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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:PEMT-SCNN1A (FusionGDB2 ID:63868)

Fusion Gene Summary for PEMT-SCNN1A

check button Fusion gene summary
Fusion gene informationFusion gene name: PEMT-SCNN1A
Fusion gene ID: 63868
HgeneTgene
Gene symbol

PEMT

SCNN1A

Gene ID

10400

6337

Gene namephosphatidylethanolamine N-methyltransferasesodium channel epithelial 1 subunit alpha
SynonymsPEAMT|PEMPT|PEMT2|PLMT|PNMTBESC2|ENaCa|ENaCalpha|LIDLS3|SCNEA|SCNN1
Cytomap

17p11.2

12p13.31

Type of geneprotein-codingprotein-coding
Descriptionphosphatidylethanolamine N-methyltransferasephospholipid methyltransferaseamiloride-sensitive sodium channel subunit alphaalpha ENaC-2alpha-ENaCalpha-NaCHamiloride-sensitive epithelial sodium channel alpha subunitamiloride-sensitive sodium channel subunit alpha 2epithelial Na(+) channel subunit alphanasal epithelial sodi
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000395782, ENST00000395783, 
ENST00000435340, ENST00000255389, 
ENST00000395781, ENST00000484838, 
ENST00000360168, ENST00000358945, 
ENST00000540037, ENST00000228916, 
ENST00000396966, ENST00000543768, 
ENST00000538979, 
Fusion gene scores* DoF score11 X 7 X 6=4625 X 6 X 4=120
# samples 116
** MAII scorelog2(11/462*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/120*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PEMT [Title/Abstract] AND SCNN1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPEMT(17427066)-SCNN1A(6457185), # samples:1
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
TgeneSCNN1A

GO:0035725

sodium ion transmembrane transport

24124190

TgeneSCNN1A

GO:0050891

multicellular organismal water homeostasis

24124190

TgeneSCNN1A

GO:0055078

sodium ion homeostasis

24124190


check buttonFusion gene breakpoints across PEMT (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 SCNN1A (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/AAA035445PEMTchr17

17427066

+SCNN1Achr12

6457185

+


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Fusion Gene ORF analysis for PEMT-SCNN1A

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-3CDSENST00000395782ENST00000360168PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000395782ENST00000358945PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000395782ENST00000540037PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000395782ENST00000228916PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3UTRENST00000395782ENST00000396966PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3UTRENST00000395782ENST00000543768PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-intronENST00000395782ENST00000538979PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000395783ENST00000360168PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000395783ENST00000358945PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000395783ENST00000540037PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000395783ENST00000228916PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3UTRENST00000395783ENST00000396966PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3UTRENST00000395783ENST00000543768PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-intronENST00000395783ENST00000538979PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000435340ENST00000360168PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000435340ENST00000358945PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000435340ENST00000540037PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000435340ENST00000228916PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3UTRENST00000435340ENST00000396966PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3UTRENST00000435340ENST00000543768PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-intronENST00000435340ENST00000538979PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000255389ENST00000360168PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000255389ENST00000358945PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000255389ENST00000540037PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000255389ENST00000228916PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3UTRENST00000255389ENST00000396966PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3UTRENST00000255389ENST00000543768PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-intronENST00000255389ENST00000538979PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000395781ENST00000360168PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000395781ENST00000358945PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000395781ENST00000540037PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000395781ENST00000228916PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3UTRENST00000395781ENST00000396966PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3UTRENST00000395781ENST00000543768PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-intronENST00000395781ENST00000538979PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000484838ENST00000360168PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000484838ENST00000358945PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000484838ENST00000540037PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3CDSENST00000484838ENST00000228916PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3UTRENST00000484838ENST00000396966PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-3UTRENST00000484838ENST00000543768PEMTchr17

17427066

+SCNN1Achr12

6457185

+
intron-intronENST00000484838ENST00000538979PEMTchr17

17427066

+SCNN1Achr12

6457185

+

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 PEMT-SCNN1A


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 PEMT-SCNN1A


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
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.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.
- 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 PEMT-SCNN1A


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 PEMT-SCNN1A


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 PEMT-SCNN1A


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 PEMT-SCNN1A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePEMTC0036341Schizophrenia2PSYGENET
HgenePEMTC0023890Liver Cirrhosis1CTD_human
HgenePEMTC0239946Fibrosis, Liver1CTD_human
HgenePEMTC0400966Non-alcoholic Fatty Liver Disease1CTD_human
HgenePEMTC3241937Nonalcoholic Steatohepatitis1CTD_human
TgeneSCNN1AC1449843Pseudohypoaldosteronism, Type I, Autosomal Recessive7CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneSCNN1AC0010674Cystic Fibrosis2CTD_human
TgeneSCNN1AC0020538Hypertensive disease2CTD_human
TgeneSCNN1AC0024115Lung diseases2CTD_human;GENOMICS_ENGLAND
TgeneSCNN1AC0221043Liddle Syndrome2CTD_human;ORPHANET
TgeneSCNN1AC0392164Pulmonary Cystic Fibrosis2CTD_human
TgeneSCNN1AC1527396Fibrocystic Disease of Pancreas2CTD_human
TgeneSCNN1AC2751666BRONCHIECTASIS WITH OR WITHOUT ELEVATED SWEAT CHLORIDE 22CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneSCNN1AC4748292LIDDLE SYNDROME 32GENOMICS_ENGLAND;UNIPROT
TgeneSCNN1AC0027654Embryonal Neoplasm1CTD_human
TgeneSCNN1AC0027658Neoplasms, Germ Cell and Embryonal1CTD_human
TgeneSCNN1AC0032460Polycystic Ovary Syndrome1CTD_human
TgeneSCNN1AC0032914Pre-Eclampsia1CTD_human
TgeneSCNN1AC0033687Proteinuria1CTD_human
TgeneSCNN1AC0033805Pseudohypoaldosteronism1CTD_human
TgeneSCNN1AC0205851Germ cell tumor1CTD_human
TgeneSCNN1AC0205852Neoplasms, Embryonal and Mixed1CTD_human
TgeneSCNN1AC0268436Pseudohypoaldosteronism, Type I1CTD_human
TgeneSCNN1AC0339985Idiopathic bronchiectasis1ORPHANET
TgeneSCNN1AC0740345Germ Cell Cancer1CTD_human
TgeneSCNN1AC0751364Cancer, Embryonal1CTD_human
TgeneSCNN1AC0751365Cancer, Embryonal and Mixed1CTD_human
TgeneSCNN1AC1136382Sclerocystic Ovaries1CTD_human
TgeneSCNN1AC1449842Pseudohypoaldosteronism, Type I, Autosomal Dominant1CTD_human
TgeneSCNN1AC1449844Pseudohypoaldosteronism, Type II1CTD_human
TgeneSCNN1AC2713447Hyperpotassemia and Hypertension, Familial1CTD_human