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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:ABCA1-NDUFB2 (FusionGDB2 ID:168)

Fusion Gene Summary for ABCA1-NDUFB2

check button Fusion gene summary
Fusion gene informationFusion gene name: ABCA1-NDUFB2
Fusion gene ID: 168
HgeneTgene
Gene symbol

ABCA1

NDUFB2

Gene ID

19

4708

Gene nameATP binding cassette subfamily A member 1NADH:ubiquinone oxidoreductase subunit B2
SynonymsABC-1|ABC1|CERP|HDLCQTL13|HDLDT1|HPALP1|TGDAGGG|CI-AGGG
Cytomap

9q31.1

7q34

Type of geneprotein-codingprotein-coding
Descriptionphospholipid-transporting ATPase ABCA1ATP-binding cassette sub-family A member 1ATP-binding cassette transporter A1ATP-binding cassette, sub-family A (ABC1), member 1cholesterol efflux regulatory proteinmembrane-boundNADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialNADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2, 8kDaNADH-ubiquinone oxidoreductase AGGG subunitcomplex I AGGG subunitcomplex I-AGGG
Modification date2020031320200313
UniProtAcc

O95477

O95178

Ensembl transtripts involved in fusion geneENST00000374733, ENST00000374736, 
ENST00000423487, ENST00000494467, 
ENST00000204307, ENST00000464564, 
ENST00000247866, ENST00000460088, 
ENST00000471136, ENST00000472695, 
ENST00000475276, ENST00000476279, 
ENST00000476470, ENST00000482954, 
ENST00000461457, ENST00000465506, 
Fusion gene scores* DoF score13 X 9 X 9=105315 X 5 X 9=675
# samples 1316
** MAII scorelog2(13/1053*10)=-3.01792190799726
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/675*10)=-2.07681559705083
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ABCA1 [Title/Abstract] AND NDUFB2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointABCA1(107690215)-NDUFB2(140402665), # samples:2
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
HgeneABCA1

GO:0007040

lysosome organization

15163665

HgeneABCA1

GO:0008203

cholesterol metabolic process

14747463

HgeneABCA1

GO:0016197

endosomal transport

14747463

HgeneABCA1

GO:0033344

cholesterol efflux

10431236|11162594|16702602|23931754

HgeneABCA1

GO:0033700

phospholipid efflux

10431236|11162594

HgeneABCA1

GO:0042632

cholesterol homeostasis

10431236

HgeneABCA1

GO:0045332

phospholipid translocation

24097981


check buttonFusion gene breakpoints across ABCA1 (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 NDUFB2 (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
ChimerDB4HNSCTCGA-CQ-6223ABCA1chr9

107690215

-NDUFB2chr7

140402665

+


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Fusion Gene ORF analysis for ABCA1-NDUFB2

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
5UTR-3UTRENST00000374733ENST00000204307ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-3UTRENST00000374733ENST00000464564ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-3UTRENST00000374736ENST00000204307ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-3UTRENST00000374736ENST00000464564ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-3UTRENST00000423487ENST00000204307ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-3UTRENST00000423487ENST00000464564ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374733ENST00000247866ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374733ENST00000460088ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374733ENST00000471136ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374733ENST00000472695ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374733ENST00000475276ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374733ENST00000476279ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374733ENST00000476470ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374733ENST00000482954ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374736ENST00000247866ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374736ENST00000460088ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374736ENST00000471136ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374736ENST00000472695ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374736ENST00000475276ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374736ENST00000476279ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374736ENST00000476470ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000374736ENST00000482954ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000423487ENST00000247866ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000423487ENST00000460088ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000423487ENST00000471136ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000423487ENST00000472695ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000423487ENST00000475276ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000423487ENST00000476279ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000423487ENST00000476470ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-5UTRENST00000423487ENST00000482954ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-intronENST00000374733ENST00000461457ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-intronENST00000374733ENST00000465506ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-intronENST00000374736ENST00000461457ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-intronENST00000374736ENST00000465506ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-intronENST00000423487ENST00000461457ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
5UTR-intronENST00000423487ENST00000465506ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
intron-3UTRENST00000494467ENST00000204307ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
intron-3UTRENST00000494467ENST00000464564ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
intron-5UTRENST00000494467ENST00000247866ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
intron-5UTRENST00000494467ENST00000460088ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
intron-5UTRENST00000494467ENST00000471136ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
intron-5UTRENST00000494467ENST00000472695ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
intron-5UTRENST00000494467ENST00000475276ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
intron-5UTRENST00000494467ENST00000476279ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
intron-5UTRENST00000494467ENST00000476470ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
intron-5UTRENST00000494467ENST00000482954ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
intron-intronENST00000494467ENST00000461457ABCA1chr9

107690215

-NDUFB2chr7

140402665

+
intron-intronENST00000494467ENST00000465506ABCA1chr9

107690215

-NDUFB2chr7

140402665

+

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 ABCA1-NDUFB2


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)
ABCA1chr9107690215-NDUFB2chr7140402665+8.16E-080.9999999
ABCA1chr9107690215-NDUFB2chr7140402665+8.16E-080.9999999

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.

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 ABCA1-NDUFB2


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/:107690215/:140402665)
- 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
ABCA1

O95477

NDUFB2

O95178

FUNCTION: Catalyzes the translocation of specific phospholipids from the cytoplasmic to the extracellular/lumenal leaflet of membrane coupled to the hydrolysis of ATP (PubMed:24097981). Thereby, participates in phospholipid transfer to apoliproteins to form nascent high density lipoproteins/HDLs (PubMed:14754908). Transports preferentially phosphatidylcholine over phosphatidylserine (PubMed:24097981). May play a similar role in the efflux of intracellular cholesterol to apoliproteins and the formation of nascent high density lipoproteins/HDLs (PubMed:10533863, PubMed:14754908, PubMed:24097981). {ECO:0000269|PubMed:10533863, ECO:0000269|PubMed:14754908, ECO:0000269|PubMed:24097981}.FUNCTION: Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. {ECO:0000269|PubMed:27626371}.

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 ABCA1-NDUFB2


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 ABCA1-NDUFB2


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 ABCA1-NDUFB2


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 ABCA1-NDUFB2


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