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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:ACER3-PPME1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ACER3-PPME1
FusionPDB ID: 1297
FusionGDB2.0 ID: 1297
HgeneTgene
Gene symbol

ACER3

PPME1

Gene ID

55331

51400

Gene namealkaline ceramidase 3protein phosphatase methylesterase 1
SynonymsAPHC|PHCA|PLDECOABDH19|PME-1
Cytomap

11q13.5

11q13.4

Type of geneprotein-codingprotein-coding
Descriptionalkaline ceramidase 3alkCDase 3alkaline CDase 3alkaline dihydroceramidase SB89alkaline phytoceramidasephytoceramidase, alkalineprotein phosphatase methylesterase 1testicular secretory protein Li 39
Modification date2020032020200313
UniProtAcc

Q9NUN7

.
Ensembl transtripts involved in fusion geneENST idsENST00000530182, ENST00000532485, 
ENST00000533873, ENST00000538157, 
ENST00000526597, ENST00000544113, 
ENST00000328257, ENST00000398427, 
ENST00000542710, ENST00000543525, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 7 X 7=68610 X 7 X 6=420
# samples 1712
** MAII scorelog2(17/686*10)=-2.01267383003511
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/420*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: ACER3 [Title/Abstract] AND PPME1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ACER3(76670075)-PPME1(73933357), # samples:3
Anticipated loss of major functional domain due to fusion event.ACER3-PPME1 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.
ACER3-PPME1 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
HgeneACER3

GO:0043067

regulation of programmed cell death

20068046

HgeneACER3

GO:0046512

sphingosine biosynthetic process

20068046

HgeneACER3

GO:0046514

ceramide catabolic process

30575723

HgeneACER3

GO:0071602

phytosphingosine biosynthetic process

11356846|20068046

TgenePPME1

GO:0006482

protein demethylation

10318862


check buttonFusion gene breakpoints across ACER3 (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 PPME1 (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
ChimerDB4LUADTCGA-05-5425-01AACER3chr11

76670075

-PPME1chr11

73933357

+
ChimerDB4LUADTCGA-05-5425-01AACER3chr11

76670075

+PPME1chr11

73933357

+


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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)
ENST00000532485ACER3chr1176670075+ENST00000328257PPME1chr1173933357+2437371801243387
ENST00000532485ACER3chr1176670075+ENST00000398427PPME1chr1173933357+2479371801285401
ENST00000533873ACER3chr1176670075+ENST00000328257PPME1chr1173933357+2257191111063350
ENST00000533873ACER3chr1176670075+ENST00000398427PPME1chr1173933357+2299191111105364
ENST00000538157ACER3chr1176670075+ENST00000328257PPME1chr1173933357+24043381911210339
ENST00000538157ACER3chr1176670075+ENST00000398427PPME1chr1173933357+24463381911252353

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
ENST00000532485ENST00000328257ACER3chr1176670075+PPME1chr1173933357+0.0018671880.9981329
ENST00000532485ENST00000398427ACER3chr1176670075+PPME1chr1173933357+0.0019667590.9980332
ENST00000533873ENST00000328257ACER3chr1176670075+PPME1chr1173933357+0.0012046080.9987954
ENST00000533873ENST00000398427ACER3chr1176670075+PPME1chr1173933357+0.001066120.99893385
ENST00000538157ENST00000328257ACER3chr1176670075+PPME1chr1173933357+0.0012483210.99875164
ENST00000538157ENST00000398427ACER3chr1176670075+PPME1chr1173933357+0.0012153310.9987847

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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

>1297_1297_1_ACER3-PPME1_ACER3_chr11_76670075_ENST00000532485_PPME1_chr11_73933357_ENST00000328257_length(amino acids)=387AA_BP=97
MGGGGGGVMAPAADREGYWGPTTSTLDWCEENYSVTWYIAEFWNTVSNLIMIIPPMFGAVQSVRDGLEKRYIASYLALTVVGMGSWCFHM
TLKYEMQAAIISRVQCRIVALDLRSHGETKVKNPEDLSAETMAKDVGNVVEAMYGDLPPPIMLIGHSMGGAIAVHTASSNLVPSLLGLCM
IDVVEGTAMDALNSMQNFLRGRPKTFKSLENAIEWSVKSGQIRNLESARVSMVGQVKQCEGITSPEGSKSIVEGIIEEEEEDEEGSESIS
KRKKEDDMETKKDHPYTWRIELAKTEKYWDGWFRGLSNLFLSCPIPKLLLLAGVDRLDKDLTIGQMQGKFQMQVLPQCGHAVHEDAPDKV

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

>1297_1297_2_ACER3-PPME1_ACER3_chr11_76670075_ENST00000532485_PPME1_chr11_73933357_ENST00000398427_length(amino acids)=401AA_BP=97
MGGGGGGVMAPAADREGYWGPTTSTLDWCEENYSVTWYIAEFWNTVSNLIMIIPPMFGAVQSVRDGLEKRYIASYLALTVVGMGSWCFHM
TLKYEMQAAIISRVQCRIVALDLRSHGETKVKNPEDLSAETMAKDVGNVVEAMYGDLPPPIMLIGHSMGGAIAVHTASSNLVPSLLGLCM
IDVVEGTAMDALNSMQNFLRGRPKTFKSLENAIEWSVKSGQIRNLESARVSMVGQVKQCEGITSPEGSKSIVEGIIEEEEEDEEGSESIS
KRKKEDDMEGLPSETQNLLLFLQTKKDHPYTWRIELAKTEKYWDGWFRGLSNLFLSCPIPKLLLLAGVDRLDKDLTIGQMQGKFQMQVLP

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

>1297_1297_3_ACER3-PPME1_ACER3_chr11_76670075_ENST00000533873_PPME1_chr11_73933357_ENST00000328257_length(amino acids)=350AA_BP=60
MGGGGGGVMAPAADREGYWGPTTSTLDWCEENYSVTWYIAEFLVGMGSWCFHMTLKYEMQAAIISRVQCRIVALDLRSHGETKVKNPEDL
SAETMAKDVGNVVEAMYGDLPPPIMLIGHSMGGAIAVHTASSNLVPSLLGLCMIDVVEGTAMDALNSMQNFLRGRPKTFKSLENAIEWSV
KSGQIRNLESARVSMVGQVKQCEGITSPEGSKSIVEGIIEEEEEDEEGSESISKRKKEDDMETKKDHPYTWRIELAKTEKYWDGWFRGLS

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

>1297_1297_4_ACER3-PPME1_ACER3_chr11_76670075_ENST00000533873_PPME1_chr11_73933357_ENST00000398427_length(amino acids)=364AA_BP=60
MGGGGGGVMAPAADREGYWGPTTSTLDWCEENYSVTWYIAEFLVGMGSWCFHMTLKYEMQAAIISRVQCRIVALDLRSHGETKVKNPEDL
SAETMAKDVGNVVEAMYGDLPPPIMLIGHSMGGAIAVHTASSNLVPSLLGLCMIDVVEGTAMDALNSMQNFLRGRPKTFKSLENAIEWSV
KSGQIRNLESARVSMVGQVKQCEGITSPEGSKSIVEGIIEEEEEDEEGSESISKRKKEDDMEGLPSETQNLLLFLQTKKDHPYTWRIELA
KTEKYWDGWFRGLSNLFLSCPIPKLLLLAGVDRLDKDLTIGQMQGKFQMQVLPQCGHAVHEDAPDKVAEAVATFLIRHRFAEPIGGFQCV

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

>1297_1297_5_ACER3-PPME1_ACER3_chr11_76670075_ENST00000538157_PPME1_chr11_73933357_ENST00000328257_length(amino acids)=339AA_BP=49
MIMIIPPMFGAVQSVRDGLEKRYIASYLALTVVGMGSWCFHMTLKYEMQAAIISRVQCRIVALDLRSHGETKVKNPEDLSAETMAKDVGN
VVEAMYGDLPPPIMLIGHSMGGAIAVHTASSNLVPSLLGLCMIDVVEGTAMDALNSMQNFLRGRPKTFKSLENAIEWSVKSGQIRNLESA
RVSMVGQVKQCEGITSPEGSKSIVEGIIEEEEEDEEGSESISKRKKEDDMETKKDHPYTWRIELAKTEKYWDGWFRGLSNLFLSCPIPKL

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

>1297_1297_6_ACER3-PPME1_ACER3_chr11_76670075_ENST00000538157_PPME1_chr11_73933357_ENST00000398427_length(amino acids)=353AA_BP=49
MIMIIPPMFGAVQSVRDGLEKRYIASYLALTVVGMGSWCFHMTLKYEMQAAIISRVQCRIVALDLRSHGETKVKNPEDLSAETMAKDVGN
VVEAMYGDLPPPIMLIGHSMGGAIAVHTASSNLVPSLLGLCMIDVVEGTAMDALNSMQNFLRGRPKTFKSLENAIEWSVKSGQIRNLESA
RVSMVGQVKQCEGITSPEGSKSIVEGIIEEEEEDEEGSESISKRKKEDDMEGLPSETQNLLLFLQTKKDHPYTWRIELAKTEKYWDGWFR

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

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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/chr11:76670075/chr11:73933357)
- 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
ACER3

Q9NUN7

.
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}.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
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+3111_3389.0268.0Topological domainCytoplasmic
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+31156_6189.0268.0Topological domainLumenal
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+31183_8789.0268.0Topological domainCytoplasmic
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+31134_5589.0268.0TransmembraneHelical
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+31162_8289.0268.0TransmembraneHelical
TgenePPME1chr11:76670075chr11:73933357ENST00000328257214256_26396.0387.0Compositional biasNote=Poly-Glu
TgenePPME1chr11:76670075chr11:73933357ENST0000054352508256_2630200.0Compositional biasNote=Poly-Glu

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+311109_11889.0268.0Topological domainLumenal
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+311140_14189.0268.0Topological domainCytoplasmic
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+311163_17389.0268.0Topological domainLumenal
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+311195_21589.0268.0Topological domainCytoplasmic
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+311237_26789.0268.0Topological domainLumenal
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+16109_1180.0135.0Topological domainLumenal
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+16140_1410.0135.0Topological domainCytoplasmic
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+16163_1730.0135.0Topological domainLumenal
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+16195_2150.0135.0Topological domainCytoplasmic
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+161_330.0135.0Topological domainCytoplasmic
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+16237_2670.0135.0Topological domainLumenal
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+1656_610.0135.0Topological domainLumenal
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+1683_870.0135.0Topological domainCytoplasmic
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+311119_13989.0268.0TransmembraneHelical
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+311142_16289.0268.0TransmembraneHelical
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+311174_19489.0268.0TransmembraneHelical
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+311216_23689.0268.0TransmembraneHelical
HgeneACER3chr11:76670075chr11:73933357ENST00000532485+31188_10889.0268.0TransmembraneHelical
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+16119_1390.0135.0TransmembraneHelical
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+16142_1620.0135.0TransmembraneHelical
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+16174_1940.0135.0TransmembraneHelical
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+16216_2360.0135.0TransmembraneHelical
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+1634_550.0135.0TransmembraneHelical
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+1662_820.0135.0TransmembraneHelical
HgeneACER3chr11:76670075chr11:73933357ENST00000544113+1688_1080.0135.0TransmembraneHelical


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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
ACER3
PPME1


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 ACER3-PPME1


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 ACER3-PPME1


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