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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:LSM14A-FXYD3 (FusionGDB2 ID:50185)

Fusion Gene Summary for LSM14A-FXYD3

check button Fusion gene summary
Fusion gene informationFusion gene name: LSM14A-FXYD3
Fusion gene ID: 50185
HgeneTgene
Gene symbol

LSM14A

FXYD3

Gene ID

26065

5349

Gene nameLSM14A mRNA processing body assembly factorFXYD domain containing ion transport regulator 3
SynonymsC19orf13|FAM61A|RAP55|RAP55AMAT8|PLML
Cytomap

19q13.11

19q13.12

Type of geneprotein-codingprotein-coding
Descriptionprotein LSM14 homolog ALSM14 homolog ALSM14A, SCD6 homolog ARNA-associated protein 55RNA-associated protein 55AalphaSNBPfamily with sequence similarity 61, member AhRAP55hRAP55Aprotein SCD6 homologputative alpha-synuclein-binding proteinFXYD domain-containing ion transport regulator 3chloride conductance inducer protein Mat-8mammary tumor 8 kDa proteinphospholemman-like proteinsodium/potassium-transporting ATPase subunit FXYD3
Modification date2020032720200313
UniProtAcc

Q8ND56

Q14802

Ensembl transtripts involved in fusion geneENST00000433627, ENST00000540746, 
ENST00000544216, 
ENST00000344013, 
ENST00000435734, ENST00000535103, 
ENST00000603181, ENST00000603524, 
ENST00000604255, ENST00000605552, 
ENST00000346446, ENST00000406242, 
ENST00000406988, ENST00000454903, 
ENST00000603449, ENST00000604404, 
ENST00000604621, ENST00000604804, 
ENST00000605550, ENST00000605677, 
Fusion gene scores* DoF score18 X 10 X 10=18009 X 10 X 8=720
# samples 2411
** MAII scorelog2(24/1800*10)=-2.90689059560852
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(11/720*10)=-2.71049338280502
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LSM14A [Title/Abstract] AND FXYD3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLSM14A(34706566)-FXYD3(35610072), # 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
HgeneLSM14A

GO:0033962

cytoplasmic mRNA processing body assembly

16484376


check buttonFusion gene breakpoints across LSM14A (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 FXYD3 (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
ChimerDB4BRCATCGA-A2-A04U-01ALSM14Achr19

34706566

+FXYD3chr19

35610072

+
ChimerDB4BRCATCGA-A2-A04ULSM14Achr19

34706566

+FXYD3chr19

35610071

+


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Fusion Gene ORF analysis for LSM14A-FXYD3

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
5CDS-5UTRENST00000433627ENST00000344013LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000433627ENST00000344013LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000433627ENST00000435734LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000433627ENST00000435734LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000433627ENST00000535103LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000433627ENST00000535103LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000433627ENST00000603181LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000433627ENST00000603181LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000433627ENST00000603524LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000433627ENST00000603524LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000433627ENST00000604255LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000433627ENST00000604255LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000433627ENST00000605552LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000433627ENST00000605552LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000540746ENST00000344013LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000540746ENST00000344013LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000540746ENST00000435734LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000540746ENST00000435734LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000540746ENST00000535103LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000540746ENST00000535103LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000540746ENST00000603181LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000540746ENST00000603181LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000540746ENST00000603524LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000540746ENST00000603524LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000540746ENST00000604255LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000540746ENST00000604255LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000540746ENST00000605552LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000540746ENST00000605552LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000544216ENST00000344013LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000544216ENST00000344013LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000544216ENST00000435734LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000544216ENST00000435734LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000544216ENST00000535103LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000544216ENST00000535103LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000544216ENST00000603181LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000544216ENST00000603181LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000544216ENST00000603524LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000544216ENST00000603524LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000544216ENST00000604255LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000544216ENST00000604255LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-5UTRENST00000544216ENST00000605552LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-5UTRENST00000544216ENST00000605552LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000433627ENST00000346446LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000433627ENST00000346446LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000433627ENST00000406242LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000433627ENST00000406242LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000433627ENST00000406988LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000433627ENST00000406988LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000433627ENST00000454903LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000433627ENST00000454903LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000433627ENST00000603449LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000433627ENST00000603449LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000433627ENST00000604404LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000433627ENST00000604404LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000433627ENST00000604621LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000433627ENST00000604621LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000433627ENST00000604804LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000433627ENST00000604804LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000433627ENST00000605550LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000433627ENST00000605550LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000433627ENST00000605677LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000433627ENST00000605677LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000540746ENST00000346446LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000540746ENST00000346446LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000540746ENST00000406242LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000540746ENST00000406242LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000540746ENST00000406988LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000540746ENST00000406988LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000540746ENST00000454903LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000540746ENST00000454903LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000540746ENST00000603449LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000540746ENST00000603449LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000540746ENST00000604404LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000540746ENST00000604404LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000540746ENST00000604621LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000540746ENST00000604621LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000540746ENST00000604804LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000540746ENST00000604804LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000540746ENST00000605550LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000540746ENST00000605550LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000540746ENST00000605677LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000540746ENST00000605677LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000544216ENST00000346446LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000544216ENST00000346446LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000544216ENST00000406242LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000544216ENST00000406242LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000544216ENST00000406988LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000544216ENST00000406988LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000544216ENST00000454903LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000544216ENST00000454903LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000544216ENST00000603449LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000544216ENST00000603449LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000544216ENST00000604404LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000544216ENST00000604404LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000544216ENST00000604621LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000544216ENST00000604621LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000544216ENST00000604804LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000544216ENST00000604804LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000544216ENST00000605550LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000544216ENST00000605550LSM14Achr19

34706566

+FXYD3chr19

35610071

+
5CDS-intronENST00000544216ENST00000605677LSM14Achr19

34706566

+FXYD3chr19

35610072

+
5CDS-intronENST00000544216ENST00000605677LSM14Achr19

34706566

+FXYD3chr19

35610071

+

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 LSM14A-FXYD3


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)
LSM14Achr1934706566+FXYD3chr1935610071+3.71E-091
LSM14Achr1934706566+FXYD3chr1935610071+3.71E-091
LSM14Achr1934706566+FXYD3chr1935610071+3.71E-091
LSM14Achr1934706566+FXYD3chr1935610071+3.71E-091

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 LSM14A-FXYD3


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/:34706566/:35610072)
- 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
LSM14A

Q8ND56

FXYD3

Q14802

FUNCTION: Essential for formation of P-bodies, cytoplasmic structures that provide storage sites for translationally inactive mRNAs and protect them from degradation (PubMed:16484376, PubMed:17074753, PubMed:29510985). Acts as a repressor of mRNA translation (PubMed:29510985). May play a role in mitotic spindle assembly (PubMed:26339800). {ECO:0000269|PubMed:16484376, ECO:0000269|PubMed:17074753, ECO:0000269|PubMed:26339800, ECO:0000269|PubMed:29510985}.FUNCTION: Associates with and regulates the activity of the sodium/potassium-transporting ATPase (NKA) which transports Na(+) out of the cell and K(+) into the cell (PubMed:17077088). Reduces glutathionylation of the NKA beta-1 subunit ATP1B1, thus reversing glutathionylation-mediated inhibition of ATP1B1 (PubMed:21454534). Induces a hyperpolarization-activated chloride current when expressed in Xenopus oocytes (PubMed:7836447). {ECO:0000269|PubMed:17077088, ECO:0000269|PubMed:21454534, ECO:0000269|PubMed:7836447}.; FUNCTION: [Isoform 1]: Decreases the apparent K+ and Na+ affinity of the sodium/potassium-transporting ATPase over a large range of membrane potentials. {ECO:0000269|PubMed:17077088}.; FUNCTION: [Isoform 2]: Decreases the apparent K+ affinity of the sodium/potassium-transporting ATPase only at slightly negative and positive membrane potentials and increases the apparent Na+ affinity over a large range of membrane potentials. {ECO:0000269|PubMed:17077088}.

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 LSM14A-FXYD3


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 LSM14A-FXYD3


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 LSM14A-FXYD3


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 LSM14A-FXYD3


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