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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:LMBR1L-KCNK6

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: LMBR1L-KCNK6
FusionPDB ID: 45737
FusionGDB2.0 ID: 45737
HgeneTgene
Gene symbol

LMBR1L

KCNK6

Gene ID

55716

9424

Gene namelimb development membrane protein 1 likepotassium two pore domain channel subfamily K member 6
SynonymsLIMRK2p6.1|KCNK8|TOSS|TWIK-2|TWIK2
Cytomap

12q13.12

19q13.2

Type of geneprotein-codingprotein-coding
Descriptionprotein LMBR1Llimb region 1 homolog-likelimb region 1 protein homolog-likelimb region 1-like protein -likelipocalin-1 interacting membrane receptorlipocalin-interacting membrane receptorpotassium channel subfamily K member 6K2P6.1 potassium channelTWIK-originated similarity sequenceTWIK-originated sodium similarity sequenceinward rectifying potassium channel protein TWIK-2potassium channel, two pore domain subfamily K, member 6
Modification date2020031320200313
UniProtAcc

Q6UX01

Q9Y257

Ensembl transtripts involved in fusion geneENST idsENST00000267102, ENST00000395141, 
ENST00000547382, ENST00000553204, 
ENST00000588137, ENST00000263372, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score6 X 6 X 4=1443 X 3 X 2=18
# samples 53
** MAII scorelog2(5/144*10)=-1.52606881166759
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: LMBR1L [Title/Abstract] AND KCNK6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)LMBR1L(49504267)-KCNK6(38817233), # samples:3
Anticipated loss of major functional domain due to fusion event.LMBR1L-KCNK6 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
LMBR1L-KCNK6 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
LMBR1L-KCNK6 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
HgeneLMBR1L

GO:0007165

signal transduction

11287427


check buttonFusion gene breakpoints across LMBR1L (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 KCNK6 (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
ChimerDB4BLCATCGA-CU-A0YN-01ALMBR1Lchr12

49499707

-KCNK6chr19

38817233

+
ChimerDB4BLCATCGA-CU-A0YN-01ALMBR1Lchr12

49500744

-KCNK6chr19

38817233

+
ChimerDB4BLCATCGA-CU-A0YN-01ALMBR1Lchr12

49504267

-KCNK6chr19

38817233

+


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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)
ENST00000267102LMBR1Lchr1249500744-ENST00000263372KCNK6chr1938817233+27375001901119309
ENST00000547382LMBR1Lchr1249500744-ENST00000263372KCNK6chr1938817233+26894521421071309

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
ENST00000267102ENST00000263372LMBR1Lchr1249500744-KCNK6chr1938817233+0.039950880.96004915
ENST00000547382ENST00000263372LMBR1Lchr1249500744-KCNK6chr1938817233+0.0441080630.95589197

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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

>45737_45737_1_LMBR1L-KCNK6_LMBR1L_chr12_49500744_ENST00000267102_KCNK6_chr19_38817233_ENST00000263372_length(amino acids)=309AA_BP=103
MYLSPRLPRVSVAGCEERPLGWVWVLGGGGFLPARPPRAQRHLGFSHAEQSMEAPDYEVLSVREQLFHERIRECIISTLLFATLYILCHI
FLTRFKKPAEFTTGYGYTTPLTDAGKAFSIAFALLGVPTTMLLLTASAQRLSLLLTHVPLSWLSMRWGWDPRRAACWHLVALLGVVVTVC
FLVPAVIFAHLEEAWSFLDAFYFCFISLSTIGLGDYVPGEAPGQPYRALYKVLVTVYLFLGLVAMVLVLQTFRHVSDLHGLTELILLPPP

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

>45737_45737_2_LMBR1L-KCNK6_LMBR1L_chr12_49500744_ENST00000547382_KCNK6_chr19_38817233_ENST00000263372_length(amino acids)=309AA_BP=103
MYLSPRLPRVSVAGCEERPLGWVWVLGGGGFLPARPPRAQRHLGFSHAEQSMEAPDYEVLSVREQLFHERIRECIISTLLFATLYILCHI
FLTRFKKPAEFTTGYGYTTPLTDAGKAFSIAFALLGVPTTMLLLTASAQRLSLLLTHVPLSWLSMRWGWDPRRAACWHLVALLGVVVTVC
FLVPAVIFAHLEEAWSFLDAFYFCFISLSTIGLGDYVPGEAPGQPYRALYKVLVTVYLFLGLVAMVLVLQTFRHVSDLHGLTELILLPPP

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

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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/chr12:49504267/chr19:38817233)
- 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
LMBR1L

Q6UX01

KCNK6

Q9Y257

FUNCTION: Plays an essential role in lymphocyte development by negatively regulating the canonical Wnt signaling pathway (By similarity). In association with UBAC2 and E3 ubiquitin-protein ligase AMFR, promotes the ubiquitin-mediated degradation of CTNNB1 and Wnt receptors FZD6 and LRP6 (By similarity). LMBR1L stabilizes the beta-catenin destruction complex that is required for regulating CTNNB1 levels (By similarity). Acts as a LCN1 receptor and can mediate its endocytosis (PubMed:11287427, PubMed:12591932, PubMed:23964685). {ECO:0000250|UniProtKB:Q9D1E5, ECO:0000269|PubMed:11287427, ECO:0000269|PubMed:12591932, ECO:0000269|PubMed:23964685}.FUNCTION: Exhibits outward rectification in a physiological K(+) gradient and mild inward rectification in symmetrical K(+) conditions.

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
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-2171_2152.333333333333336490.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-2171_2152.333333333333336470.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-21722_4252.333333333333336490.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-21722_4252.333333333333336470.0TransmembraneHelical
TgeneKCNK6chr12:49500744chr19:38817233ENST0000026337203199_223107.33333333333333314.0IntramembranePore-forming%3B Name%3DPore-forming 2
TgeneKCNK6chr12:49500744chr19:38817233ENST0000026337203142_172107.33333333333333314.0Topological domainCytoplasmic
TgeneKCNK6chr12:49500744chr19:38817233ENST0000026337203257_313107.33333333333333314.0Topological domainCytoplasmic
TgeneKCNK6chr12:49500744chr19:38817233ENST0000026337203121_141107.33333333333333314.0TransmembraneHelical
TgeneKCNK6chr12:49500744chr19:38817233ENST0000026337203173_193107.33333333333333314.0TransmembraneHelical
TgeneKCNK6chr12:49500744chr19:38817233ENST0000026337203236_256107.33333333333333314.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-2171_7652.333333333333336490.0RegionLCN1-binding
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-1161_760.0485.0RegionLCN1-binding
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-2171_7652.333333333333336470.0RegionLCN1-binding
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217136_15452.333333333333336490.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217176_19652.333333333333336490.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217218_30552.333333333333336490.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217327_35052.333333333333336490.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217372_38852.333333333333336490.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217410_43152.333333333333336490.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-21743_6652.333333333333336490.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217453_48952.333333333333336490.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-21788_11452.333333333333336490.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116136_1540.0485.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116176_1960.0485.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-1161_210.0485.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116218_3050.0485.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116327_3500.0485.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116372_3880.0485.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116410_4310.0485.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-11643_660.0485.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116453_4890.0485.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-11688_1140.0485.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217136_15452.333333333333336470.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217176_19652.333333333333336470.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217218_30552.333333333333336470.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217327_35052.333333333333336470.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217372_38852.333333333333336470.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217410_43152.333333333333336470.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-21743_6652.333333333333336470.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217453_48952.333333333333336470.0Topological domainCytoplasmic
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-21788_11452.333333333333336470.0Topological domainExtracellular
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217115_13552.333333333333336490.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217155_17552.333333333333336490.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217197_21752.333333333333336490.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217306_32652.333333333333336490.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217351_37152.333333333333336490.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217389_40952.333333333333336490.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-217432_45252.333333333333336490.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-21767_8752.333333333333336490.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116115_1350.0485.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116155_1750.0485.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116197_2170.0485.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-11622_420.0485.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116306_3260.0485.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116351_3710.0485.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116389_4090.0485.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-116432_4520.0485.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-11667_870.0485.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217115_13552.333333333333336470.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217155_17552.333333333333336470.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217197_21752.333333333333336470.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217306_32652.333333333333336470.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217351_37152.333333333333336470.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217389_40952.333333333333336470.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-217432_45252.333333333333336470.0TransmembraneHelical
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-21767_8752.333333333333336470.0TransmembraneHelical
TgeneKCNK6chr12:49500744chr19:38817233ENST000002633720390_115107.33333333333333314.0IntramembranePore-forming%3B Name%3DPore-forming 1
TgeneKCNK6chr12:49500744chr19:38817233ENST00000263372031_4107.33333333333333314.0Topological domainCytoplasmic
TgeneKCNK6chr12:49500744chr19:38817233ENST00000263372035_25107.33333333333333314.0TransmembraneHelical


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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
LMBR1L
KCNK6


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
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000267102-2171_5952.333333333333336490.0LGB
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000395141-1161_590.0485.0LGB
HgeneLMBR1Lchr12:49500744chr19:38817233ENST00000547382-2171_5952.333333333333336470.0LGB


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Related Drugs to LMBR1L-KCNK6


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 LMBR1L-KCNK6


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