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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:AMMECR1-PLA2G12B (FusionGDB2 ID:HG9949TG84647)

Fusion Gene Summary for AMMECR1-PLA2G12B

check button Fusion gene summary
Fusion gene informationFusion gene name: AMMECR1-PLA2G12B
Fusion gene ID: hg9949tg84647
HgeneTgene
Gene symbol

AMMECR1

PLA2G12B

Gene ID

9949

84647

Gene nameAMMECR nuclear protein 1phospholipase A2 group XIIB
SynonymsAMMERC1|MFHIENFKSG71|GXIIB|GXIIIsPLA2|PLA2G13|sPLA2-GXIIB
Cytomap('AMMECR1')('PLA2G12B')

Xq23

10q22.1

Type of geneprotein-codingprotein-coding
DescriptionAMME syndrome candidate gene 1 proteinAlport syndrome mental retardation midface hypoplasia and elliptocytosis chromosomal region protein 1Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1group XIIB secretory phospholipase A2-like proteingroup XIII secreted phospholipase A2phospholipase A2, group XIII
Modification date2020031320200313
UniProtAcc

Q9Y4X0

.
Ensembl transtripts involved in fusion geneENST00000262844, ENST00000372057, 
ENST00000372059, ENST00000496695, 
Fusion gene scores* DoF score4 X 4 X 3=482 X 2 X 2=8
# samples 42
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: AMMECR1 [Title/Abstract] AND PLA2G12B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAMMECR1(109507717)-PLA2G12B(74702498), # samples:2
Anticipated loss of major functional domain due to fusion event.AMMECR1-PLA2G12B 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.
AMMECR1-PLA2G12B 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.
AMMECR1-PLA2G12B 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.
AMMECR1-PLA2G12B 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.
AMMECR1-PLA2G12B seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
AMMECR1-PLA2G12B seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene 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

check buttonFusion gene breakpoints across AMMECR1 (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 PLA2G12B (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
ChimerDB4LUADTCGA-MN-A4N5-01AAMMECR1chrX

109507717

-PLA2G12Bchr10

74702498

-


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Fusion Gene ORF analysis for AMMECR1-PLA2G12B

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
Frame-shiftENST00000262844ENST00000373032AMMECR1chrX

109507717

-PLA2G12Bchr10

74702498

-
In-frameENST00000372057ENST00000373032AMMECR1chrX

109507717

-PLA2G12Bchr10

74702498

-
intron-3CDSENST00000372059ENST00000373032AMMECR1chrX

109507717

-PLA2G12Bchr10

74702498

-
intron-3CDSENST00000496695ENST00000373032AMMECR1chrX

109507717

-PLA2G12Bchr10

74702498

-

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)
ENST00000372057AMMECR1chrX109507717-ENST00000373032PLA2G12Bchr1074702498-1676852321965214

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
ENST00000372057ENST00000373032AMMECR1chrX109507717-PLA2G12Bchr1074702498-0.174373340.8256267

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Fusion Genomic Features for AMMECR1-PLA2G12B


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)

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

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Fusion Protein Features for AMMECR1-PLA2G12B


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/chrX:109507717/chr10:74702498)
- 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
AMMECR1

Q9Y4X0

.
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
HgeneAMMECR1chrX:109507717chr10:74702498ENST00000262844-26105_121194334.0Compositional biasNote=Ser-rich
HgeneAMMECR1chrX:109507717chr10:74702498ENST00000262844-2620_82194334.0Compositional biasNote=Gly/Ser-rich

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneAMMECR1chrX:109507717chr10:74702498ENST00000372057-48105_12171211.0Compositional biasNote=Ser-rich
HgeneAMMECR1chrX:109507717chr10:74702498ENST00000372057-4820_8271211.0Compositional biasNote=Gly/Ser-rich
HgeneAMMECR1chrX:109507717chr10:74702498ENST00000372059-15105_1210297.0Compositional biasNote=Ser-rich
HgeneAMMECR1chrX:109507717chr10:74702498ENST00000372059-1520_820297.0Compositional biasNote=Gly/Ser-rich
HgeneAMMECR1chrX:109507717chr10:74702498ENST00000262844-26119_313194334.0DomainAMMECR1
HgeneAMMECR1chrX:109507717chr10:74702498ENST00000372057-48119_31371211.0DomainAMMECR1
HgeneAMMECR1chrX:109507717chr10:74702498ENST00000372059-15119_3130297.0DomainAMMECR1


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Fusion Gene Sequence for AMMECR1-PLA2G12B


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.
>4225_4225_1_AMMECR1-PLA2G12B_AMMECR1_chrX_109507717_ENST00000372057_PLA2G12B_chr10_74702498_ENST00000373032_length(transcript)=1676nt_BP=852nt
CTCTTTCTCTGGGCTAATCGTTTAGAGGACAGTCGCTCCTGCCAACCTAATCCCATGAGCCTGACTACCTTGCCGGGCCACAGGCTCAAA
GAAGCAGTGTGGCTGCCAGCACCCTCACGGTAAGGGGCACGGAGGCACCAGGCAGTCTGGCAGGATGAGAGACATCCTGGGGGTGGTCTG
AGTTTGGATGTGGGCTGAGAAGACAAAGCAGGGGGCTTTCGGGGGACAAGATTTTCCAAACATCTTATTCTTAGGATCATCACTTCCTAA
TCTGATGCAACTGACTCGGCAGGCATTCGGGAGCCTGTAAGCTCCATTTTCCTGTTCCAAATTCTTCTGCACCTCACCATGAGTCCTCAC
CTTGACCCTAATCAACTTGGGATTCTCCTCAAAGTACTTAGAAAGGAAAAGGAAGACGGTGACTACCCTGACATGATGGCCACCCACCCG
AGCTCCAGGTATGAAGCCTGCTCCTCTGGAATTACTCTAGGGCTGCGGCGGCGGCGGCGGGGGGATCGCCCTGTCGCCACCTCCGAGCTG
CGGAGTGGGGACCCTACTTTCTACCCCGGCCGCCGCCACCTCTTCCTCACCCTCCTCATCGTCCGCCGCCTCGTCCTCATCGCCGGGCTC
CCGGAAGATGGTGGTGTCAGCAGAGATGTGCTGCTTTTGCTTCGATGTGCTCTACTGTCACCTGTATGGATACCAGCAGCCCCGGACCCC
CCGATTCACCAACGAGCCCTACCCACTGTTTGTAACATGGAAGATTGGTCGAGACAAAAGATTACGTGGATGCATAGGTACTTTTTCTGC
CATGAATTTGCATTCAGGACTCAGGGAGTACACACTTACCAGGAAAGGCACCAATGCCCAGACCTGGCTACAAGCCCCAAGAGCCCAATG
GCTGCGGCTCCTATTTCCTGGGTCTCAAGGTACCAGAAAGTATGGACTTGGGCATTCCAGCAATGACAAAGTGCTGCAACCAGCTGGATG
TCTGTTATGACACTTGCGGTGCCAACAAATATCGCTGTGATGCAAAATTCCGATGGTGTCTCCACTCGATCTGCTCTGACCTTAAGCGGA
GTCTGGGCTTTGTCTCCAAAGTGGAAGCAGCCTGTGATTCCCTGGTTGACACTGTGTTCAACACCGTGTGGACCTTGGGCTGCCGCCCCT
TTATGAATAGTCAGCGGGCAGCTTGCATCTGTGCAGAGGAGGAGAAGGAAGAGTTATGAGGAAGAAGTGATTCCTTCCTGGTTTTGAGTG
ACACCACAGCTGTCAGCCTTCAAGATGTCAAGTCTTCGAGTCAGCGTGACTCATTCATTCTTCCAACAGTTTGGACACCACAAAGCAGGA
GAAAGGGAACATTTTTCTACAGCTGGAAAGTGAGTCCTATCCTTTGAGGAAATTTGAAAAAAGACATGGAGTGGTTTGAAAGCTACTCTT
CATTTAAGACTGCTCTCCCCAACCAAGACACATTTGCCTGGAAATTCAGTTCTTAGCTTAAAGACTAAAATGCAAGCAAACCCTGCAATT
CCTGGACCTGATAGTTATATTCATGAGTGAAATTGTGGGGAGTCCAGCCATTTGGGAGGCAATGACTTTCTGCTGGCCCATGTTTCAGTT

>4225_4225_1_AMMECR1-PLA2G12B_AMMECR1_chrX_109507717_ENST00000372057_PLA2G12B_chr10_74702498_ENST00000373032_length(amino acids)=214AA_BP=177
MFQILLHLTMSPHLDPNQLGILLKVLRKEKEDGDYPDMMATHPSSRYEACSSGITLGLRRRRRGDRPVATSELRSGDPTFYPGRRHLFLT
LLIVRRLVLIAGLPEDGGVSRDVLLLLRCALLSPVWIPAAPDPPIHQRALPTVCNMEDWSRQKITWMHRYFFCHEFAFRTQGVHTYQERH

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

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Fusion Gene PPI Analysis for AMMECR1-PLA2G12B


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 AMMECR1-PLA2G12B


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 AMMECR1-PLA2G12B


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAMMECR1C1846242Alport Syndrome, Mental Retardation, Midface Hypoplasia, and Elliptocytosis2ORPHANET
HgeneAMMECR1C4310810MIDFACE HYPOPLASIA, HEARING IMPAIRMENT, ELLIPTOCYTOSIS, AND NEPHROCALCINOSIS2CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneAMMECR1C0013336Dwarfism1GENOMICS_ENGLAND
HgeneAMMECR1C0349588Short stature1GENOMICS_ENGLAND
HgeneAMMECR1C2919142Short Stature, CTCAE1GENOMICS_ENGLAND