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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:LMF1-CCDC154

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: LMF1-CCDC154
FusionPDB ID: 45772
FusionGDB2.0 ID: 45772
HgeneTgene
Gene symbol

LMF1

CCDC154

Gene ID

64788

645811

Gene namelipase maturation factor 1coiled-coil domain containing 154
SynonymsC16orf26|HMFN1876|JFP11|TMEM112|TMEM112AC16orf29
Cytomap

16p13.3

16p13.3

Type of geneprotein-codingprotein-coding
Descriptionlipase maturation factor 1transmembrane protein 112coiled-coil domain-containing protein 154
Modification date2020031320200313
UniProtAcc

Q96S06

.
Ensembl transtripts involved in fusion geneENST idsENST00000539379, ENST00000262301, 
ENST00000399843, ENST00000568897, 
ENST00000543238, ENST00000568268, 
ENST00000389176, ENST00000409671, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score1 X 1 X 1=11 X 1 X 1=1
# samples 11
** MAII scorelog2(1/1*10)=3.32192809488736log2(1/1*10)=3.32192809488736
Context (manual curation of fusion genes in FusionPDB)

PubMed: LMF1 [Title/Abstract] AND CCDC154 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)LMF1(960931)-CCDC154(1489127), # 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

check buttonFusion gene breakpoints across LMF1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across CCDC154 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4LGGTCGA-DU-A6S2-01ALMF1chr16

960931

-CCDC154chr16

1489127

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000262301LMF1chr16960931-ENST00000409671CCDC154chr161489127-2034682192010663
ENST00000262301LMF1chr16960931-ENST00000389176CCDC154chr161489127-2052682192031670
ENST00000399843LMF1chr16960931-ENST00000409671CCDC154chr161489127-201766521993663
ENST00000399843LMF1chr16960931-ENST00000389176CCDC154chr161489127-203566522014670
ENST00000568897LMF1chr16960931-ENST00000409671CCDC154chr161489127-18945423861870494
ENST00000568897LMF1chr16960931-ENST00000389176CCDC154chr161489127-19125423861891501

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
ENST00000262301ENST00000409671LMF1chr16960931-CCDC154chr161489127-0.0430095640.9569905
ENST00000262301ENST00000389176LMF1chr16960931-CCDC154chr161489127-0.044374990.955625
ENST00000399843ENST00000409671LMF1chr16960931-CCDC154chr161489127-0.04271620.9572838
ENST00000399843ENST00000389176LMF1chr16960931-CCDC154chr161489127-0.043996010.95600396
ENST00000568897ENST00000409671LMF1chr16960931-CCDC154chr161489127-0.0169467550.98305327
ENST00000568897ENST00000389176LMF1chr16960931-CCDC154chr161489127-0.0175079670.98249197

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>45772_45772_1_LMF1-CCDC154_LMF1_chr16_960931_ENST00000262301_CCDC154_chr16_1489127_ENST00000389176_length(amino acids)=670AA_BP=221
MRPDSPTMAAPAESLRRRKTGYSDPEPESPPAPGRGPAGSPAHLHTGTFWLTRIVLLKALAFVYFVAFLVAFHQNKQLIGDRGLLPCRVF
LKNFQQYFQDRTSWEVFSYMPTILWLMDWSDMNSNLDLLALLGLGISSFVLITGCANMLLMAALWGLYMSLVNVGHVWYSFGWESQLLET
GFLGIFLCPLWTLSRLPQHTPTSRIVLWGFRWLIFRIMLGAAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKASESSRLKLEGS
LRGELESRWEKLRGLMEERLRALQGQHEVGPGGRRAEESHLLEQCQGLDAAVAQLTKFVQQNQASLNRVLLAEEKAWDAKGRLEESRAGE
LAAYVQENLEAAQLAGELARQEMHGELVLLREKSRALEASVAQLAGQLKELSGHLPALSSRLDLQEQMLGLRLSEAKTEWEGAERKSLED
LARWRKEVTEHLRGVREKVDGLPQQIESVSDKCLLHKSDSDLRISAEGKAREFKVGALRQELATLLSSVQLLKEDNPGRKIAEMQGKLAT
NQIMKLENCVQANKTIQNLRFNTEARLRTQEMATLWESVLRLWSEEGPRTPLGSWKALPSLVRPRVFIKDMAPGKVVPMNCWGVYQAVRW

--------------------------------------------------------------

>45772_45772_2_LMF1-CCDC154_LMF1_chr16_960931_ENST00000262301_CCDC154_chr16_1489127_ENST00000409671_length(amino acids)=663AA_BP=221
MRPDSPTMAAPAESLRRRKTGYSDPEPESPPAPGRGPAGSPAHLHTGTFWLTRIVLLKALAFVYFVAFLVAFHQNKQLIGDRGLLPCRVF
LKNFQQYFQDRTSWEVFSYMPTILWLMDWSDMNSNLDLLALLGLGISSFVLITGCANMLLMAALWGLYMSLVNVGHVWYSFGWESQLLET
GFLGIFLCPLWTLSRLPQHTPTSRIVLWGFRWLIFRIMLGAAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKASESSRLKLEGS
LRGELESRWEKLRGLMEERLRALQGQHEESHLLEQCQGLDAAVAQLTKFVQQNQASLNRVLLAEEKAWDAKGRLEESRAGELAAYVQENL
EAAQLAGELARQEMHGELVLLREKSRALEASVAQLAGQLKELSGHLPALSSRLDLQEQMLGLRLSEAKTEWEGAERKSLEDLARWRKEVT
EHLRGVREKVDGLPQQIESVSDKCLLHKSDSDLRISAEGKAREFKVGALRQELATLLSSVQLLKEDNPGRKIAEMQGKLATFQNQIMKLE
NCVQANKTIQNLRFNTEARLRTQEMATLWESVLRLWSEEGPRTPLGSWKALPSLVRPRVFIKDMAPGKVVPMNCWGVYQAVRWLRWKASL

--------------------------------------------------------------

>45772_45772_3_LMF1-CCDC154_LMF1_chr16_960931_ENST00000399843_CCDC154_chr16_1489127_ENST00000389176_length(amino acids)=670AA_BP=221
MRPDSPTMAAPAESLRRRKTGYSDPEPESPPAPGRGPAGSPAHLHTGTFWLTRIVLLKALAFVYFVAFLVAFHQNKQLIGDRGLLPCRVF
LKNFQQYFQDRTSWEVFSYMPTILWLMDWSDMNSNLDLLALLGLGISSFVLITGCANMLLMAALWGLYMSLVNVGHVWYSFRWESQLLET
GFLGIFLCPLWTLSRLPQHTPTSRIVLWGFRWLIFRIMLGAAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKASESSRLKLEGS
LRGELESRWEKLRGLMEERLRALQGQHEVGPGGRRAEESHLLEQCQGLDAAVAQLTKFVQQNQASLNRVLLAEEKAWDAKGRLEESRAGE
LAAYVQENLEAAQLAGELARQEMHGELVLLREKSRALEASVAQLAGQLKELSGHLPALSSRLDLQEQMLGLRLSEAKTEWEGAERKSLED
LARWRKEVTEHLRGVREKVDGLPQQIESVSDKCLLHKSDSDLRISAEGKAREFKVGALRQELATLLSSVQLLKEDNPGRKIAEMQGKLAT
NQIMKLENCVQANKTIQNLRFNTEARLRTQEMATLWESVLRLWSEEGPRTPLGSWKALPSLVRPRVFIKDMAPGKVVPMNCWGVYQAVRW

--------------------------------------------------------------

>45772_45772_4_LMF1-CCDC154_LMF1_chr16_960931_ENST00000399843_CCDC154_chr16_1489127_ENST00000409671_length(amino acids)=663AA_BP=221
MRPDSPTMAAPAESLRRRKTGYSDPEPESPPAPGRGPAGSPAHLHTGTFWLTRIVLLKALAFVYFVAFLVAFHQNKQLIGDRGLLPCRVF
LKNFQQYFQDRTSWEVFSYMPTILWLMDWSDMNSNLDLLALLGLGISSFVLITGCANMLLMAALWGLYMSLVNVGHVWYSFRWESQLLET
GFLGIFLCPLWTLSRLPQHTPTSRIVLWGFRWLIFRIMLGAAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKASESSRLKLEGS
LRGELESRWEKLRGLMEERLRALQGQHEESHLLEQCQGLDAAVAQLTKFVQQNQASLNRVLLAEEKAWDAKGRLEESRAGELAAYVQENL
EAAQLAGELARQEMHGELVLLREKSRALEASVAQLAGQLKELSGHLPALSSRLDLQEQMLGLRLSEAKTEWEGAERKSLEDLARWRKEVT
EHLRGVREKVDGLPQQIESVSDKCLLHKSDSDLRISAEGKAREFKVGALRQELATLLSSVQLLKEDNPGRKIAEMQGKLATFQNQIMKLE
NCVQANKTIQNLRFNTEARLRTQEMATLWESVLRLWSEEGPRTPLGSWKALPSLVRPRVFIKDMAPGKVVPMNCWGVYQAVRWLRWKASL

--------------------------------------------------------------

>45772_45772_5_LMF1-CCDC154_LMF1_chr16_960931_ENST00000568897_CCDC154_chr16_1489127_ENST00000389176_length(amino acids)=501AA_BP=52
MVRWESQLLETGFLGIFLCPLWTLSRLPQHTPTSRIVLWGFRWLIFRIMLGAAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKA
SESSRLKLEGSLRGELESRWEKLRGLMEERLRALQGQHEVGPGGRRAEESHLLEQCQGLDAAVAQLTKFVQQNQASLNRVLLAEEKAWDA
KGRLEESRAGELAAYVQENLEAAQLAGELARQEMHGELVLLREKSRALEASVAQLAGQLKELSGHLPALSSRLDLQEQMLGLRLSEAKTE
WEGAERKSLEDLARWRKEVTEHLRGVREKVDGLPQQIESVSDKCLLHKSDSDLRISAEGKAREFKVGALRQELATLLSSVQLLKEDNPGR
KIAEMQGKLATNQIMKLENCVQANKTIQNLRFNTEARLRTQEMATLWESVLRLWSEEGPRTPLGSWKALPSLVRPRVFIKDMAPGKVVPM

--------------------------------------------------------------

>45772_45772_6_LMF1-CCDC154_LMF1_chr16_960931_ENST00000568897_CCDC154_chr16_1489127_ENST00000409671_length(amino acids)=494AA_BP=52
MVRWESQLLETGFLGIFLCPLWTLSRLPQHTPTSRIVLWGFRWLIFRIMLGAAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKA
SESSRLKLEGSLRGELESRWEKLRGLMEERLRALQGQHEESHLLEQCQGLDAAVAQLTKFVQQNQASLNRVLLAEEKAWDAKGRLEESRA
GELAAYVQENLEAAQLAGELARQEMHGELVLLREKSRALEASVAQLAGQLKELSGHLPALSSRLDLQEQMLGLRLSEAKTEWEGAERKSL
EDLARWRKEVTEHLRGVREKVDGLPQQIESVSDKCLLHKSDSDLRISAEGKAREFKVGALRQELATLLSSVQLLKEDNPGRKIAEMQGKL
ATFQNQIMKLENCVQANKTIQNLRFNTEARLRTQEMATLWESVLRLWSEEGPRTPLGSWKALPSLVRPRVFIKDMAPGKVVPMNCWGVYQ

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Fusion Protein Functional Features


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/chr16:960931/chr16:1489127)
- 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
LMF1

Q96S06

.
FUNCTION: Involved in the maturation of specific proteins in the endoplasmic reticulum. Required for maturation and transport of active lipoprotein lipase (LPL) through the secretory pathway. Each LMF1 molecule chaperones 50 or more molecules of LPL. {ECO:0000250|UniProtKB:Q3U3R4, ECO:0000269|PubMed:24909692}.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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneLMF1chr16:960931chr16:1489127ENST00000262301-411152_207221.0568.0Topological domainCytoplasmic
HgeneLMF1chr16:960931chr16:1489127ENST00000262301-4111_49221.0568.0Topological domainCytoplasmic
HgeneLMF1chr16:960931chr16:1489127ENST00000262301-41173_127221.0568.0Topological domainLumenal
HgeneLMF1chr16:960931chr16:1489127ENST00000262301-411128_151221.0568.0TransmembraneHelical
HgeneLMF1chr16:960931chr16:1489127ENST00000262301-411208_221221.0568.0TransmembraneHelical
HgeneLMF1chr16:960931chr16:1489127ENST00000262301-41150_72221.0568.0TransmembraneHelical
TgeneCCDC154chr16:960931chr16:1489127ENST00000389176517384_410225.0675.0Coiled coilOntology_term=ECO:0000255
TgeneCCDC154chr16:960931chr16:1489127ENST00000389176517457_521225.0675.0Coiled coilOntology_term=ECO:0000255

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneLMF1chr16:960931chr16:1489127ENST00000262301-411222_292221.0568.0Topological domainLumenal
HgeneLMF1chr16:960931chr16:1489127ENST00000262301-411322_367221.0568.0Topological domainCytoplasmic
HgeneLMF1chr16:960931chr16:1489127ENST00000262301-411389_567221.0568.0Topological domainLumenal
HgeneLMF1chr16:960931chr16:1489127ENST00000262301-411293_321221.0568.0TransmembraneHelical
HgeneLMF1chr16:960931chr16:1489127ENST00000262301-411368_388221.0568.0TransmembraneHelical
TgeneCCDC154chr16:960931chr16:1489127ENST00000389176517215_302225.0675.0Coiled coilOntology_term=ECO:0000255
TgeneCCDC154chr16:960931chr16:1489127ENST0000038917651776_182225.0675.0Coiled coilOntology_term=ECO:0000255


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
LMF1
CCDC154


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to LMF1-CCDC154


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to LMF1-CCDC154


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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