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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:ATL2-ACER3

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ATL2-ACER3
FusionPDB ID: 7637
FusionGDB2.0 ID: 7637
HgeneTgene
Gene symbol

ATL2

ACER3

Gene ID

64225

55331

Gene nameatlastin GTPase 2alkaline ceramidase 3
SynonymsARL3IP2|ARL6IP2|aip-2|atlastin2APHC|PHCA|PLDECO
Cytomap

2p22.2-p22.1

11q13.5

Type of geneprotein-codingprotein-coding
Descriptionatlastin-2ADP-ribosylation factor-like protein 6-interacting protein 2ARL-6-interacting protein 2alkaline ceramidase 3alkCDase 3alkaline CDase 3alkaline dihydroceramidase SB89alkaline phytoceramidasephytoceramidase, alkaline
Modification date2020031320200320
UniProtAcc

Q8NHH9

Q9NUN7

Ensembl transtripts involved in fusion geneENST idsENST00000332337, ENST00000378954, 
ENST00000402054, ENST00000406122, 
ENST00000419554, ENST00000452935, 
ENST00000539122, ENST00000546051, 
ENST00000486927, 		ENST00000530182, 
ENST00000526597, ENST00000538157, 
ENST00000533873, ENST00000544113, 
ENST00000532485, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 10 X 5=70013 X 10 X 5=650
# samples 1615
** MAII scorelog2(16/700*10)=-2.12928301694497
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/650*10)=-2.11547721741994
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: ATL2 [Title/Abstract] AND ACER3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ATL2(38540292)-ACER3(76637600), # samples:1
Anticipated loss of major functional domain due to fusion event.ATL2-ACER3 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.
ATL2-ACER3 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.
ATL2-ACER3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ATL2-ACER3 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
ATL2-ACER3 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
HgeneATL2

GO:0051260

protein homooligomerization

18270207

TgeneACER3

GO:0043067

regulation of programmed cell death

20068046

TgeneACER3

GO:0046512

sphingosine biosynthetic process

20068046

TgeneACER3

GO:0046514

ceramide catabolic process

30575723

TgeneACER3

GO:0071602

phytosphingosine biosynthetic process

11356846|20068046


check buttonFusion gene breakpoints across ATL2 (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 ACER3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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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
ChimerDB4STADTCGA-BR-7958ATL2chr2

38540292

-ACER3chr11

76637600

+


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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)
ENST00000402054ATL2chr238540292-ENST00000532485ACER3chr1176637600+77215505671250227
ENST00000546051ATL2chr238540292-ENST00000532485ACER3chr1176637600+77215505671250227

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
ENST00000402054ENST00000532485ATL2chr238540292-ACER3chr1176637600+0.036059590.96394044
ENST00000546051ENST00000532485ATL2chr238540292-ACER3chr1176637600+0.036059590.96394044

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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

>7637_7637_1_ATL2-ACER3_ATL2_chr2_38540292_ENST00000402054_ACER3_chr11_76637600_ENST00000532485_length(amino acids)=227AA_BP=
MIMIIPPMFGAVQSVRDGLEKRYIASYLALTVVGMGSWCFHMTLKYEMQLLDELPMIYSCCIFVYCMFECFKIKNSVNYHLLFTLVLFSL
IVTTVYLKVKEPIFHQVMYGMLVFTLVLRSIYIVTWVYPWLRGLGYTSLGIFLLGFLFWNIDNIFCESLRNFRKKVPPIIGITTQFHAWW

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

>7637_7637_2_ATL2-ACER3_ATL2_chr2_38540292_ENST00000546051_ACER3_chr11_76637600_ENST00000532485_length(amino acids)=227AA_BP=
MIMIIPPMFGAVQSVRDGLEKRYIASYLALTVVGMGSWCFHMTLKYEMQLLDELPMIYSCCIFVYCMFECFKIKNSVNYHLLFTLVLFSL
IVTTVYLKVKEPIFHQVMYGMLVFTLVLRSIYIVTWVYPWLRGLGYTSLGIFLLGFLFWNIDNIFCESLRNFRKKVPPIIGITTQFHAWW

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

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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/chr2:38540292/chr11:76637600)
- 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
ATL2

Q8NHH9

ACER3

Q9NUN7

FUNCTION: GTPase tethering membranes through formation of trans-homooligomers and mediating homotypic fusion of endoplasmic reticulum membranes. Functions in endoplasmic reticulum tubular network biogenesis (PubMed:18270207, PubMed:19665976, PubMed:27619977). {ECO:0000269|PubMed:18270207, ECO:0000269|PubMed:19665976, ECO:0000269|PubMed:27619977}.FUNCTION: Endoplasmic reticulum and Golgi ceramidase that catalyzes the hydrolysis of unsaturated long-chain C18:1-, C20:1- and C20:4-ceramides, dihydroceramides and phytoceramides into sphingoid bases like sphingosine and free fatty acids at alkaline pH (PubMed:20068046, PubMed:26792856, PubMed:20207939, PubMed:11356846, PubMed:30575723). Ceramides, sphingosine, and its phosphorylated form sphingosine-1-phosphate are bioactive lipids that mediate cellular signaling pathways regulating several biological processes including cell proliferation, apoptosis and differentiation (PubMed:20068046). Controls the generation of sphingosine in erythrocytes, and thereby sphingosine-1-phosphate in plasma (PubMed:20207939). Through the regulation of ceramides and sphingosine-1-phosphate homeostasis in the brain may play a role in neurons survival and function (By similarity). By regulating the levels of proinflammatory ceramides in immune cells and tissues, may modulate the inflammatory response (By similarity). {ECO:0000250|UniProtKB:Q9D099, ECO:0000269|PubMed:11356846, ECO:0000269|PubMed:20068046, ECO:0000269|PubMed:20207939, ECO:0000269|PubMed:26792856, ECO:0000269|PubMed:30575723, ECO:0000303|PubMed:20068046}.

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
HgeneATL2chr2:38540292chr11:76637600ENST00000332337-714101_108250.0567.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000332337-714145_147250.0567.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000332337-714244_245250.0567.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000378954-713101_108268.0584.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000378954-713145_147268.0584.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000378954-713244_245268.0584.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000419554-713101_108268.0580.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000419554-713145_147268.0580.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000419554-713244_245268.0580.0Nucleotide bindingGTP
TgeneACER3chr2:38540292chr11:76637600ENST00000532485011109_11834.333333333333336268.0Topological domainLumenal
TgeneACER3chr2:38540292chr11:76637600ENST00000532485011140_14134.333333333333336268.0Topological domainCytoplasmic
TgeneACER3chr2:38540292chr11:76637600ENST00000532485011163_17334.333333333333336268.0Topological domainLumenal
TgeneACER3chr2:38540292chr11:76637600ENST00000532485011195_21534.333333333333336268.0Topological domainCytoplasmic
TgeneACER3chr2:38540292chr11:76637600ENST00000532485011237_26734.333333333333336268.0Topological domainLumenal
TgeneACER3chr2:38540292chr11:76637600ENST0000053248501156_6134.333333333333336268.0Topological domainLumenal
TgeneACER3chr2:38540292chr11:76637600ENST0000053248501183_8734.333333333333336268.0Topological domainCytoplasmic
TgeneACER3chr2:38540292chr11:76637600ENST0000054411306109_1180.0135.0Topological domainLumenal
TgeneACER3chr2:38540292chr11:76637600ENST0000054411306140_1410.0135.0Topological domainCytoplasmic
TgeneACER3chr2:38540292chr11:76637600ENST0000054411306163_1730.0135.0Topological domainLumenal
TgeneACER3chr2:38540292chr11:76637600ENST0000054411306195_2150.0135.0Topological domainCytoplasmic
TgeneACER3chr2:38540292chr11:76637600ENST00000544113061_330.0135.0Topological domainCytoplasmic
TgeneACER3chr2:38540292chr11:76637600ENST0000054411306237_2670.0135.0Topological domainLumenal
TgeneACER3chr2:38540292chr11:76637600ENST000005441130656_610.0135.0Topological domainLumenal
TgeneACER3chr2:38540292chr11:76637600ENST000005441130683_870.0135.0Topological domainCytoplasmic
TgeneACER3chr2:38540292chr11:76637600ENST00000532485011119_13934.333333333333336268.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST00000532485011142_16234.333333333333336268.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST00000532485011174_19434.333333333333336268.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST00000532485011216_23634.333333333333336268.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST0000053248501134_5534.333333333333336268.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST0000053248501162_8234.333333333333336268.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST0000053248501188_10834.333333333333336268.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST0000054411306119_1390.0135.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST0000054411306142_1620.0135.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST0000054411306174_1940.0135.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST0000054411306216_2360.0135.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST000005441130634_550.0135.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST000005441130662_820.0135.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST000005441130688_1080.0135.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneATL2chr2:38540292chr11:76637600ENST00000332337-714256_284250.0567.0Coiled coilOntology_term=ECO:0000255
HgeneATL2chr2:38540292chr11:76637600ENST00000378954-713256_284268.0584.0Coiled coilOntology_term=ECO:0000255
HgeneATL2chr2:38540292chr11:76637600ENST00000402054-612256_28497.0413.0Coiled coilOntology_term=ECO:0000255
HgeneATL2chr2:38540292chr11:76637600ENST00000419554-713256_284268.0580.0Coiled coilOntology_term=ECO:0000255
HgeneATL2chr2:38540292chr11:76637600ENST00000539122-612256_28497.0413.0Coiled coilOntology_term=ECO:0000255
HgeneATL2chr2:38540292chr11:76637600ENST00000332337-71491_336250.0567.0DomainGB1/RHD3-type G
HgeneATL2chr2:38540292chr11:76637600ENST00000378954-71391_336268.0584.0DomainGB1/RHD3-type G
HgeneATL2chr2:38540292chr11:76637600ENST00000402054-61291_33697.0413.0DomainGB1/RHD3-type G
HgeneATL2chr2:38540292chr11:76637600ENST00000419554-71391_336268.0580.0DomainGB1/RHD3-type G
HgeneATL2chr2:38540292chr11:76637600ENST00000539122-61291_33697.0413.0DomainGB1/RHD3-type G
HgeneATL2chr2:38540292chr11:76637600ENST00000332337-714303_306250.0567.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000378954-713303_306268.0584.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000402054-612101_10897.0413.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000402054-612145_14797.0413.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000402054-612244_24597.0413.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000402054-612303_30697.0413.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000419554-713303_306268.0580.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000539122-612101_10897.0413.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000539122-612145_14797.0413.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000539122-612244_24597.0413.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000539122-612303_30697.0413.0Nucleotide bindingGTP
HgeneATL2chr2:38540292chr11:76637600ENST00000332337-7141_476250.0567.0Topological domainCytoplasmic
HgeneATL2chr2:38540292chr11:76637600ENST00000332337-714498_499250.0567.0Topological domainLumenal
HgeneATL2chr2:38540292chr11:76637600ENST00000332337-714521_583250.0567.0Topological domainCytoplasmic
HgeneATL2chr2:38540292chr11:76637600ENST00000378954-7131_476268.0584.0Topological domainCytoplasmic
HgeneATL2chr2:38540292chr11:76637600ENST00000378954-713498_499268.0584.0Topological domainLumenal
HgeneATL2chr2:38540292chr11:76637600ENST00000378954-713521_583268.0584.0Topological domainCytoplasmic
HgeneATL2chr2:38540292chr11:76637600ENST00000402054-6121_47697.0413.0Topological domainCytoplasmic
HgeneATL2chr2:38540292chr11:76637600ENST00000402054-612498_49997.0413.0Topological domainLumenal
HgeneATL2chr2:38540292chr11:76637600ENST00000402054-612521_58397.0413.0Topological domainCytoplasmic
HgeneATL2chr2:38540292chr11:76637600ENST00000419554-7131_476268.0580.0Topological domainCytoplasmic
HgeneATL2chr2:38540292chr11:76637600ENST00000419554-713498_499268.0580.0Topological domainLumenal
HgeneATL2chr2:38540292chr11:76637600ENST00000419554-713521_583268.0580.0Topological domainCytoplasmic
HgeneATL2chr2:38540292chr11:76637600ENST00000539122-6121_47697.0413.0Topological domainCytoplasmic
HgeneATL2chr2:38540292chr11:76637600ENST00000539122-612498_49997.0413.0Topological domainLumenal
HgeneATL2chr2:38540292chr11:76637600ENST00000539122-612521_58397.0413.0Topological domainCytoplasmic
HgeneATL2chr2:38540292chr11:76637600ENST00000332337-714477_497250.0567.0TransmembraneHelical
HgeneATL2chr2:38540292chr11:76637600ENST00000332337-714500_520250.0567.0TransmembraneHelical
HgeneATL2chr2:38540292chr11:76637600ENST00000378954-713477_497268.0584.0TransmembraneHelical
HgeneATL2chr2:38540292chr11:76637600ENST00000378954-713500_520268.0584.0TransmembraneHelical
HgeneATL2chr2:38540292chr11:76637600ENST00000402054-612477_49797.0413.0TransmembraneHelical
HgeneATL2chr2:38540292chr11:76637600ENST00000402054-612500_52097.0413.0TransmembraneHelical
HgeneATL2chr2:38540292chr11:76637600ENST00000419554-713477_497268.0580.0TransmembraneHelical
HgeneATL2chr2:38540292chr11:76637600ENST00000419554-713500_520268.0580.0TransmembraneHelical
HgeneATL2chr2:38540292chr11:76637600ENST00000539122-612477_49797.0413.0TransmembraneHelical
HgeneATL2chr2:38540292chr11:76637600ENST00000539122-612500_52097.0413.0TransmembraneHelical
TgeneACER3chr2:38540292chr11:76637600ENST000005324850111_3334.333333333333336268.0Topological domainCytoplasmic


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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
ATL2
ACER3


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


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Related Drugs to ATL2-ACER3


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

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Related Diseases to ATL2-ACER3


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