UTHEALTH HOME    ABOUT SBMI    A-Z    WEBMAIL    INSIDE THE UNIVERSITY
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use
Center for Computational Systems Medicine level1
leaf

Fusion Gene Summary

leaf

Fusion Gene Sample Information

leaf

Fusion ORF Analysis

leaf

Fusion Amino Acid Sequences

leaf

Fusion Protein Functional Features

leaf

Fusion Protein-Protein Interaction

leaf

Related drugs with this fusion protein

leaf

Related disease with this fusion protein

Fusion Protein:ABCA1-RAB5C

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ABCA1-RAB5C
FusionPDB ID: 173
FusionGDB2.0 ID: 173
HgeneTgene
Gene symbol

ABCA1

RAB5C

Gene ID

19

5878

Gene nameATP binding cassette subfamily A member 1RAB5C, member RAS oncogene family
SynonymsABC-1|ABC1|CERP|HDLCQTL13|HDLDT1|HPALP1|TGDL1880|RAB5CL|RAB5L|RABL
Cytomap

9q31.1

17q21.2

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-boundras-related protein Rab-5CRAB5C, member of RAS oncogene family
Modification date2020031320200313
UniProtAcc

Q86UQ4

.
Ensembl transtripts involved in fusion geneENST idsENST00000374733, ENST00000374736, 
ENST00000423487, ENST00000494467, 
ENST00000346213, ENST00000393860, 
ENST00000547517, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score13 X 9 X 9=10538 X 7 X 6=336
# samples 1310
** MAII scorelog2(13/1053*10)=-3.01792190799726
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/336*10)=-1.74846123300404
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: ABCA1 [Title/Abstract] AND RAB5C [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ABCA1(107645320)-RAB5C(40278866), # samples:1
Anticipated loss of major functional domain due to fusion event.ABCA1-RAB5C 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.
ABCA1-RAB5C 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.
ABCA1-RAB5C seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
ABCA1-RAB5C seems lost the major protein functional domain in Hgene 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
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.
all structure

check buttonFusion gene breakpoints across RAB5C (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4BLCATCGA-4Z-AA7Q-01AABCA1chr9

107645320

-RAB5Cchr17

40278866

-


Top

Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000374736ABCA1chr9107645320-ENST00000346213RAB5Cchr1740278866-183381612661784172
ENST00000374736ABCA1chr9107645320-ENST00000393860RAB5Cchr1740278866-182981612661784172
ENST00000374736ABCA1chr9107645320-ENST00000547517RAB5Cchr1740278866-1142816395913172
ENST00000423487ABCA1chr9107645320-ENST00000346213RAB5Cchr1740278866-1735718297815172
ENST00000423487ABCA1chr9107645320-ENST00000393860RAB5Cchr1740278866-1731718297815172
ENST00000423487ABCA1chr9107645320-ENST00000547517RAB5Cchr1740278866-1044718297815172

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
ENST00000374736ENST00000346213ABCA1chr9107645320-RAB5Cchr1740278866-0.137937160.8620629
ENST00000374736ENST00000393860ABCA1chr9107645320-RAB5Cchr1740278866-0.137625950.862374
ENST00000374736ENST00000547517ABCA1chr9107645320-RAB5Cchr1740278866-0.0888052360.91119474
ENST00000423487ENST00000346213ABCA1chr9107645320-RAB5Cchr1740278866-0.102874220.8971258
ENST00000423487ENST00000393860ABCA1chr9107645320-RAB5Cchr1740278866-0.101674950.8983251
ENST00000423487ENST00000547517ABCA1chr9107645320-RAB5Cchr1740278866-0.055887520.9441124

Top

Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>173_173_1_ABCA1-RAB5C_ABCA1_chr9_107645320_ENST00000374736_RAB5C_chr17_40278866_ENST00000346213_length(amino acids)=172AA_BP=
MLFPLPPLSTALPFSLAGSSHMLLPPNPCIWGQWGQCSYPFFPSCGTADPARASTSSLCSEWSLVWAVGQTLGRGLGRERQLFLQLALIR

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

>173_173_2_ABCA1-RAB5C_ABCA1_chr9_107645320_ENST00000374736_RAB5C_chr17_40278866_ENST00000393860_length(amino acids)=172AA_BP=
MLFPLPPLSTALPFSLAGSSHMLLPPNPCIWGQWGQCSYPFFPSCGTADPARASTSSLCSEWSLVWAVGQTLGRGLGRERQLFLQLALIR

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

>173_173_3_ABCA1-RAB5C_ABCA1_chr9_107645320_ENST00000374736_RAB5C_chr17_40278866_ENST00000547517_length(amino acids)=172AA_BP=141
MACWPQLRLLLWKNLTFRRRQTCQLLLEVAWPLFIFLILISVRLSYPPYEQHECHFPNKAMPSAGTLPWVQGIICNANNPCFRYPTPGEA

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

>173_173_4_ABCA1-RAB5C_ABCA1_chr9_107645320_ENST00000423487_RAB5C_chr17_40278866_ENST00000346213_length(amino acids)=172AA_BP=141
MACWPQLRLLLWKNLTFRRRQTCQLLLEVAWPLFIFLILISVRLSYPPYEQHECHFPNKAMPSAGTLPWVQGIICNANNPCFRYPTPGEA

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

>173_173_5_ABCA1-RAB5C_ABCA1_chr9_107645320_ENST00000423487_RAB5C_chr17_40278866_ENST00000393860_length(amino acids)=172AA_BP=141
MACWPQLRLLLWKNLTFRRRQTCQLLLEVAWPLFIFLILISVRLSYPPYEQHECHFPNKAMPSAGTLPWVQGIICNANNPCFRYPTPGEA

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

>173_173_6_ABCA1-RAB5C_ABCA1_chr9_107645320_ENST00000423487_RAB5C_chr17_40278866_ENST00000547517_length(amino acids)=172AA_BP=141
MACWPQLRLLLWKNLTFRRRQTCQLLLEVAWPLFIFLILISVRLSYPPYEQHECHFPNKAMPSAGTLPWVQGIICNANNPCFRYPTPGEA

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

Top

Fusion Protein Functional Features


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/chr9:107645320/chr17:40278866)
- 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

Q86UQ4

.
FUNCTION: May mediate the cholesterol and gangliosides transport from the plasma membrane to intracellular vesicles in an ATP hydrolysis dependent manner, thus playing a role in their internalization by endocytic retrograde transport and may also participate in the endocytosis of synaptic vesicle in cortical neurons. {ECO:0000269|PubMed:33293368}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-55022_42140.333333333333342262.0TransmembraneHelical
TgeneRAB5Cchr9:107645320chr17:40278866ENST0000034621336164_166147.0217.0Nucleotide bindingGTP
TgeneRAB5Cchr9:107645320chr17:40278866ENST0000039386047164_166147.0217.0Nucleotide bindingGTP

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-5501912_2144140.333333333333342262.0DomainABC transporter 2
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-550899_1131140.333333333333342262.0DomainABC transporter 1
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-5501946_1953140.333333333333342262.0Nucleotide bindingATP 2
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-550933_940140.333333333333342262.0Nucleotide bindingATP 1
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-5501372_1656140.333333333333342262.0Topological domainNote=Extracellular
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-55043_639140.333333333333342262.0Topological domainNote=Extracellular
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-5501041_1057140.333333333333342262.0TransmembraneHelical
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-5501351_1371140.333333333333342262.0TransmembraneHelical
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-5501657_1677140.333333333333342262.0TransmembraneHelical
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-5501703_1723140.333333333333342262.0TransmembraneHelical
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-5501735_1755140.333333333333342262.0TransmembraneHelical
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-5501768_1788140.333333333333342262.0TransmembraneHelical
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-5501802_1822140.333333333333342262.0TransmembraneHelical
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-5501852_1872140.333333333333342262.0TransmembraneHelical
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-550640_660140.333333333333342262.0TransmembraneHelical
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-550683_703140.333333333333342262.0TransmembraneHelical
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-550716_736140.333333333333342262.0TransmembraneHelical
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-550745_765140.333333333333342262.0TransmembraneHelical
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-550777_797140.333333333333342262.0TransmembraneHelical
HgeneABCA1chr9:107645320chr17:40278866ENST00000374736-550827_847140.333333333333342262.0TransmembraneHelical
TgeneRAB5Cchr9:107645320chr17:40278866ENST000003462133650_58147.0217.0MotifEffector region
TgeneRAB5Cchr9:107645320chr17:40278866ENST000003938604750_58147.0217.0MotifEffector region
TgeneRAB5Cchr9:107645320chr17:40278866ENST000005475174750_58180.0250.0MotifEffector region
TgeneRAB5Cchr9:107645320chr17:40278866ENST0000034621336134_137147.0217.0Nucleotide bindingGTP
TgeneRAB5Cchr9:107645320chr17:40278866ENST000003462133628_36147.0217.0Nucleotide bindingGTP
TgeneRAB5Cchr9:107645320chr17:40278866ENST000003462133647_53147.0217.0Nucleotide bindingGTP
TgeneRAB5Cchr9:107645320chr17:40278866ENST000003462133676_80147.0217.0Nucleotide bindingGTP
TgeneRAB5Cchr9:107645320chr17:40278866ENST0000039386047134_137147.0217.0Nucleotide bindingGTP
TgeneRAB5Cchr9:107645320chr17:40278866ENST000003938604728_36147.0217.0Nucleotide bindingGTP
TgeneRAB5Cchr9:107645320chr17:40278866ENST000003938604747_53147.0217.0Nucleotide bindingGTP
TgeneRAB5Cchr9:107645320chr17:40278866ENST000003938604776_80147.0217.0Nucleotide bindingGTP
TgeneRAB5Cchr9:107645320chr17:40278866ENST0000054751747134_137180.0250.0Nucleotide bindingGTP
TgeneRAB5Cchr9:107645320chr17:40278866ENST0000054751747164_166180.0250.0Nucleotide bindingGTP
TgeneRAB5Cchr9:107645320chr17:40278866ENST000005475174728_36180.0250.0Nucleotide bindingGTP
TgeneRAB5Cchr9:107645320chr17:40278866ENST000005475174747_53180.0250.0Nucleotide bindingGTP
TgeneRAB5Cchr9:107645320chr17:40278866ENST000005475174776_80180.0250.0Nucleotide bindingGTP


Top

Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
ABCA1
RAB5C


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


Top

Related Drugs to ABCA1-RAB5C


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

Top

Related Diseases to ABCA1-RAB5C


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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