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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:LRRC23-CAMKK2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: LRRC23-CAMKK2
FusionPDB ID: 49888
FusionGDB2.0 ID: 49888
HgeneTgene
Gene symbol

LRRC23

CAMKK2

Gene ID

10233

10645

Gene nameleucine rich repeat containing 23calcium/calmodulin dependent protein kinase kinase 2
SynonymsLRPB7CAMKK|CAMKKB
Cytomap

12p13.31

12q24.31

Type of geneprotein-codingprotein-coding
Descriptionleucine-rich repeat-containing protein 23leucine-rich protein B7calcium/calmodulin-dependent protein kinase kinase 2CAMKK beta proteincaM-KK 2caM-KK betacaM-kinase kinase 2caM-kinase kinase betacalcium/calmodulin-dependent protein kinase betacalcium/calmodulin-dependent protein kinase kinase 2, beta
Modification date2020031320200313
UniProtAcc

Q53EV4

Main function of 5'-partner protein:

Q96RR4

Main function of 5'-partner protein: FUNCTION: Calcium/calmodulin-dependent protein kinase belonging to a proposed calcium-triggered signaling cascade involved in a number of cellular processes. Isoform 1, isoform 2 and isoform 3 phosphorylate CAMK1 and CAMK4. Isoform 3 phosphorylates CAMK1D. Isoform 4, isoform 5 and isoform 6 lacking part of the calmodulin-binding domain are inactive. Efficiently phosphorylates 5'-AMP-activated protein kinase (AMPK) trimer, including that consisting of PRKAA1, PRKAB1 and PRKAG1. This phosphorylation is stimulated in response to Ca(2+) signals (By similarity). Seems to be involved in hippocampal activation of CREB1 (By similarity). May play a role in neurite growth. Isoform 3 may promote neurite elongation, while isoform 1 may promoter neurite branching. {ECO:0000250, ECO:0000269|PubMed:11395482, ECO:0000269|PubMed:12935886, ECO:0000269|PubMed:21957496, ECO:0000269|PubMed:9662074}.
Ensembl transtripts involved in fusion geneENST idsENST00000007969, ENST00000323702, 
ENST00000429740, ENST00000433346, 
ENST00000436789, ENST00000443597, 
ENST00000449039, 		ENST00000535524, 
ENST00000324774, ENST00000337174, 
ENST00000347034, ENST00000392473, 
ENST00000392474, ENST00000402834, 
ENST00000404169, ENST00000412367, 
ENST00000446440, ENST00000538733, 
ENST00000545538, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score6 X 5 X 4=1204 X 4 X 3=48
# samples 64
** MAII scorelog2(6/120*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: LRRC23 [Title/Abstract] AND CAMKK2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: LRRC23 [Title/Abstract] AND CAMKK2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)LRRC23(7015826)-CAMKK2(121691277), # samples:1
Anticipated loss of major functional domain due to fusion event.LRRC23-CAMKK2 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.
LRRC23-CAMKK2 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.
LRRC23-CAMKK2 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.
LRRC23-CAMKK2 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.
* 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
TgeneCAMKK2

GO:0006468

protein phosphorylation

11395482

TgeneCAMKK2

GO:0046777

protein autophosphorylation

11395482



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/chr12:7015826/chr12:121691277)
- 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 buttonRetention analysis results 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, are available here.

check buttonFusion gene breakpoints across LRRC23 (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 CAMKK2 (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 Amino Acid Sequences


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)
ENST00000433346LRRC23chr127015826+ENST00000392474CAMKK2chr12121691277-45069684781731417
ENST00000433346LRRC23chr127015826+ENST00000538733CAMKK2chr12121691277-46589684781557359
ENST00000433346LRRC23chr127015826+ENST00000337174CAMKK2chr12121691277-47879684781686402
ENST00000433346LRRC23chr127015826+ENST00000347034CAMKK2chr12121691277-47019684781698406
ENST00000433346LRRC23chr127015826+ENST00000324774CAMKK2chr12121691277-48309684781827449
ENST00000433346LRRC23chr127015826+ENST00000545538CAMKK2chr12121691277-44309684781731417
ENST00000433346LRRC23chr127015826+ENST00000412367CAMKK2chr12121691277-19599684781686402
ENST00000433346LRRC23chr127015826+ENST00000404169CAMKK2chr12121691277-20029684781827449
ENST00000433346LRRC23chr127015826+ENST00000402834CAMKK2chr12121691277-19809684781827449
ENST00000433346LRRC23chr127015826+ENST00000446440CAMKK2chr12121691277-20709684781533351
ENST00000433346LRRC23chr127015826+ENST00000392473CAMKK2chr12121691277-21999684781662394
ENST00000007969LRRC23chr127015826+ENST00000392474CAMKK2chr12121691277-42487102201473417
ENST00000007969LRRC23chr127015826+ENST00000538733CAMKK2chr12121691277-44007102201299359
ENST00000007969LRRC23chr127015826+ENST00000337174CAMKK2chr12121691277-45297102201428402
ENST00000007969LRRC23chr127015826+ENST00000347034CAMKK2chr12121691277-44437102201440406
ENST00000007969LRRC23chr127015826+ENST00000324774CAMKK2chr12121691277-45727102201569449
ENST00000007969LRRC23chr127015826+ENST00000545538CAMKK2chr12121691277-41727102201473417
ENST00000007969LRRC23chr127015826+ENST00000412367CAMKK2chr12121691277-17017102201428402
ENST00000007969LRRC23chr127015826+ENST00000404169CAMKK2chr12121691277-17447102201569449
ENST00000007969LRRC23chr127015826+ENST00000402834CAMKK2chr12121691277-17227102201569449
ENST00000007969LRRC23chr127015826+ENST00000446440CAMKK2chr12121691277-18127102201275351
ENST00000007969LRRC23chr127015826+ENST00000392473CAMKK2chr12121691277-19417102201404394
ENST00000323702LRRC23chr127015826+ENST00000392474CAMKK2chr12121691277-41406021121365417
ENST00000323702LRRC23chr127015826+ENST00000538733CAMKK2chr12121691277-42926021121191359
ENST00000323702LRRC23chr127015826+ENST00000337174CAMKK2chr12121691277-44216021121320402
ENST00000323702LRRC23chr127015826+ENST00000347034CAMKK2chr12121691277-43356021121332406
ENST00000323702LRRC23chr127015826+ENST00000324774CAMKK2chr12121691277-44646021121461449
ENST00000323702LRRC23chr127015826+ENST00000545538CAMKK2chr12121691277-40646021121365417
ENST00000323702LRRC23chr127015826+ENST00000412367CAMKK2chr12121691277-15936021121320402
ENST00000323702LRRC23chr127015826+ENST00000404169CAMKK2chr12121691277-16366021121461449
ENST00000323702LRRC23chr127015826+ENST00000402834CAMKK2chr12121691277-16146021121461449
ENST00000323702LRRC23chr127015826+ENST00000446440CAMKK2chr12121691277-17046021121167351
ENST00000323702LRRC23chr127015826+ENST00000392473CAMKK2chr12121691277-18336021121296394
ENST00000443597LRRC23chr127015826+ENST00000392474CAMKK2chr12121691277-42477092191472417
ENST00000443597LRRC23chr127015826+ENST00000538733CAMKK2chr12121691277-43997092191298359
ENST00000443597LRRC23chr127015826+ENST00000337174CAMKK2chr12121691277-45287092191427402
ENST00000443597LRRC23chr127015826+ENST00000347034CAMKK2chr12121691277-44427092191439406
ENST00000443597LRRC23chr127015826+ENST00000324774CAMKK2chr12121691277-45717092191568449
ENST00000443597LRRC23chr127015826+ENST00000545538CAMKK2chr12121691277-41717092191472417
ENST00000443597LRRC23chr127015826+ENST00000412367CAMKK2chr12121691277-17007092191427402
ENST00000443597LRRC23chr127015826+ENST00000404169CAMKK2chr12121691277-17437092191568449
ENST00000443597LRRC23chr127015826+ENST00000402834CAMKK2chr12121691277-17217092191568449
ENST00000443597LRRC23chr127015826+ENST00000446440CAMKK2chr12121691277-18117092191274351
ENST00000443597LRRC23chr127015826+ENST00000392473CAMKK2chr12121691277-19407092191403394
ENST00000436789LRRC23chr127015826+ENST00000392474CAMKK2chr12121691277-4125587971350417
ENST00000436789LRRC23chr127015826+ENST00000538733CAMKK2chr12121691277-4277587971176359
ENST00000436789LRRC23chr127015826+ENST00000337174CAMKK2chr12121691277-4406587971305402
ENST00000436789LRRC23chr127015826+ENST00000347034CAMKK2chr12121691277-4320587971317406
ENST00000436789LRRC23chr127015826+ENST00000324774CAMKK2chr12121691277-4449587971446449
ENST00000436789LRRC23chr127015826+ENST00000545538CAMKK2chr12121691277-4049587971350417
ENST00000436789LRRC23chr127015826+ENST00000412367CAMKK2chr12121691277-1578587971305402
ENST00000436789LRRC23chr127015826+ENST00000404169CAMKK2chr12121691277-1621587971446449
ENST00000436789LRRC23chr127015826+ENST00000402834CAMKK2chr12121691277-1599587971446449
ENST00000436789LRRC23chr127015826+ENST00000446440CAMKK2chr12121691277-1689587971152351
ENST00000436789LRRC23chr127015826+ENST00000392473CAMKK2chr12121691277-1818587971281394
ENST00000429740LRRC23chr127015826+ENST00000392474CAMKK2chr12121691277-402849001253417
ENST00000429740LRRC23chr127015826+ENST00000538733CAMKK2chr12121691277-418049001079359
ENST00000429740LRRC23chr127015826+ENST00000337174CAMKK2chr12121691277-430949001208402
ENST00000429740LRRC23chr127015826+ENST00000347034CAMKK2chr12121691277-422349001220406
ENST00000429740LRRC23chr127015826+ENST00000324774CAMKK2chr12121691277-435249001349449
ENST00000429740LRRC23chr127015826+ENST00000545538CAMKK2chr12121691277-395249001253417
ENST00000429740LRRC23chr127015826+ENST00000412367CAMKK2chr12121691277-148149001208402
ENST00000429740LRRC23chr127015826+ENST00000404169CAMKK2chr12121691277-152449001349449
ENST00000429740LRRC23chr127015826+ENST00000402834CAMKK2chr12121691277-150249001349449
ENST00000429740LRRC23chr127015826+ENST00000446440CAMKK2chr12121691277-159249001055351
ENST00000429740LRRC23chr127015826+ENST00000392473CAMKK2chr12121691277-172149001184394

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
ENST00000433346ENST00000392474LRRC23chr127015826+CAMKK2chr12121691277-0.0017988920.99820113
ENST00000433346ENST00000538733LRRC23chr127015826+CAMKK2chr12121691277-0.0015932040.9984068
ENST00000433346ENST00000337174LRRC23chr127015826+CAMKK2chr12121691277-0.001904210.9980958
ENST00000433346ENST00000347034LRRC23chr127015826+CAMKK2chr12121691277-0.0019972940.9980027
ENST00000433346ENST00000324774LRRC23chr127015826+CAMKK2chr12121691277-0.0020469530.99795306
ENST00000433346ENST00000545538LRRC23chr127015826+CAMKK2chr12121691277-0.0018991120.99810094
ENST00000433346ENST00000412367LRRC23chr127015826+CAMKK2chr12121691277-0.0033762820.99662375
ENST00000433346ENST00000404169LRRC23chr127015826+CAMKK2chr12121691277-0.0041537870.9958462
ENST00000433346ENST00000402834LRRC23chr127015826+CAMKK2chr12121691277-0.0047328620.99526715
ENST00000433346ENST00000446440LRRC23chr127015826+CAMKK2chr12121691277-0.0022905720.9977094
ENST00000433346ENST00000392473LRRC23chr127015826+CAMKK2chr12121691277-0.0026862970.9973137
ENST00000007969ENST00000392474LRRC23chr127015826+CAMKK2chr12121691277-0.0016028570.9983972
ENST00000007969ENST00000538733LRRC23chr127015826+CAMKK2chr12121691277-0.0014460570.99855393
ENST00000007969ENST00000337174LRRC23chr127015826+CAMKK2chr12121691277-0.0017171870.9982828
ENST00000007969ENST00000347034LRRC23chr127015826+CAMKK2chr12121691277-0.0017849270.9982151
ENST00000007969ENST00000324774LRRC23chr127015826+CAMKK2chr12121691277-0.0018437760.99815625
ENST00000007969ENST00000545538LRRC23chr127015826+CAMKK2chr12121691277-0.0016966230.9983034
ENST00000007969ENST00000412367LRRC23chr127015826+CAMKK2chr12121691277-0.0029678630.99703217
ENST00000007969ENST00000404169LRRC23chr127015826+CAMKK2chr12121691277-0.0037575590.9962424
ENST00000007969ENST00000402834LRRC23chr127015826+CAMKK2chr12121691277-0.004468020.9955319
ENST00000007969ENST00000446440LRRC23chr127015826+CAMKK2chr12121691277-0.0020243710.99797565
ENST00000007969ENST00000392473LRRC23chr127015826+CAMKK2chr12121691277-0.0025458840.9974541
ENST00000323702ENST00000392474LRRC23chr127015826+CAMKK2chr12121691277-0.0015922430.9984078
ENST00000323702ENST00000538733LRRC23chr127015826+CAMKK2chr12121691277-0.0014013310.99859864
ENST00000323702ENST00000337174LRRC23chr127015826+CAMKK2chr12121691277-0.0016899550.9983101
ENST00000323702ENST00000347034LRRC23chr127015826+CAMKK2chr12121691277-0.0017560840.9982439
ENST00000323702ENST00000324774LRRC23chr127015826+CAMKK2chr12121691277-0.0018185310.99818146
ENST00000323702ENST00000545538LRRC23chr127015826+CAMKK2chr12121691277-0.0016897060.9983103
ENST00000323702ENST00000412367LRRC23chr127015826+CAMKK2chr12121691277-0.0025640540.997436
ENST00000323702ENST00000404169LRRC23chr127015826+CAMKK2chr12121691277-0.0033124920.9966875
ENST00000323702ENST00000402834LRRC23chr127015826+CAMKK2chr12121691277-0.0040248810.9959751
ENST00000323702ENST00000446440LRRC23chr127015826+CAMKK2chr12121691277-0.0021477140.9978523
ENST00000323702ENST00000392473LRRC23chr127015826+CAMKK2chr12121691277-0.0025876710.9974124
ENST00000443597ENST00000392474LRRC23chr127015826+CAMKK2chr12121691277-0.0017309180.9982691
ENST00000443597ENST00000538733LRRC23chr127015826+CAMKK2chr12121691277-0.001538790.99846125
ENST00000443597ENST00000337174LRRC23chr127015826+CAMKK2chr12121691277-0.0018458980.9981541
ENST00000443597ENST00000347034LRRC23chr127015826+CAMKK2chr12121691277-0.0019295970.9980704
ENST00000443597ENST00000324774LRRC23chr127015826+CAMKK2chr12121691277-0.0019979040.9980021
ENST00000443597ENST00000545538LRRC23chr127015826+CAMKK2chr12121691277-0.0018388160.99816114
ENST00000443597ENST00000412367LRRC23chr127015826+CAMKK2chr12121691277-0.003095050.9969049
ENST00000443597ENST00000404169LRRC23chr127015826+CAMKK2chr12121691277-0.0041740350.995826
ENST00000443597ENST00000402834LRRC23chr127015826+CAMKK2chr12121691277-0.0048958450.9951042
ENST00000443597ENST00000446440LRRC23chr127015826+CAMKK2chr12121691277-0.0023367810.99766326
ENST00000443597ENST00000392473LRRC23chr127015826+CAMKK2chr12121691277-0.002925860.9970741
ENST00000436789ENST00000392474LRRC23chr127015826+CAMKK2chr12121691277-0.0016291170.99837095
ENST00000436789ENST00000538733LRRC23chr127015826+CAMKK2chr12121691277-0.001437330.99856263
ENST00000436789ENST00000337174LRRC23chr127015826+CAMKK2chr12121691277-0.0017390290.99826103
ENST00000436789ENST00000347034LRRC23chr127015826+CAMKK2chr12121691277-0.0017937160.99820626
ENST00000436789ENST00000324774LRRC23chr127015826+CAMKK2chr12121691277-0.0018760270.99812394
ENST00000436789ENST00000545538LRRC23chr127015826+CAMKK2chr12121691277-0.0017358090.99826425
ENST00000436789ENST00000412367LRRC23chr127015826+CAMKK2chr12121691277-0.0026344580.99736553
ENST00000436789ENST00000404169LRRC23chr127015826+CAMKK2chr12121691277-0.0033429890.996657
ENST00000436789ENST00000402834LRRC23chr127015826+CAMKK2chr12121691277-0.0040348210.9959651
ENST00000436789ENST00000446440LRRC23chr127015826+CAMKK2chr12121691277-0.0022696140.99773043
ENST00000436789ENST00000392473LRRC23chr127015826+CAMKK2chr12121691277-0.0027514230.9972486
ENST00000429740ENST00000392474LRRC23chr127015826+CAMKK2chr12121691277-0.0015170960.9984829
ENST00000429740ENST00000538733LRRC23chr127015826+CAMKK2chr12121691277-0.0013644270.9986356
ENST00000429740ENST00000337174LRRC23chr127015826+CAMKK2chr12121691277-0.0016324440.9983676
ENST00000429740ENST00000347034LRRC23chr127015826+CAMKK2chr12121691277-0.0016805980.9983193
ENST00000429740ENST00000324774LRRC23chr127015826+CAMKK2chr12121691277-0.001771270.9982287
ENST00000429740ENST00000545538LRRC23chr127015826+CAMKK2chr12121691277-0.0016281270.9983719
ENST00000429740ENST00000412367LRRC23chr127015826+CAMKK2chr12121691277-0.002556010.99744403
ENST00000429740ENST00000404169LRRC23chr127015826+CAMKK2chr12121691277-0.0033476950.9966523
ENST00000429740ENST00000402834LRRC23chr127015826+CAMKK2chr12121691277-0.0041392640.99586076
ENST00000429740ENST00000446440LRRC23chr127015826+CAMKK2chr12121691277-0.0018348590.9981652
ENST00000429740ENST00000392473LRRC23chr127015826+CAMKK2chr12121691277-0.0023908080.99760914

check button Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for LRRC23-CAMKK2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
LRRC23chr127015826CAMKK2chr12121691277490163GISHPRLETLNLKVHYQKIIHRDIKP
LRRC23chr127015826CAMKK2chr12121691277587163GISHPRLETLNLKVHYQKIIHRDIKP
LRRC23chr127015826CAMKK2chr12121691277602163GISHPRLETLNLKVHYQKIIHRDIKP
LRRC23chr127015826CAMKK2chr12121691277709163GISHPRLETLNLKVHYQKIIHRDIKP
LRRC23chr127015826CAMKK2chr12121691277710163GISHPRLETLNLKVHYQKIIHRDIKP
LRRC23chr127015826CAMKK2chr12121691277968163GISHPRLETLNLKVHYQKIIHRDIKP

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Potential FusionNeoAntigen Information of LRRC23-CAMKK2 in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
LRRC23-CAMKK2_7015826_121691277.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)
LRRC23-CAMKK2chr127015826chr12121691277710HLA-B15:02ETLNLKVHY0.88330.7261716
LRRC23-CAMKK2chr127015826chr12121691277710HLA-B44:03LETLNLKVHY0.99850.9073616
LRRC23-CAMKK2chr127015826chr12121691277710HLA-A30:08KVHYQKIIHR0.99440.57381222
LRRC23-CAMKK2chr127015826chr12121691277710HLA-B15:31ETLNLKVHY0.93510.6107716
LRRC23-CAMKK2chr127015826chr12121691277710HLA-A25:01ETLNLKVHY0.99550.7164716
LRRC23-CAMKK2chr127015826chr12121691277710HLA-B35:20ETLNLKVHY0.92660.7029716
LRRC23-CAMKK2chr127015826chr12121691277710HLA-B15:11ETLNLKVHY0.68590.6061716
LRRC23-CAMKK2chr127015826chr12121691277710HLA-B15:08ETLNLKVHY0.67140.5978716
LRRC23-CAMKK2chr127015826chr12121691277710HLA-B18:04ETLNLKVHY0.30920.6813716
LRRC23-CAMKK2chr127015826chr12121691277710HLA-B44:07LETLNLKVHY0.99850.9073616
LRRC23-CAMKK2chr127015826chr12121691277710HLA-B44:26LETLNLKVHY0.99850.9073616
LRRC23-CAMKK2chr127015826chr12121691277710HLA-B44:13LETLNLKVHY0.99850.9073616
LRRC23-CAMKK2chr127015826chr12121691277710HLA-A30:01KVHYQKIIHR0.99480.69311222
LRRC23-CAMKK2chr127015826chr12121691277710HLA-B18:11LETLNLKVHY0.90190.6534616

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Potential FusionNeoAntigen Information of LRRC23-CAMKK2 in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
LRRC23-CAMKK2_7015826_121691277.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)
LRRC23-CAMKK2chr127015826chr12121691277710DRB1-0807LKVHYQKIIHRDIKP1126
LRRC23-CAMKK2chr127015826chr12121691277710DRB1-1429NLKVHYQKIIHRDIK1025
LRRC23-CAMKK2chr127015826chr12121691277710DRB1-1452NLKVHYQKIIHRDIK1025
LRRC23-CAMKK2chr127015826chr12121691277710DRB4-0104NLKVHYQKIIHRDIK1025
LRRC23-CAMKK2chr127015826chr12121691277710DRB5-0106NLKVHYQKIIHRDIK1025
LRRC23-CAMKK2chr127015826chr12121691277710DRB5-0106LNLKVHYQKIIHRDI924
LRRC23-CAMKK2chr127015826chr12121691277710DRB5-0106TLNLKVHYQKIIHRD823
LRRC23-CAMKK2chr127015826chr12121691277710DRB5-0202NLKVHYQKIIHRDIK1025
LRRC23-CAMKK2chr127015826chr12121691277710DRB5-0204NLKVHYQKIIHRDIK1025
LRRC23-CAMKK2chr127015826chr12121691277710DRB5-0205NLKVHYQKIIHRDIK1025

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Fusion breakpoint peptide structures of LRRC23-CAMKK2

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
4937LETLNLKVHYQKIILRRC23CAMKK2chr127015826chr12121691277710

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of LRRC23-CAMKK2

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score
HLA-B14:023BVN4937LETLNLKVHYQKII-7.9962-8.1096
HLA-B14:023BVN4937LETLNLKVHYQKII-5.70842-6.74372
HLA-B52:013W394937LETLNLKVHYQKII-6.83737-6.95077
HLA-B52:013W394937LETLNLKVHYQKII-4.4836-5.5189
HLA-A11:014UQ24937LETLNLKVHYQKII-10.0067-10.1201
HLA-A11:014UQ24937LETLNLKVHYQKII-9.03915-10.0745
HLA-A24:025HGA4937LETLNLKVHYQKII-6.56204-6.67544
HLA-A24:025HGA4937LETLNLKVHYQKII-5.42271-6.45801
HLA-B44:053DX84937LETLNLKVHYQKII-7.85648-8.89178
HLA-B44:053DX84937LETLNLKVHYQKII-5.3978-5.5112
HLA-A02:016TDR4937LETLNLKVHYQKII-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of LRRC23-CAMKK2

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence
LRRC23-CAMKK2chr127015826chr121216912771222KVHYQKIIHRAAGTACACTACCAGAAGATCATCCACCGTG
LRRC23-CAMKK2chr127015826chr12121691277616LETLNLKVHYTTGAAACCCTGAATCTCAAAGTACACTACC
LRRC23-CAMKK2chr127015826chr12121691277716ETLNLKVHYAAACCCTGAATCTCAAAGTACACTACC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
LRRC23-CAMKK2chr127015826chr121216912771025NLKVHYQKIIHRDIKATCTCAAAGTACACTACCAGAAGATCATCCACCGTGACATCAAAC
LRRC23-CAMKK2chr127015826chr121216912771126LKVHYQKIIHRDIKPTCAAAGTACACTACCAGAAGATCATCCACCGTGACATCAAACCTT
LRRC23-CAMKK2chr127015826chr12121691277823TLNLKVHYQKIIHRDCCCTGAATCTCAAAGTACACTACCAGAAGATCATCCACCGTGACA
LRRC23-CAMKK2chr127015826chr12121691277924LNLKVHYQKIIHRDITGAATCTCAAAGTACACTACCAGAAGATCATCCACCGTGACATCA

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Information of the samples that have these potential fusion neoantigens of LRRC23-CAMKK2

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample
N/ALRRC23-CAMKK2chr127015826ENST00000007969chr12121691277ENST00000324774DA116260

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Potential target of CAR-T therapy development for LRRC23-CAMKK2

check button Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to LRRC23-CAMKK2

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 LRRC23-CAMKK2

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