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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 19633

FusionGeneSummary for LETM1_NELFA

check button Fusion gene summary
Fusion gene informationFusion gene name: LETM1_NELFA
Fusion gene ID: 19633
HgeneTgene
Gene symbol

LETM1

NELFA

Gene ID

3954

7469

Gene nameleucine zipper and EF-hand containing transmembrane protein 1negative elongation factor complex member A
SynonymsSLC55A1NELF-A|P/OKcl.15|WHSC2
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 1negative elongation factor Awolf-Hirschhorn syndrome candidate 2 protein
Modification date2018052320180522
UniProtAcc

O95202

Q9H3P2

Ensembl transtripts involved in fusion geneENST00000302787, ENST00000512189, 
ENST00000382882, ENST00000411638, 
ENST00000542778, 
Fusion gene scores* DoF score5 X 5 X 4=1001 X 1 X 1=1
# samples 61
** MAII scorelog2(6/100*10)=-0.736965594166206
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

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

Functional or gene categories assigned by FusionGDB annotation
* 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


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGALDUCECTCGA-PG-A914-01ALETM1chr4

1823908

-NELFAchr4

2025263

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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-intronENST00000302787ENST00000382882LETM1chr4

1823908

-NELFAchr4

2025263

-
5CDS-intronENST00000302787ENST00000411638LETM1chr4

1823908

-NELFAchr4

2025263

-
5CDS-intronENST00000302787ENST00000542778LETM1chr4

1823908

-NELFAchr4

2025263

-
intron-intronENST00000512189ENST00000382882LETM1chr4

1823908

-NELFAchr4

2025263

-
intron-intronENST00000512189ENST00000411638LETM1chr4

1823908

-NELFAchr4

2025263

-
intron-intronENST00000512189ENST00000542778LETM1chr4

1823908

-NELFAchr4

2025263

-

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FusionProtFeatures for LETM1_NELFA


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LETM1

O95202

NELFA

Q9H3P2

Mitochondrial proton/calcium antiporter that mediatesproton-dependent calcium efflux from mitochondrion(PubMed:19797662). Crucial for the maintenance of mitochondrialtubular networks and for the assembly of the supercomplexes of therespiratory chain (PubMed:18628306). Required for the maintenanceof the tubular shape and cristae organization (PubMed:18628306).In contrast to SLC8B1/NCLX, does not constitute the major factorfor mitochondrial calcium extrusion (PubMed:24898248).{ECO:0000269|PubMed:18628306, ECO:0000269|PubMed:19797662,ECO:0000269|PubMed:24898248}. Essential component of the NELF complex, a complex thatnegatively regulates the elongation of transcription by RNApolymerase II. The NELF complex, which acts via an associationwith the DSIF complex and causes transcriptional pausing, iscounteracted by the P-TEFb kinase complex. The NELF complex isinvolved in HIV-1 latency possibly involving recruitment of PCF11to paused RNA polymerase II. In vitro, the NELFA:NELFCD subcomplexbinds to ssDNA and ssRNA in a sequence- and structure-dependentmanner. Probably required to interact with the RNA polymerase IIcomplex. {ECO:0000269|PubMed:10199401,ECO:0000269|PubMed:12563561, ECO:0000269|PubMed:12612062,ECO:0000305}.

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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FusionGeneSequence for LETM1_NELFA


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for LETM1_NELFA


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
LETM1ICT1, TBK1, ILF3, C12orf57, SYNCRIP, LATS2, PSMA3, CYP1A1, NTRK1, NDUFA4, COQ9, PTPMT1, C15orf48, PPM1A, USP47, SNRNP27, PCDHGB4, HSD3B2, FGB, MRPS11, LYPD4, RNF19B, ATP6V0D1NELFANELFE, NELFB, NELFCD, POLR2A, TCEA2, ATP1A1, APP, POLR2C, YWHAB, HECW2, SIAH1, PRR22, NXF1, NTRK1, POLR2B, SUPT5H, NCBP1, ATL2, INTS12, WIBG, FEZ1, PROSER2, MCM9, IGHMBP2, TMOD4


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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RelatedDrugs for LETM1_NELFA


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for LETM1_NELFA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLETM1C0026827Muscle hypotonia1CTD_human;HPO
HgeneLETM1C0036572Seizures1CTD_human;HPO
HgeneLETM1C0376634Craniofacial Abnormalities1CTD_human
HgeneLETM1C1956097Wolf-Hirschhorn Syndrome1CTD_human;ORPHANET
HgeneLETM1C2239176Liver carcinoma1CTD_human
HgeneLETM1C3714756Intellectual Disability1CTD_human