 1
SynonymsDELGEF|GnefrEPM7|KV3.1|KV4|NGK2
Cytomap

11p15.1

11p15.1

Type of geneprotein-codingprotein-coding
Descriptionsecretion-regulating guanine nucleotide exchange factordeafness locus associated putative guanine nucleotide exchange factorguanine nucleotide exchange factor-related proteinpotassium voltage-gated channel subfamily C member 1potassium channel, voltage gated Shaw related subfamily C, member 1voltage-gated potassium channel protein KV3.1voltage-gated potassium channel subunit Kv4
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000265965, ENST00000528200, 
ENST00000532212, ENST00000532265, 
ENST00000525802, ENST00000379472, 
ENST00000265969, 
Fusion gene scores* DoF score9 X 8 X 7=5041 X 1 X 1=1
# samples 101
** MAII scorelog2(10/504*10)=-2.33342373372519
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(1/1*10)=3.32192809488736
Context

PubMed: SERGEF [Title/Abstract] AND KCNC1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSERGEF(17981017)-KCNC1(17793212), # samples:3
Anticipated loss of major functional domain due to fusion event.SERGEF-KCNC1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
HgeneSERGEF

GO:0050709

negative regulation of protein secretion

12459492

TgeneKCNC1

GO:0051262

protein tetramerization

23734863


check buttonFusion gene breakpoints across SERGEF (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 KCNC1 (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
ChimerDB4SKCMTCGA-DA-A1HW-06ASERGEFchr11

17981017

-KCNC1chr11

17793212

+


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Fusion Gene ORF analysis for SERGEF-KCNC1

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-intronENST00000265965ENST00000525802SERGEFchr11

17981017

-KCNC1chr11

17793212

+
Frame-shiftENST00000265965ENST00000379472SERGEFchr11

17981017

-KCNC1chr11

17793212

+
In-frameENST00000265965ENST00000265969SERGEFchr11

17981017

-KCNC1chr11

17793212

+
intron-3CDSENST00000528200ENST00000265969SERGEFchr11

17981017

-KCNC1chr11

17793212

+
intron-3CDSENST00000528200ENST00000379472SERGEFchr11

17981017

-KCNC1chr11

17793212

+
intron-3CDSENST00000532212ENST00000265969SERGEFchr11

17981017

-KCNC1chr11

17793212

+
intron-3CDSENST00000532212ENST00000379472SERGEFchr11

17981017

-KCNC1chr11

17793212

+
intron-3CDSENST00000532265ENST00000265969SERGEFchr11

17981017

-KCNC1chr11

17793212

+
intron-3CDSENST00000532265ENST00000379472SERGEFchr11

17981017

-KCNC1chr11

17793212

+
intron-intronENST00000528200ENST00000525802SERGEFchr11

17981017

-KCNC1chr11

17793212

+
intron-intronENST00000532212ENST00000525802SERGEFchr11

17981017

-KCNC1chr11

17793212

+
intron-intronENST00000532265ENST00000525802SERGEFchr11

17981017

-KCNC1chr11

17793212

+

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)
ENST00000265965SERGEFchr1117981017-ENST00000265969KCNC1chr1117793212+328911631522350732

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
ENST00000265965ENST00000265969SERGEFchr1117981017-KCNC1chr1117793212+0.0027330070.997267

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Fusion Genomic Features for SERGEF-KCNC1


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)
SERGEFchr1117981016-KCNC1chr1117793211+1.25E-070.9999999
SERGEFchr1117981016-KCNC1chr1117793211+1.25E-070.9999999

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 SERGEF-KCNC1


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/chr11:17981017/chr11:17793212)
- 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
HgeneSERGEFchr11:17981017chr11:17793212ENST00000265965-911120_171337459.0RepeatNote=RCC1 3
HgeneSERGEFchr11:17981017chr11:17793212ENST00000265965-91115_67337459.0RepeatNote=RCC1 1
HgeneSERGEFchr11:17981017chr11:17793212ENST00000265965-911172_230337459.0RepeatNote=RCC1 4
HgeneSERGEFchr11:17981017chr11:17793212ENST00000265965-911231_283337459.0RepeatNote=RCC1 5
HgeneSERGEFchr11:17981017chr11:17793212ENST00000265965-91168_119337459.0RepeatNote=RCC1 2
TgeneKCNC1chr11:17981017chr11:17793212ENST0000037947202400_405190512.0MotifSelectivity filter
TgeneKCNC1chr11:17981017chr11:17793212ENST0000037947202268_276190512.0Topological domainCytoplasmic
TgeneKCNC1chr11:17981017chr11:17793212ENST0000037947202332_344190512.0Topological domainCytoplasmic
TgeneKCNC1chr11:17981017chr11:17793212ENST0000037947202437_511190512.0Topological domainCytoplasmic
TgeneKCNC1chr11:17981017chr11:17793212ENST0000037947202191_209190512.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNC1chr11:17981017chr11:17793212ENST0000037947202248_267190512.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNC1chr11:17981017chr11:17793212ENST0000037947202277_295190512.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNC1chr11:17981017chr11:17793212ENST0000037947202309_331190512.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNC1chr11:17981017chr11:17793212ENST0000037947202345_366190512.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNC1chr11:17981017chr11:17793212ENST0000037947202415_436190512.0TransmembraneHelical%3B Name%3DSegment S6

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSERGEFchr11:17981017chr11:17793212ENST00000265965-911284_351337459.0RepeatNote=RCC1 6
HgeneSERGEFchr11:17981017chr11:17793212ENST00000265965-911352_402337459.0RepeatNote=RCC1 7
HgeneSERGEFchr11:17981017chr11:17793212ENST00000528200-110120_1710351.6666666666667RepeatNote=RCC1 3
HgeneSERGEFchr11:17981017chr11:17793212ENST00000528200-11015_670351.6666666666667RepeatNote=RCC1 1
HgeneSERGEFchr11:17981017chr11:17793212ENST00000528200-110172_2300351.6666666666667RepeatNote=RCC1 4
HgeneSERGEFchr11:17981017chr11:17793212ENST00000528200-110231_2830351.6666666666667RepeatNote=RCC1 5
HgeneSERGEFchr11:17981017chr11:17793212ENST00000528200-110284_3510351.6666666666667RepeatNote=RCC1 6
HgeneSERGEFchr11:17981017chr11:17793212ENST00000528200-110352_4020351.6666666666667RepeatNote=RCC1 7
HgeneSERGEFchr11:17981017chr11:17793212ENST00000528200-11068_1190351.6666666666667RepeatNote=RCC1 2
TgeneKCNC1chr11:17981017chr11:17793212ENST00000379472021_190190512.0Topological domainCytoplasmic


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Fusion Gene Sequence for SERGEF-KCNC1


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.
>80634_80634_1_SERGEF-KCNC1_SERGEF_chr11_17981017_ENST00000265965_KCNC1_chr11_17793212_ENST00000265969_length(transcript)=3289nt_BP=1163nt
CTCTCTCCCGGCCTGCGGGCCGCTTCCCACCACAGACCCCGCCCCGCGCCCTACCCATCACGCGTCCCCGGTCCGGCTCCGGCGCTCACC
TACCCCCGGCAGGCGCCGCCCCCGTGCCGTCCCTCCCGGAAGCGCCGGCGGAGCGTCCTCGCATGGAGCGCGAGCCCAGCGCCTCGGAGG
CCGCCCCCGCGGCGGCCGCGCTCTTCGCCTGGGGTGCAAATAGCTATGGGCAACTTGGCCTCGGCCATAAGGAAGATGTGCTGTTGCCCC
AGCAACTGAATGACTTCTGTAAACCCAGGAGTGTCAGGAGGATCACAGGAGGAGGGGGCCACTCTGCAGTTGTCACAGATGGAGGAGACC
TCTTTGTTTGTGGCCTGAACAAAGATGGGCAACTGGGGCTTGGTCACACAGAGGATATCCCATATTTTACCCCCTGCAAATCCCTCTTTG
GCTGTCCCATCCAACAGGTGGCCTGTGGCTGGGATTTTACGATTATGCTCACAGAAAATGGTCAAGTTCTATCATGTGGATCCAACTCCT
TTGGCCAGTTAGGAGTTCCTCATGGACCTCGAAGATGTGTGGTTCCCCAGGCCATTGAGCTCCATAAAGAGAAGGTTGTTTGTATTGCTG
CTGGACTGAGGCATGCAGTAGCTGCTACAGCGAGTGGCATCGTGTTCCAGTGGGGGACTGGTTTGGCATCATGTGGACGACGGTTGTGCC
CTGGGCAGACTCTTCCATTGTTTTTCACAGCAAAGGAACCAAGCAGAGTGACAGGTCTAGAGAATTCTAAAGCAATGTGTGTTCTTGCTG
GCTCAGACCACTCAGCTTCATTAACAGATGCAGGAGAGGTGTATGTTTGGGGAAGCAACAAGCATGGGCAACTGGCTAATGAGGCTGCTT
TCCTTCCTGTGCCCCAGAAAATAGAAGCACATTGTTTCCAGAATGAAAAGGTCACTGCCATCTGGAGTGGATGGACACACCTGGTTGCTC
AGACAGAAACTGGCAAGATGTTTACCTGGGGCCGAGCAGACTATGGTCAGCTAGGGAGGAAGTTGGAGACTTATGAAGGCTGGAAACTAG
AAAAGCAAGATTCATTTCTCCCCTGTTCAAGACCACCGAACAGCATGCCTTCGTCTCCGCATTGCTTAACTGGAGCAACTGAGTATGTGG
CCTTCGCTTCCCTCTTCTTCATCCTGGTCTCCATCACCACCTTCTGCCTGGAGACCCACGAGCGCTTCAACCCCATCGTGAACAAGACGG
AGATCGAGAACGTTCGCAATGGCACGCAAGTGCGCTACTACCGGGAGGCCGAGACGGAGGCCTTCCTTACCTACATCGAGGGCGTCTGTG
TGGTCTGGTTCACCTTCGAGTTCCTCATGCGTGTCATCTTCTGCCCCAACAAGGTAGAGTTCATCAAGAACTCGCTCAACATCATTGACT
TTGTGGCCATCCTGCCCTTCTACCTGGAGGTGGGGCTGAGCGGCCTGTCCTCCAAGGCAGCCAAGGACGTGCTGGGCTTCCTGCGCGTCG
TCCGCTTCGTGCGCATCTTGCGCATCTTTAAGCTGACCCGCCACTTTGTGGGCCTGCGGGTCCTGGGCCACACGCTCCGAGCCAGCACCA
ACGAGTTCCTGCTGCTCATCATCTTCCTGGCCTTGGGCGTGCTGATCTTCGCCACCATGATCTACTACGCCGAGAGGATAGGGGCACAGC
CCAATGACCCCAGCGCCAGTGAGCACACGCACTTTAAGAACATCCCCATCGGCTTCTGGTGGGCCGTGGTCACCATGACGACCCTGGGCT
ATGGAGACATGTACCCGCAGACGTGGTCCGGCATGCTGGTGGGGGCTCTGTGTGCGCTGGCGGGCGTGCTCACCATCGCCATGCCCGTGC
CCGTCATCGTGAACAATTTCGGGATGTATTACTCCTTAGCCATGGCTAAGCAGAAACTACCAAAGAAAAAAAAGAAGCATATTCCGCGGC
CACCGCAGCTGGGATCTCCCAATTATTGTAAATCTGTCGTAAACTCTCCACACCACAGTACTCAGAGTGACACATGTCCGCTGGCCCAGG
AAGAAATTTTAGAAATTAACAGAGCAGATTCCAAACTGAATGGGGAGGTGGCGAAGGCCGCGCTGGCGAACGAAGACTGCCCCCACATAG
ACCAGGCCCTCACTCCCGATGAGGGCCTGCCCTTTACGCGCTCGGGCACCCGCGAGAGATACGGACCCTGCTTCCTCTTATCAACCGGGG
AGTACGCGTGCCCACCTGGTGGAGGAATGAGAAAGGATCTTTGCAAAGAAAGCCCTGTCATTGCTAAGTATATGCCGACAGAGGCTGTGA
GAGTGACTTGACCAGGCGGCTTGGCCGAGGACACTGGTGGCTATTAAGCATCTGGGTGGACCTGCAGCCCCTCCTCACCCTCGGACAGAG
TAAATTCACGCCATGCAGGTTTGCCGGACGAGTCCGAGTGGCCCAGGCATTGTACTAGGACGGACGTAGCTTTTTCTACGGCCAAATGGT
AACTGACCGTAGAGGATTTCTTTTCCTTCTTTTCATTTTTTAAAATTTTATTTTATTTGGGGAGGGGGGGTGGAGGGGCTCCTTAGCATG
ACTTGCATGAAGTTAAACAGAAAACCCAGCAAACCAAACCCACCAACCCCCTGCAACTGTATGATTACCCTGAACAACAATAATGAAAAG
AAAAACATCAAAGCCCTCTATTTTCTTTCAAAGCTCTTGACTTTCACACACGTTGTTGGAGCCAAACTGTAACGGCGTTCAGTAGAAACC
TGTACATTTCTGGGGGTGAGGGGCGAGGGGAGGAGGGACAGAGATGGGGAATGGATTGCTTCCTTTTTGTACACAAGATCAAGAGGAAAG
CTTCCAAAAAGGGCAGTCGGTCAGTCATCGGTCATATTGACCTCACCTTCATAGTTCATCTCTCACGTGGAAACTGAGAACTTTGCTCCA
AATAGAATTGTGGAAACTCGCACGGCTGCCTTCTTCCCCGTTTGGCATGCTTGTGACCCAGCGGATGTCTCCCCAAGACCCCTGACAGCA
GCTAGTCTAGGTTGATTCTCTCATCTTATCGGTGTGTAGATCCAGTGTGACCAACTTTCATAACAAATTGTTCATAGTAAATAATCACCA
CCGTATGGATTTTCCAAGTGTTCCATTAAAACCAGGATGTAGAGCACCAAAAGATCAGGACCACGGGAGGAGCAGCCTCCTCCACCTTTA

>80634_80634_1_SERGEF-KCNC1_SERGEF_chr11_17981017_ENST00000265965_KCNC1_chr11_17793212_ENST00000265969_length(amino acids)=732AA_BP=337
MEREPSASEAAPAAAALFAWGANSYGQLGLGHKEDVLLPQQLNDFCKPRSVRRITGGGGHSAVVTDGGDLFVCGLNKDGQLGLGHTEDIP
YFTPCKSLFGCPIQQVACGWDFTIMLTENGQVLSCGSNSFGQLGVPHGPRRCVVPQAIELHKEKVVCIAAGLRHAVAATASGIVFQWGTG
LASCGRRLCPGQTLPLFFTAKEPSRVTGLENSKAMCVLAGSDHSASLTDAGEVYVWGSNKHGQLANEAAFLPVPQKIEAHCFQNEKVTAI
WSGWTHLVAQTETGKMFTWGRADYGQLGRKLETYEGWKLEKQDSFLPCSRPPNSMPSSPHCLTGATEYVAFASLFFILVSITTFCLETHE
RFNPIVNKTEIENVRNGTQVRYYREAETEAFLTYIEGVCVVWFTFEFLMRVIFCPNKVEFIKNSLNIIDFVAILPFYLEVGLSGLSSKAA
KDVLGFLRVVRFVRILRIFKLTRHFVGLRVLGHTLRASTNEFLLLIIFLALGVLIFATMIYYAERIGAQPNDPSASEHTHFKNIPIGFWW
AVVTMTTLGYGDMYPQTWSGMLVGALCALAGVLTIAMPVPVIVNNFGMYYSLAMAKQKLPKKKKKHIPRPPQLGSPNYCKSVVNSPHHST
QSDTCPLAQEEILEINRADSKLNGEVAKAALANEDCPHIDQALTPDEGLPFTRSGTRERYGPCFLLSTGEYACPPGGGMRKDLCKESPVI

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Fusion Gene PPI Analysis for SERGEF-KCNC1


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 SERGEF-KCNC1


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 SERGEF-KCNC1


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