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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:LRP3-LSM14A

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: LRP3-LSM14A
FusionPDB ID: 49770
FusionGDB2.0 ID: 49770
HgeneTgene
Gene symbol

LRP3

LSM14A

Gene ID

4037

26065

Gene nameLDL receptor related protein 3LSM14A mRNA processing body assembly factor
Synonyms-C19orf13|FAM61A|RAP55|RAP55A
Cytomap

19q13.11

19q13.11

Type of geneprotein-codingprotein-coding
Descriptionlow-density lipoprotein receptor-related protein 3105 kDa low-density lipoprotein receptor-related proteinCTD-2540B15.13LRP-3hLRp105protein LSM14 homolog ALSM14 homolog ALSM14A, SCD6 homolog ARNA-associated protein 55RNA-associated protein 55AalphaSNBPfamily with sequence similarity 61, member AhRAP55hRAP55Aprotein SCD6 homologputative alpha-synuclein-binding protein
Modification date2020031320200327
UniProtAcc

O75074

Q8ND56

Ensembl transtripts involved in fusion geneENST idsENST00000253193, ENST00000433627, 
ENST00000540746, ENST00000544216, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score6 X 6 X 4=14416 X 15 X 8=1920
# samples 720
** MAII scorelog2(7/144*10)=-1.04064198449735
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(20/1920*10)=-3.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: LRP3 [Title/Abstract] AND LSM14A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)LRP3(33685764)-LSM14A(34685382), # samples:2
Anticipated loss of major functional domain due to fusion event.LRP3-LSM14A 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.
LRP3-LSM14A 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.
LRP3-LSM14A 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.
LRP3-LSM14A 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
TgeneLSM14A

GO:0033962

cytoplasmic mRNA processing body assembly

16484376


check buttonFusion gene breakpoints across LRP3 (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 LSM14A (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
ChimerDB4PRADTCGA-J4-A83I-01ALRP3chr19

33685764

+LSM14Achr19

34685383

+
ChimerDB4PRADTCGA-J4-A83ILRP3chr19

33685764

+LSM14Achr19

34685382

+


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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)
ENST00000253193LRP3chr1933685764+ENST00000540746LSM14Achr1934685383+21882752021422406
ENST00000253193LRP3chr1933685764+ENST00000544216LSM14Achr1934685383+36732752021545447
ENST00000253193LRP3chr1933685764+ENST00000433627LSM14Achr1934685383+35032752021545447
ENST00000253193LRP3chr1933685764+ENST00000540746LSM14Achr1934685382+21882752021422406
ENST00000253193LRP3chr1933685764+ENST00000544216LSM14Achr1934685382+36732752021545447
ENST00000253193LRP3chr1933685764+ENST00000433627LSM14Achr1934685382+35032752021545447

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
ENST00000253193ENST00000540746LRP3chr1933685764+LSM14Achr1934685383+0.0008580110.99914193
ENST00000253193ENST00000544216LRP3chr1933685764+LSM14Achr1934685383+0.0003832130.99961674
ENST00000253193ENST00000433627LRP3chr1933685764+LSM14Achr1934685383+0.0005924720.99940753
ENST00000253193ENST00000540746LRP3chr1933685764+LSM14Achr1934685382+0.0008580110.99914193
ENST00000253193ENST00000544216LRP3chr1933685764+LSM14Achr1934685382+0.0003832130.99961674
ENST00000253193ENST00000433627LRP3chr1933685764+LSM14Achr1934685382+0.0005924720.99940753

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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

>49770_49770_1_LRP3-LSM14A_LRP3_chr19_33685764_ENST00000253193_LSM14A_chr19_34685382_ENST00000433627_length(amino acids)=447AA_BP=24
MEKRAAAGLEGAPGARAQLAVVCLVRSFGTEDRPTDRPIPPRDEVFEYIIFRGSDIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSTSSFQ
SMGSYGPFGRMPTYSQFSPSSLVGQQFGAVGVAGSSLTSFGTETSNSGTLPQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTME
QAVQTASAHLPAPAAVGRRSPVSTRPLPSASQKAGENQEHRRAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRGGHRGGRGRFGIRR
DGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLEKQEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDKTKSFFDNISCD

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

>49770_49770_2_LRP3-LSM14A_LRP3_chr19_33685764_ENST00000253193_LSM14A_chr19_34685382_ENST00000540746_length(amino acids)=406AA_BP=24
MEKRAAAGLEGAPGARAQLAVVCLVRSFGTEDRPTDRPIPPRDEVFEYIIFRGSDIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSTSSFQ
SMGSYGPFGRMPTYSQFSPSSLVGQQFGAVGVGRSSPQLDPLRKSPTMEQAVQTASAHLPAPAAVGRRSPVSTRPLPSASQKAGENQEHR
RAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRGGHRGGRGRFGIRRDGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLEK
QEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDKTKSFFDNISCDDNRERRPTWAEERRLNAETFGIPLRPNRGRGGYRGRGGLGF

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

>49770_49770_3_LRP3-LSM14A_LRP3_chr19_33685764_ENST00000253193_LSM14A_chr19_34685382_ENST00000544216_length(amino acids)=447AA_BP=24
MEKRAAAGLEGAPGARAQLAVVCLVRSFGTEDRPTDRPIPPRDEVFEYIIFRGSDIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSTSSFQ
SMGSYGPFGRMPTYSQFSPSSLVGQQFGAVGVAGSSLTSFGTETSNSGTLPQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTME
QAVQTASAHLPAPAAVGRRSPVSTRPLPSASQKAGENQEHRRAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRGGHRGGRGRFGIRR
DGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLEKQEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDKTKSFFDNISCD

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

>49770_49770_4_LRP3-LSM14A_LRP3_chr19_33685764_ENST00000253193_LSM14A_chr19_34685383_ENST00000433627_length(amino acids)=447AA_BP=24
MEKRAAAGLEGAPGARAQLAVVCLVRSFGTEDRPTDRPIPPRDEVFEYIIFRGSDIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSTSSFQ
SMGSYGPFGRMPTYSQFSPSSLVGQQFGAVGVAGSSLTSFGTETSNSGTLPQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTME
QAVQTASAHLPAPAAVGRRSPVSTRPLPSASQKAGENQEHRRAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRGGHRGGRGRFGIRR
DGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLEKQEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDKTKSFFDNISCD

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

>49770_49770_5_LRP3-LSM14A_LRP3_chr19_33685764_ENST00000253193_LSM14A_chr19_34685383_ENST00000540746_length(amino acids)=406AA_BP=24
MEKRAAAGLEGAPGARAQLAVVCLVRSFGTEDRPTDRPIPPRDEVFEYIIFRGSDIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSTSSFQ
SMGSYGPFGRMPTYSQFSPSSLVGQQFGAVGVGRSSPQLDPLRKSPTMEQAVQTASAHLPAPAAVGRRSPVSTRPLPSASQKAGENQEHR
RAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRGGHRGGRGRFGIRRDGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLEK
QEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDKTKSFFDNISCDDNRERRPTWAEERRLNAETFGIPLRPNRGRGGYRGRGGLGF

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

>49770_49770_6_LRP3-LSM14A_LRP3_chr19_33685764_ENST00000253193_LSM14A_chr19_34685383_ENST00000544216_length(amino acids)=447AA_BP=24
MEKRAAAGLEGAPGARAQLAVVCLVRSFGTEDRPTDRPIPPRDEVFEYIIFRGSDIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSTSSFQ
SMGSYGPFGRMPTYSQFSPSSLVGQQFGAVGVAGSSLTSFGTETSNSGTLPQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTME
QAVQTASAHLPAPAAVGRRSPVSTRPLPSASQKAGENQEHRRAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRGGHRGGRGRFGIRR
DGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLEKQEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDKTKSFFDNISCD

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

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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/chr19:33685764/chr19:34685382)
- 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
LRP3

O75074

LSM14A

Q8ND56

FUNCTION: Probable receptor, which may be involved in the internalization of lipophilic molecules and/or signal transduction. Its precise role is however unclear, since it does not bind to very low density lipoprotein (VLDL) or to LRPAP1 in vitro.FUNCTION: Essential for formation of P-bodies, cytoplasmic structures that provide storage sites for translationally inactive mRNAs and protect them from degradation (PubMed:16484376, PubMed:17074753, PubMed:29510985). Acts as a repressor of mRNA translation (PubMed:29510985). May play a role in mitotic spindle assembly (PubMed:26339800). {ECO:0000269|PubMed:16484376, ECO:0000269|PubMed:17074753, ECO:0000269|PubMed:26339800, ECO:0000269|PubMed:29510985}.

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
TgeneLSM14Achr19:33685764chr19:34685382ENST00000433627011284_32040.3333333333333361040.0DomainDFDF
TgeneLSM14Achr19:33685764chr19:34685382ENST00000544216010284_32040.333333333333336464.0DomainDFDF
TgeneLSM14Achr19:33685764chr19:34685383ENST00000433627011284_32040.3333333333333361040.0DomainDFDF
TgeneLSM14Achr19:33685764chr19:34685383ENST00000544216010284_32040.333333333333336464.0DomainDFDF
TgeneLSM14Achr19:33685764chr19:34685382ENST00000433627011361_37740.3333333333333361040.0MotifNote=FFD box
TgeneLSM14Achr19:33685764chr19:34685382ENST00000433627011380_40040.3333333333333361040.0MotifNote=TFG box
TgeneLSM14Achr19:33685764chr19:34685382ENST00000544216010361_37740.333333333333336464.0MotifNote=FFD box
TgeneLSM14Achr19:33685764chr19:34685382ENST00000544216010380_40040.333333333333336464.0MotifNote=TFG box
TgeneLSM14Achr19:33685764chr19:34685383ENST00000433627011361_37740.3333333333333361040.0MotifNote=FFD box
TgeneLSM14Achr19:33685764chr19:34685383ENST00000433627011380_40040.3333333333333361040.0MotifNote=TFG box
TgeneLSM14Achr19:33685764chr19:34685383ENST00000544216010361_37740.333333333333336464.0MotifNote=FFD box
TgeneLSM14Achr19:33685764chr19:34685383ENST00000544216010380_40040.333333333333336464.0MotifNote=TFG box

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneLRP3chr19:33685764chr19:34685382ENST00000253193+17751_75424.333333333333332771.0Compositional biasNote=Poly-Pro
HgeneLRP3chr19:33685764chr19:34685383ENST00000253193+17751_75424.333333333333332771.0Compositional biasNote=Poly-Pro
HgeneLRP3chr19:33685764chr19:34685382ENST00000253193+17165_20124.333333333333332771.0DomainLDL-receptor class A 1
HgeneLRP3chr19:33685764chr19:34685382ENST00000253193+17211_25024.333333333333332771.0DomainLDL-receptor class A 2
HgeneLRP3chr19:33685764chr19:34685382ENST00000253193+17254_36524.333333333333332771.0DomainCUB 2
HgeneLRP3chr19:33685764chr19:34685382ENST00000253193+17415_45324.333333333333332771.0DomainLDL-receptor class A 3
HgeneLRP3chr19:33685764chr19:34685382ENST00000253193+1743_15924.333333333333332771.0DomainCUB 1
HgeneLRP3chr19:33685764chr19:34685382ENST00000253193+17454_49024.333333333333332771.0DomainLDL-receptor class A 4
HgeneLRP3chr19:33685764chr19:34685383ENST00000253193+17165_20124.333333333333332771.0DomainLDL-receptor class A 1
HgeneLRP3chr19:33685764chr19:34685383ENST00000253193+17211_25024.333333333333332771.0DomainLDL-receptor class A 2
HgeneLRP3chr19:33685764chr19:34685383ENST00000253193+17254_36524.333333333333332771.0DomainCUB 2
HgeneLRP3chr19:33685764chr19:34685383ENST00000253193+17415_45324.333333333333332771.0DomainLDL-receptor class A 3
HgeneLRP3chr19:33685764chr19:34685383ENST00000253193+1743_15924.333333333333332771.0DomainCUB 1
HgeneLRP3chr19:33685764chr19:34685383ENST00000253193+17454_49024.333333333333332771.0DomainLDL-receptor class A 4
HgeneLRP3chr19:33685764chr19:34685382ENST00000253193+1737_49624.333333333333332771.0Topological domainExtracellular
HgeneLRP3chr19:33685764chr19:34685382ENST00000253193+17518_77024.333333333333332771.0Topological domainCytoplasmic
HgeneLRP3chr19:33685764chr19:34685383ENST00000253193+1737_49624.333333333333332771.0Topological domainExtracellular
HgeneLRP3chr19:33685764chr19:34685383ENST00000253193+17518_77024.333333333333332771.0Topological domainCytoplasmic
HgeneLRP3chr19:33685764chr19:34685382ENST00000253193+17497_51724.333333333333332771.0TransmembraneHelical
HgeneLRP3chr19:33685764chr19:34685383ENST00000253193+17497_51724.333333333333332771.0TransmembraneHelical


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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
LSM14ALsm14a, ELAVL1, RAE1, HNRNPDL, SYNCRIP, CIRBP, HNRNPH1, DDX1, HNRNPU, HNRNPL, CSNK2A1, HECW2, TP53, PRMT8, NTRK1, XPO1, AHSA1, SORT1, EGFR, SFPQ, STRAP, G3BP1, PHACTR3, PTCH1, ESR2, HEXIM1, MEPCE, LARP7, SNAI1, RECQL4, ATG16L1, ZC3H7A, EIF4ENIF1, DDX6, C1QBP, PRMT1, EDC4, PATL1, LSM1, LSM2, LSM3, LSM4, LSM6, LSM7, DCP1A, EDC3, UBQLN2, ZBTB10, HDAC2, APEX1, ITFG1, PLEKHA4, ORF9b, ENG, ZC3H18, N, nsp9, nsp3, ESR1, CELF1, DAZL, FAM120C, FMR1, FUBP3, FXR1, IGF2BP2, AGO1, AGO2, AGO3, ALG13, ANKRD17, ATXN2, CAPRIN1, CNOT1, CNOT10, CNOT3, CNOT4, RQCD1, CPEB4, DCP1B, FAM120A, G3BP2, GIGYF1, GTPBP1, HELZ, IGF2BP1, LSM12, LSM14B, KIAA0430, MEX3A, MKRN2, OTUD4, PRRC2A, PRRC2B, PRRC2C, PUM1, R3HDM1, RC3H1, RC3H2, SECISBP2, SMG1, SMG5, SMG7, SMG8, STAU2, TDRD3, TNRC6B, TOP3B, TRIM56, UBAP2L, UPF1, USP10, YTHDF1, YTHDF2, YTHDF3, ZC3HAV1, ZCCHC11, MEX3B, MOV10, DDX3X, FXR2, ANKHD1-EIF4EBP3, CNOT2, KIAA0355, LARP1B, PUM2, RBMS1, ZCCHC3, UNK, XRN1, CEP85, LARP4B, RNF214, UBAP2, RBM47, NUFIP2, TAF15, CNOT6, NUPL2, PARP12, SPATS2L, ARHGAP11B, ARHGAP23, CIC, FBP1, INSIG1, INSIG2, NUP37, DDX58, OGT, CD274, UFL1, FBL, MAPRE1, MYCBP2, NAA40, TMEM14B, IFI27L1, COL8A1, KIF2C, TMC4, GAGE2E, PEA15, SEPT9, CPEB1, KLF15, KLF16, KLF5, KLF8, SOX15, SOX5, SOX6, TLX2, TLX3,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
LRP3
LSM14Aall structure


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 LRP3-LSM14A


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 LRP3-LSM14A


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