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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:LETM1-SLBP (FusionGDB2 ID:44248)

Fusion Gene Summary for LETM1-SLBP

check button Fusion gene summary
Fusion gene informationFusion gene name: LETM1-SLBP
Fusion gene ID: 44248
HgeneTgene
Gene symbol

LETM1

SLBP

Gene ID

3954

7884

Gene nameleucine zipper and EF-hand containing transmembrane protein 1stem-loop binding protein
SynonymsSLC55A1HBP
Cytomap

4p16.3

4p16.3

Type of geneprotein-codingprotein-coding
Descriptionmitochondrial proton/calcium exchanger proteinLETM1 and EF-hand domain-containing protein 1, mitochondrialMdm38 homologleucine zipper-EF-hand containing transmembrane protein 1histone RNA hairpin-binding proteinhairpin binding protein, histonehistone binding proteinhistone stem-loop binding proteinstem-loop (histone) binding protein
Modification date2020032820200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000302787, ENST00000512189, 
ENST00000429429, ENST00000489418, 
ENST00000318386, ENST00000488267, 
Fusion gene scores* DoF score10 X 13 X 7=9103 X 3 X 2=18
# samples 124
** MAII scorelog2(12/910*10)=-2.92283213947754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/18*10)=1.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: LETM1 [Title/Abstract] AND SLBP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSLBP(1696501)-LETM1(1827410), # samples:3
SLBP(1713601)-LETM1(1817529), # samples:3
LETM1(1821065)-SLBP(1705427), # samples:2
Anticipated loss of major functional domain due to fusion event.LETM1-SLBP seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
LETM1-SLBP seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
LETM1-SLBP seems lost the major protein functional domain in Tgene partner, which is a essential 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
HgeneLETM1

GO:0006851

mitochondrial calcium ion transmembrane transport

19797662

HgeneLETM1

GO:0051560

mitochondrial calcium ion homeostasis

19797662

HgeneLETM1

GO:0099093

calcium export from the mitochondrion

19797662

TgeneSLBP

GO:0051028

mRNA transport

19155325


check buttonFusion gene breakpoints across LETM1 (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 SLBP (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
ChimerDB4STADTCGA-VQ-A8PE-01ALETM1chr4

1821065

-SLBPchr4

1705427

-
ChimerDB4STADTCGA-VQ-A8PELETM1chr4

1821064

-SLBPchr4

1705427

-
ChimerDB4STADTCGA-VQ-A8PE-01ALETM1chr4

1821065

-SLBPchr4

1705427

-


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Fusion Gene ORF analysis for LETM1-SLBP

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-shiftENST00000302787ENST00000429429LETM1chr4

1821065

-SLBPchr4

1705427

-
Frame-shiftENST00000302787ENST00000489418LETM1chr4

1821065

-SLBPchr4

1705427

-
Frame-shiftENST00000302787ENST00000318386LETM1chr4

1821065

-SLBPchr4

1705427

-
5CDS-intronENST00000302787ENST00000488267LETM1chr4

1821065

-SLBPchr4

1705427

-
intron-3CDSENST00000512189ENST00000429429LETM1chr4

1821065

-SLBPchr4

1705427

-
intron-3CDSENST00000512189ENST00000489418LETM1chr4

1821065

-SLBPchr4

1705427

-
intron-3CDSENST00000512189ENST00000318386LETM1chr4

1821065

-SLBPchr4

1705427

-
intron-intronENST00000512189ENST00000488267LETM1chr4

1821065

-SLBPchr4

1705427

-
Frame-shiftENST00000302787ENST00000429429LETM1chr4

1821064

-SLBPchr4

1705427

-
Frame-shiftENST00000302787ENST00000489418LETM1chr4

1821064

-SLBPchr4

1705427

-
Frame-shiftENST00000302787ENST00000318386LETM1chr4

1821064

-SLBPchr4

1705427

-
5CDS-intronENST00000302787ENST00000488267LETM1chr4

1821064

-SLBPchr4

1705427

-
intron-3CDSENST00000512189ENST00000429429LETM1chr4

1821064

-SLBPchr4

1705427

-
intron-3CDSENST00000512189ENST00000489418LETM1chr4

1821064

-SLBPchr4

1705427

-
intron-3CDSENST00000512189ENST00000318386LETM1chr4

1821064

-SLBPchr4

1705427

-
intron-intronENST00000512189ENST00000488267LETM1chr4

1821064

-SLBPchr4

1705427

-

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 LETM1-SLBP


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 LETM1-SLBP


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 LETM1-SLBP


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 LETM1-SLBP


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 LETM1-SLBP


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 LETM1-SLBP


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLETM1C0020796Profound Mental Retardation1CTD_human
HgeneLETM1C0022333Jacksonian Seizure1CTD_human
HgeneLETM1C0025363Mental Retardation, Psychosocial1CTD_human
HgeneLETM1C0026825Flaccid Muscle Tone1CTD_human
HgeneLETM1C0026827Muscle hypotonia1CTD_human
HgeneLETM1C0036572Seizures1CTD_human
HgeneLETM1C0149958Complex partial seizures1CTD_human
HgeneLETM1C0234533Generalized seizures1CTD_human
HgeneLETM1C0234535Clonic Seizures1CTD_human
HgeneLETM1C0270824Visual seizure1CTD_human
HgeneLETM1C0270844Tonic Seizures1CTD_human
HgeneLETM1C0270846Epileptic drop attack1CTD_human
HgeneLETM1C0376634Craniofacial Abnormalities1CTD_human
HgeneLETM1C0422850Seizures, Somatosensory1CTD_human
HgeneLETM1C0422852Seizures, Auditory1CTD_human
HgeneLETM1C0422853Olfactory seizure1CTD_human
HgeneLETM1C0422854Gustatory seizure1CTD_human
HgeneLETM1C0422855Vertiginous seizure1CTD_human
HgeneLETM1C0427201Floppy Muscles1CTD_human
HgeneLETM1C0427202Muscle Tone Atonic1CTD_human
HgeneLETM1C0494475Tonic - clonic seizures1CTD_human
HgeneLETM1C0751056Non-epileptic convulsion1CTD_human
HgeneLETM1C0751110Single Seizure1CTD_human
HgeneLETM1C0751123Atonic Absence Seizures1CTD_human
HgeneLETM1C0751330Unilateral Hypotonia1CTD_human
HgeneLETM1C0751494Convulsive Seizures1CTD_human
HgeneLETM1C0751495Seizures, Focal1CTD_human
HgeneLETM1C0751496Seizures, Sensory1CTD_human
HgeneLETM1C0796117Pitt-Rogers-Danks Syndrome1CTD_human
HgeneLETM1C0917816Mental deficiency1CTD_human
HgeneLETM1C1956097Wolf-Hirschhorn Syndrome1CTD_human;ORPHANET
HgeneLETM1C2239176Liver carcinoma1CTD_human
HgeneLETM1C2267233Neonatal Hypotonia1CTD_human
HgeneLETM1C3495874Nonepileptic Seizures1CTD_human
HgeneLETM1C3714756Intellectual Disability1CTD_human
HgeneLETM1C4048158Convulsions1CTD_human
HgeneLETM1C4316903Absence Seizures1CTD_human
HgeneLETM1C4317109Epileptic Seizures1CTD_human
HgeneLETM1C4317123Myoclonic Seizures1CTD_human
HgeneLETM1C4505436Generalized Absence Seizures1CTD_human
TgeneSLBPC0009363Congenital ocular coloboma (disorder)1CTD_human
TgeneSLBPC0029124Optic Atrophy1CTD_human
TgeneSLBPC0035313Retinal Dysplasia1CTD_human
TgeneSLBPC4554007Uveoretinal Coloboma1CTD_human