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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:SC5D-BCL11A (FusionGDB2 ID:HG6309TG53335)

Fusion Gene Summary for SC5D-BCL11A

check button Fusion gene summary
Fusion gene informationFusion gene name: SC5D-BCL11A
Fusion gene ID: hg6309tg53335
HgeneTgene
Gene symbol

SC5D

BCL11A

Gene ID

6309

53335

Gene namesterol-C5-desaturaseBAF chromatin remodeling complex subunit BCL11A
SynonymsERG3|S5DES|SC5DLBCL11A-L|BCL11A-S|BCL11A-XL|BCL11a-M|CTIP1|DILOS|EVI9|HBFQTL5|ZNF856
Cytomap('SC5D')('BCL11A')

11q23.3-q24.1

2p16.1

Type of geneprotein-codingprotein-coding
Descriptionlathosterol oxidase3beta-hydroxysteroid-delta5-desaturaseC-5 sterol desaturasedelta(7)-sterol 5(6)-desaturasedelta(7)-sterol 5-desaturasedelta(7)-sterol C5(6)-desaturasefungal ERG3, delta-5-desaturase-likelathosterol 5-desaturaselathosterol dehydrB-cell lymphoma/leukemia 11AB cell CLL/lymphoma 11AB-cell CLL/lymphoma 11A (zinc finger protein) isoform 2BCL11A B-cell CLL/lymphoma 11A (zinc finger protein) isoform 1BCL11A, BAF complex componentC2H2-type zinc finger proteinCOUP-TF-interacting pro
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000264027, ENST00000392789, 
ENST00000528991, ENST00000534230, 
Fusion gene scores* DoF score6 X 6 X 2=7210 X 9 X 3=270
# samples 59
** MAII scorelog2(5/72*10)=-0.526068811667588
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/270*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SC5D [Title/Abstract] AND BCL11A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSC5D(121169803)-BCL11A(60733201), # 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
TgeneBCL11A

GO:0000122

negative regulation of transcription by RNA polymerase II

19153051



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/AAI655175SC5Dchr11

121169803

-BCL11Achr2

60733201

+


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Fusion Gene ORF analysis for SC5D-BCL11A

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
intron-intronENST00000264027ENST00000335712SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000264027ENST00000356842SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000264027ENST00000358510SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000264027ENST00000359629SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000264027ENST00000477659SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000264027ENST00000537768SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000264027ENST00000538214SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000392789ENST00000335712SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000392789ENST00000356842SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000392789ENST00000358510SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000392789ENST00000359629SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000392789ENST00000477659SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000392789ENST00000537768SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000392789ENST00000538214SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000528991ENST00000335712SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000528991ENST00000356842SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000528991ENST00000358510SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000528991ENST00000359629SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000528991ENST00000477659SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000528991ENST00000537768SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000528991ENST00000538214SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000534230ENST00000335712SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000534230ENST00000356842SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000534230ENST00000358510SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000534230ENST00000359629SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000534230ENST00000477659SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000534230ENST00000537768SC5Dchr11

121169803

-BCL11Achr2

60733201

+
intron-intronENST00000534230ENST00000538214SC5Dchr11

121169803

-BCL11Achr2

60733201

+

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 SC5D-BCL11A


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)


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Fusion Protein Features for SC5D-BCL11A


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/:121169803/:60733201)
- 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

- 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 SC5D-BCL11A


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 SC5D-BCL11A


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 SC5D-BCL11A


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 SC5D-BCL11A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSC5DC1846421Lathosterolosis3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneSC5DC3714756Intellectual Disability2CTD_human;GENOMICS_ENGLAND
HgeneSC5DC0020796Profound Mental Retardation1CTD_human
HgeneSC5DC0023895Liver diseases1CTD_human
HgeneSC5DC0025363Mental Retardation, Psychosocial1CTD_human
HgeneSC5DC0086543Cataract1GENOMICS_ENGLAND
HgeneSC5DC0086565Liver Dysfunction1CTD_human
HgeneSC5DC0917816Mental deficiency1CTD_human
TgeneC4310833INTELLECTUAL DEVELOPMENTAL DISORDER WITH PERSISTENCE OF FETAL HEMOGLOBIN2CTD_human;UNIPROT
TgeneC0003635Apraxias1CTD_human
TgeneC0010606Adenoid Cystic Carcinoma1CTD_human
TgeneC0023012Language Delay1CTD_human
TgeneC0023014Language Development Disorders1CTD_human
TgeneC0032460Polycystic Ovary Syndrome1CTD_human
TgeneC0036095Salivary Gland Neoplasms1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0220636Malignant neoplasm of salivary gland1CTD_human
TgeneC0234526Ideational Apraxia1CTD_human
TgeneC0234527Apraxia, Motor1CTD_human
TgeneC0234529Dressing Apraxia1CTD_human
TgeneC0241210Speech Delay1CTD_human
TgeneC0264611Apraxia of Phonation1CTD_human
TgeneC0349391Apraxia, Verbal1CTD_human
TgeneC0422892Apraxia, Gestural1CTD_human
TgeneC0454608Apraxia, Oral1CTD_human
TgeneC0454655Semantic-Pragmatic Disorder1CTD_human
TgeneC0750927Apraxia, Developmental Verbal1CTD_human
TgeneC0750928Apraxia, Facial-Oral1CTD_human
TgeneC0751257Auditory Processing Disorder, Central1CTD_human
TgeneC1136382Sclerocystic Ovaries1CTD_human
TgeneC3495144Apraxia, Articulatory1CTD_human
TgeneC3714756Intellectual Disability1GENOMICS_ENGLAND