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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:SLC12A6-EMC4 (FusionGDB2 ID:82228)

Fusion Gene Summary for SLC12A6-EMC4

check button Fusion gene summary
Fusion gene informationFusion gene name: SLC12A6-EMC4
Fusion gene ID: 82228
HgeneTgene
Gene symbol

SLC12A6

EMC4

Gene ID

9990

51234

Gene namesolute carrier family 12 member 6ER membrane protein complex subunit 4
SynonymsACCPN|KCC3|KCC3A|KCC3BPIG17|TMEM85
Cytomap

15q14

15q14

Type of geneprotein-codingprotein-coding
Descriptionsolute carrier family 12 member 6K-Cl cotransporter 3electroneutral potassium-chloride cotransporter 3potassium chloride cotransporter 3potassium chloride cotransporter KCC3a-S3potassium-chloride transporter-3apotassium-chloride transporter-3bsolutER membrane protein complex subunit 4cell proliferation-inducing gene 17 proteintransmembrane protein 85
Modification date2020031320200313
UniProtAcc.

Q5J8M3

Ensembl transtripts involved in fusion geneENST00000290209, ENST00000354181, 
ENST00000397702, ENST00000397707, 
ENST00000451844, ENST00000458406, 
ENST00000558589, ENST00000558667, 
ENST00000560164, ENST00000560611, 
ENST00000249209, ENST00000267750, 
ENST00000557879, ENST00000559078, 
ENST00000559421, 
Fusion gene scores* DoF score6 X 6 X 2=723 X 4 X 2=24
# samples 74
** MAII scorelog2(7/72*10)=-0.0406419844973459
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SLC12A6 [Title/Abstract] AND EMC4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSLC12A6(34521954)-EMC4(34520790), # 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
HgeneSLC12A6

GO:0006811

ion transport

10187864

HgeneSLC12A6

GO:0071477

cellular hypotonic salinity response

16048901


check buttonFusion gene breakpoints across SLC12A6 (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 EMC4 (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
ChiTaRS5.0N/AAW606410SLC12A6chr15

34522275

-EMC4chr15

34522273

-
ChiTaRS5.0N/ABE855820SLC12A6chr15

34521954

-EMC4chr15

34520790

-
ChiTaRS5.0N/ABF594188SLC12A6chr15

34521954

-EMC4chr15

34520790

-


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Fusion Gene ORF analysis for SLC12A6-EMC4

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
intron-3UTRENST00000290209ENST00000249209SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000290209ENST00000267750SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000290209ENST00000557879SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-3UTRENST00000354181ENST00000249209SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000354181ENST00000267750SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000354181ENST00000557879SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-3UTRENST00000397702ENST00000249209SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000397702ENST00000267750SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000397702ENST00000557879SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-3UTRENST00000397707ENST00000249209SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000397707ENST00000267750SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000397707ENST00000557879SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-3UTRENST00000451844ENST00000249209SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000451844ENST00000267750SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000451844ENST00000557879SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-3UTRENST00000458406ENST00000249209SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000458406ENST00000267750SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000458406ENST00000557879SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-3UTRENST00000558589ENST00000249209SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000558589ENST00000267750SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000558589ENST00000557879SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-3UTRENST00000558667ENST00000249209SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000558667ENST00000267750SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000558667ENST00000557879SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-3UTRENST00000560164ENST00000249209SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000560164ENST00000267750SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000560164ENST00000557879SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-3UTRENST00000560611ENST00000249209SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000560611ENST00000267750SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-3UTRENST00000560611ENST00000557879SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000290209ENST00000249209SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000290209ENST00000267750SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000290209ENST00000557879SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000290209ENST00000559078SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000290209ENST00000559078SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000290209ENST00000559421SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000290209ENST00000559421SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000354181ENST00000249209SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000354181ENST00000267750SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000354181ENST00000557879SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000354181ENST00000559078SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000354181ENST00000559078SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000354181ENST00000559421SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000354181ENST00000559421SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000397702ENST00000249209SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000397702ENST00000267750SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000397702ENST00000557879SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000397702ENST00000559078SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000397702ENST00000559078SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000397702ENST00000559421SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000397702ENST00000559421SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000397707ENST00000249209SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000397707ENST00000267750SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000397707ENST00000557879SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000397707ENST00000559078SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000397707ENST00000559078SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000397707ENST00000559421SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000397707ENST00000559421SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000451844ENST00000249209SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000451844ENST00000267750SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000451844ENST00000557879SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000451844ENST00000559078SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000451844ENST00000559078SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000451844ENST00000559421SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000451844ENST00000559421SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000458406ENST00000249209SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000458406ENST00000267750SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000458406ENST00000557879SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000458406ENST00000559078SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000458406ENST00000559078SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000458406ENST00000559421SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000458406ENST00000559421SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000558589ENST00000249209SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000558589ENST00000267750SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000558589ENST00000557879SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000558589ENST00000559078SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000558589ENST00000559078SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000558589ENST00000559421SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000558589ENST00000559421SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000558667ENST00000249209SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000558667ENST00000267750SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000558667ENST00000557879SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000558667ENST00000559078SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000558667ENST00000559078SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000558667ENST00000559421SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000558667ENST00000559421SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000560164ENST00000249209SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000560164ENST00000267750SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000560164ENST00000557879SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000560164ENST00000559078SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000560164ENST00000559078SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000560164ENST00000559421SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000560164ENST00000559421SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000560611ENST00000249209SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000560611ENST00000267750SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000560611ENST00000557879SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000560611ENST00000559078SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000560611ENST00000559078SLC12A6chr15

34521954

-EMC4chr15

34520790

-
intron-intronENST00000560611ENST00000559421SLC12A6chr15

34522275

-EMC4chr15

34522273

-
intron-intronENST00000560611ENST00000559421SLC12A6chr15

34521954

-EMC4chr15

34520790

-

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 SLC12A6-EMC4


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.

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.

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Fusion Protein Features for SLC12A6-EMC4


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/:34521954/:34520790)
- 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
.EMC4

Q5J8M3

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}.FUNCTION: Part of the endoplasmic reticulum membrane protein complex (EMC) that enables the energy-independent insertion into endoplasmic reticulum membranes of newly synthesized membrane proteins (PubMed:30415835, PubMed:29809151, PubMed:29242231, PubMed:32459176, PubMed:32439656). Preferentially accommodates proteins with transmembrane domains that are weakly hydrophobic or contain destabilizing features such as charged and aromatic residues (PubMed:30415835, PubMed:29809151, PubMed:29242231). Involved in the cotranslational insertion of multi-pass membrane proteins in which stop-transfer membrane-anchor sequences become ER membrane spanning helices (PubMed:30415835, PubMed:29809151). It is also required for the post-translational insertion of tail-anchored/TA proteins in endoplasmic reticulum membranes (PubMed:29809151, PubMed:29242231). By mediating the proper cotranslational insertion of N-terminal transmembrane domains in an N-exo topology, with translocated N-terminus in the lumen of the ER, controls the topology of multi-pass membrane proteins like the G protein-coupled receptors (PubMed:30415835). By regulating the insertion of various proteins in membranes, it is indirectly involved in many cellular processes (Probable). {ECO:0000269|PubMed:29242231, ECO:0000269|PubMed:29809151, ECO:0000269|PubMed:30415835, ECO:0000269|PubMed:32439656, ECO:0000269|PubMed:32459176, ECO:0000305|PubMed:18586032}.

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 SLC12A6-EMC4


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 SLC12A6-EMC4


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 SLC12A6-EMC4


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 SLC12A6-EMC4


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