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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:ABCA3-XRCC6BP1 (FusionGDB2 ID:HG21TG91419)

Fusion Gene Summary for ABCA3-XRCC6BP1

check button Fusion gene summary
Fusion gene informationFusion gene name: ABCA3-XRCC6BP1
Fusion gene ID: hg21tg91419
HgeneTgene
Gene symbol

ABCA3

XRCC6BP1

Gene ID

21

91419

Gene nameATP binding cassette subfamily A member 3ATP23 metallopeptidase and ATP synthase assembly factor homolog
SynonymsABC-C|ABC3|EST111653|LBM180|SMDP3KUB3|XRCC6BP1
Cytomap('ABCA3')('XRCC6BP1')

16p13.3

12q14.1

Type of geneprotein-codingprotein-coding
DescriptionATP-binding cassette sub-family A member 3ABC transporter 3ABC-C transporterATP-binding cassette transporter 3ATP-binding cassette, sub-family A (ABC1), member 3mitochondrial inner membrane protease ATP23 homologKu70-binding protein 3XRCC6-binding protein 1
Modification date2020031320200320
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000301732, ENST00000382381, 
ENST00000567910, 
Fusion gene scores* DoF score5 X 7 X 3=10518 X 7 X 5=630
# samples 721
** MAII scorelog2(7/105*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(21/630*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ABCA3 [Title/Abstract] AND XRCC6BP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointABCA3(2358451)-XRCC6BP1(58340778), # samples:1
Anticipated loss of major functional domain due to fusion event.ABCA3-XRCC6BP1 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.
ABCA3-XRCC6BP1 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.
* 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 ABCA3 (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 XRCC6BP1 (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
ChimerDB4LGGTCGA-TM-A84I-01AABCA3chr16

2358451

-XRCC6BP1chr12

58340778

+


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Fusion Gene ORF analysis for ABCA3-XRCC6BP1

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-intronENST00000301732ENST00000546709ABCA3chr16

2358451

-XRCC6BP1chr12

58340778

+
In-frameENST00000301732ENST00000300145ABCA3chr16

2358451

-XRCC6BP1chr12

58340778

+
intron-3CDSENST00000382381ENST00000300145ABCA3chr16

2358451

-XRCC6BP1chr12

58340778

+
intron-3CDSENST00000567910ENST00000300145ABCA3chr16

2358451

-XRCC6BP1chr12

58340778

+
intron-intronENST00000382381ENST00000546709ABCA3chr16

2358451

-XRCC6BP1chr12

58340778

+
intron-intronENST00000567910ENST00000546709ABCA3chr16

2358451

-XRCC6BP1chr12

58340778

+

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)
ENST00000301732ABCA3chr162358451-ENST00000300145XRCC6BP1chr1258340778+287319865392071510

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
ENST00000301732ENST00000300145ABCA3chr162358451-XRCC6BP1chr1258340778+0.0256300250.97436994

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Fusion Genomic Features for ABCA3-XRCC6BP1


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)
ABCA3chr162358450-XRCC6BP1chr1258340777+1.57E-050.9999844
ABCA3chr162358450-XRCC6BP1chr1258340777+1.57E-050.9999844

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 ABCA3-XRCC6BP1


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/chr16:2358451/chr12:58340778)
- 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
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-113322_424281705.0TransmembraneHelical
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-1133261_2834281705.0TransmembraneHelical
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-1133307_3274281705.0TransmembraneHelical
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-1133344_3644281705.0TransmembraneHelical
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-1133373_3934281705.0TransmembraneHelical
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-1133405_4254281705.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-11331381_16144281705.0DomainABC transporter 2
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-1133530_7634281705.0DomainABC transporter 1
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-11331416_14234281705.0Nucleotide bindingATP 2
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-1133566_5734281705.0Nucleotide bindingATP 1
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-11331100_11204281705.0TransmembraneHelical
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-11331144_11644281705.0TransmembraneHelical
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-11331183_12034281705.0TransmembraneHelical
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-11331213_12334281705.0TransmembraneHelical
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-11331245_12654281705.0TransmembraneHelical
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-11331306_13264281705.0TransmembraneHelical
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-1133447_4674281705.0TransmembraneHelical
HgeneABCA3chr16:2358451chr12:58340778ENST00000301732-1133925_9454281705.0TransmembraneHelical


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Fusion Gene Sequence for ABCA3-XRCC6BP1


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.
>190_190_1_ABCA3-XRCC6BP1_ABCA3_chr16_2358451_ENST00000301732_XRCC6BP1_chr12_58340778_ENST00000300145_length(transcript)=2873nt_BP=1986nt
GTCCGCCAGTAGCGGGTTGCAGGCGCACCCTCCCCTCCAGGGCGGCCACGCAGCTGTCAGTGCCGCCGCCACTGCGAGGCTGGAGCGGAG
CCCGGGTGGCCGAGGGAGGGGACCCCGCGAGAGGGCCGCGCGCCGGCCGCCGCCGCCCCGGCGCCCAGGCTCGGTGCTGGAGAGTCATGC
CTGTGAGCCCTGGGCACCTCCTGATGTCCTGCGAGGTCACGGTGTTCCCAAACCTCAGGGTTGCCCTGCCCCACTCCAGAGGCTCTCAGG
CCCCACCCCGGAGCCCTCTGTGCGGAGCCGCCTCCTCCTGGCCAGTTCCCCAGTAGTCCTGAAGGGAGACCTGCTGTGTGGAGCCTCTTC
TGGGACCCAGCCATGAGTGTGGAGCTGAGCAACTGAACCTGAAACTCTTCCACTGTGAGTCAAGGAGGCTTTTCCGCACATGAAGGACGC
TGAGCGGGAAGGACTCCTCTCTGCCTGCAGTTGTAGCGAGTGGACCAGCACCAGGGGCTCTCTAGACTGCCCCTCCTCCATCGCCTTCCC
TGCCTCTCCAGGACAGAGCAGCCACGTCTGCACACCTCGCCCTCTTTACACTCAGTTTTCAGAGCACGTTTCTCCTATTTCCTGCGGGTT
GCAGCGCCTACTTGAACTTACTCAGACCACCTACTTCTCTAGCAGCACTGGGCGTCCCTTTCAGCAAGACGATGGCTGTGCTCAGGCAGC
TGGCGCTCCTCCTCTGGAAGAACTACACCCTGCAGAAGCGGAAGGTCCTGGTGACGGTCCTGGAACTCTTCCTGCCATTGCTGTTTTCTG
GGATCCTCATCTGGCTCCGCTTGAAGATTCAGTCGGAAAATGTGCCCAACGCCACCATCTACCCGGGCCAGTCCATCCAGGAGCTGCCTC
TGTTCTTCACCTTCCCTCCGCCAGGAGACACCTGGGAGCTTGCCTACATCCCTTCTCACAGTGACGCTGCCAAGACCGTCACTGAGACAG
TGCGCAGGGCACTTGTGATCAACATGCGAGTGCGCGGCTTTCCCTCCGAGAAGGACTTTGAGGACTACATTAGGTACGACAACTGCTCGT
CCAGCGTGCTGGCCGCCGTGGTCTTCGAGCACCCCTTCAACCACAGCAAGGAGCCCCTGCCGCTGGCGGTGAAATATCACCTACGGTTCA
GTTACACACGGAGAAATTACATGTGGACCCAAACAGGCTCCTTTTTCCTGAAAGAGACAGAAGGCTGGCACACTACTTCCCTTTTCCCGC
TTTTCCCAAACCCAGGACCAAGGGAACCTACATCCCCTGATGGCGGAGAACCTGGGTACATCCGGGAAGGCTTCCTGGCCGTGCAGCATG
CTGTGGACCGGGCCATCATGGAGTACCATGCCGATGCCGCCACACGCCAGCTGTTCCAGAGACTGACGGTGACCATCAAGAGGTTCCCGT
ACCCGCCGTTCATCGCAGACCCCTTCCTCGTGGCCATCCAGTACCAGCTGCCCCTGCTGCTGCTGCTCAGCTTCACCTACACCGCGCTCA
CCATTGCCCGTGCTGTCGTGCAGGAGAAGGAAAGGAGGCTGAAGGAGTACATGCGCATGATGGGGCTCAGCAGCTGGCTGCACTGGAGTG
CCTGGTTCCTCTTGTTCTTCCTCTTCCTCCTCATCGCCGCCTCCTTCATGACCCTGCTCTTCTGTGTCAAGGTGAAGCCAAATGTAGCCG
TGCTGTCCCGCAGCGACCCCTCCCTGGTGCTCGCCTTCCTGCTGTGCTTCGCCATCTCTACCATCTCCTTCAGCTTCATGGTCAGCACCT
TCTTCAGCAAAGCCAACATGGCAGCAGCCTTCGGAGGCTTCCTCTACTTCTTCACCTACATCCCCTACTTCTTCGTGGCCCCTCGGTACA
ACTGGATGACTCTGAGCCAGAAGCTCTGCTCCTGCCTCCTGTCTAATGTCGCCATGGCAATGGGAGCCCAGCTCATTGGGAAATTTGAGG
CGAAAGTGCTGTTAACAAAGATAGACACTTTTCTTGCGAAGACTGTAATGGAAATGTCAGTGGAGGTTTTGATGCTTCAACATCTCAGAT
AGTTTTGTGCCAGAATAATATCCATAATCAGGCCCATATGAACAGAGTGGTCACACACGAGCTTATTCATGCATTTGATCATTGTCGTGC
CCATGTCGACTGGTTCACCAACATCAGACATTTGGCGTGCTCAGAGGTTCGAGCTGCTAACCTTAGTGGAGACTGCTCACTTGTCAATGA
AATATTCAGGTTACATTTTGGATTAAAACAACACCACCAGACTTGTGTGCGAGACAGAGCCACTCTTTCTATCCTGGCTGTTAGGAATAT
CAGCAAAGAAGTAGCTAAAAAGGCTGTTGATGAAGTTTTTGAATCTTGTTTCAATGACCATGAACCTTTTGGAAGGATCCCACATAACAA
GACTTATGCAAGATATGCTCACAGAGACTTTGAAAACCGTGATCGGTATTATTCAAATATATGAGCACAATGACATTTTTATATTACAGA
GCTTCCATCATCATGAAGAAAAAAAAATTTGGTTCTCAAGTGAACAAACATATAAAATGTAAACAATCCCTACAATCCAGATAAAACAGA
GAAGACTGTGATTCTAGCATATTATCAGAAAAAGTAACTATGGCAAAAAATGAAACTGCTTTAAACTCCAAGGCAGAAATTGTATCTTTA
TAGCTAACCATTTAGTAAATAAATACATTACATTTTTGTATTTTAGTCATTTGTTTTTATTACATGTGATTATTTTAAAATTTGATTATG

>190_190_1_ABCA3-XRCC6BP1_ABCA3_chr16_2358451_ENST00000301732_XRCC6BP1_chr12_58340778_ENST00000300145_length(amino acids)=510AA_BP=482
MPLQDRAATSAHLALFTLSFQSTFLLFPAGCSAYLNLLRPPTSLAALGVPFSKTMAVLRQLALLLWKNYTLQKRKVLVTVLELFLPLLFS
GILIWLRLKIQSENVPNATIYPGQSIQELPLFFTFPPPGDTWELAYIPSHSDAAKTVTETVRRALVINMRVRGFPSEKDFEDYIRYDNCS
SSVLAAVVFEHPFNHSKEPLPLAVKYHLRFSYTRRNYMWTQTGSFFLKETEGWHTTSLFPLFPNPGPREPTSPDGGEPGYIREGFLAVQH
AVDRAIMEYHADAATRQLFQRLTVTIKRFPYPPFIADPFLVAIQYQLPLLLLLSFTYTALTIARAVVQEKERRLKEYMRMMGLSSWLHWS
AWFLLFFLFLLIAASFMTLLFCVKVKPNVAVLSRSDPSLVLAFLLCFAISTISFSFMVSTFFSKANMAAAFGGFLYFFTYIPYFFVAPRY

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Fusion Gene PPI Analysis for ABCA3-XRCC6BP1


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 ABCA3-XRCC6BP1


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 ABCA3-XRCC6BP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneABCA3C1970456Surfactant Metabolism Dysfunction, Pulmonary, 34CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneABCA3C0009402Colorectal Carcinoma1CTD_human
HgeneABCA3C0009404Colorectal Neoplasms1CTD_human
HgeneABCA3C0013990Pathological accumulation of air in tissues1CTD_human
HgeneABCA3C0020192Hyaline Membrane Disease1ORPHANET
HgeneABCA3C0020542Pulmonary Hypertension1CTD_human
HgeneABCA3C0034069Pulmonary Fibrosis1CTD_human
HgeneABCA3C0035220Respiratory Distress Syndrome, Newborn1ORPHANET
HgeneABCA3C0085786Hamman-Rich syndrome1ORPHANET
HgeneABCA3C0852283Respiratory Distress Syndrome1ORPHANET
HgeneABCA3C1800706Idiopathic Pulmonary Fibrosis1ORPHANET
HgeneABCA3C1861829Cataract microcornea syndrome1GENOMICS_ENGLAND
HgeneABCA3C4721507Alveolitis, Fibrosing1CTD_human