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Fusion gene ID: 19588 |
FusionGeneSummary for LDLR_CALR |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LDLR_CALR | Fusion gene ID: 19588 | Hgene | Tgene | Gene symbol | LDLR | CALR | Gene ID | 3949 | 811 |
| Gene name | low density lipoprotein receptor | calreticulin | |
| Synonyms | FH|FHC|LDLCQ2 | CRT|HEL-S-99n|RO|SSA|cC1qR | |
| Cytomap | 19p13.2 | 19p13.13 | |
| Type of gene | protein-coding | protein-coding | |
| Description | low-density lipoprotein receptorLDL receptorlow-density lipoprotein receptor class A domain-containing protein 3 | calreticulinCRP55ERp60HACBPSicca syndrome antigen A (autoantigen Ro; calreticulin)calregulinendoplasmic reticulum resident protein 60epididymis secretory sperm binding protein Li 99ngrp60 | |
| Modification date | 20180520 | 20180527 | |
| UniProtAcc | P01130 | P27797 | |
| Ensembl transtripts involved in fusion gene | ENST00000558518, ENST00000557933, ENST00000455727, ENST00000535915, ENST00000545707, ENST00000558013, ENST00000560628, | ENST00000316448, | |
| Fusion gene scores | * DoF score | 14 X 9 X 11=1386 | 12 X 15 X 3=540 |
| # samples | 17 | 18 | |
| ** MAII score | log2(17/1386*10)=-3.02732060599951 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(18/540*10)=-1.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: LDLR [Title/Abstract] AND CALR [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) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Tgene | CALR | GO:0000122 | negative regulation of transcription by RNA polymerase II | 8107809 |
| Tgene | CALR | GO:0006611 | protein export from nucleus | 11149926 |
| Tgene | CALR | GO:0017148 | negative regulation of translation | 14726956 |
| Tgene | CALR | GO:0033144 | negative regulation of intracellular steroid hormone receptor signaling pathway | 8107809 |
| Tgene | CALR | GO:0034504 | protein localization to nucleus | 15998798 |
| Tgene | CALR | GO:0045665 | negative regulation of neuron differentiation | 8107809 |
| Tgene | CALR | GO:0045892 | negative regulation of transcription, DNA-templated | 8107809 |
| Tgene | CALR | GO:0048387 | negative regulation of retinoic acid receptor signaling pathway | 8107809 |
| 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 type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| TCGA | LD | CESC | TCGA-VS-A8Q9-01A | LDLR | chr19 | 11227674 | + | CALR | chr19 | 13049948 | + |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| 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. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| Frame-shift | ENST00000558518 | ENST00000316448 | LDLR | chr19 | 11227674 | + | CALR | chr19 | 13049948 | + |
| Frame-shift | ENST00000557933 | ENST00000316448 | LDLR | chr19 | 11227674 | + | CALR | chr19 | 13049948 | + |
| Frame-shift | ENST00000455727 | ENST00000316448 | LDLR | chr19 | 11227674 | + | CALR | chr19 | 13049948 | + |
| Frame-shift | ENST00000535915 | ENST00000316448 | LDLR | chr19 | 11227674 | + | CALR | chr19 | 13049948 | + |
| Frame-shift | ENST00000545707 | ENST00000316448 | LDLR | chr19 | 11227674 | + | CALR | chr19 | 13049948 | + |
| Frame-shift | ENST00000558013 | ENST00000316448 | LDLR | chr19 | 11227674 | + | CALR | chr19 | 13049948 | + |
| intron-3CDS | ENST00000560628 | ENST00000316448 | LDLR | chr19 | 11227674 | + | CALR | chr19 | 13049948 | + |
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FusionProtFeatures for LDLR_CALR |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LDLR | CALR |
| Calcium-binding chaperone that promotes folding,oligomeric assembly and quality control in the endoplasmicreticulum (ER) via the calreticulin/calnexin cycle. This lectininteracts transiently with almost all of the monoglucosylatedglycoproteins that are synthesized in the ER. Interacts with theDNA-binding domain of NR3C1 and mediates its nuclear export.Involved in maternal gene expression regulation. May participatein oocyte maturation via the regulation of calcium homeostasis (Bysimilarity). {ECO:0000250, ECO:0000269|PubMed:11149926,ECO:0000269|PubMed:7876246}. |
| Retention 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 . * 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. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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FusionGeneSequence for LDLR_CALR |
| 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 LDLR_CALR |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| LDLR | DAB1, PF4, CD36, DAB2, AP1M2, LDLRAP1, LRPAP1, SNX17, HSPA5, MYLIP, HSP90B1, PDIA4, CANX, PDIA3, CREBBP, MAP4, PCSK9, GINM1, B3GNT2, ZFP41, PRG2, CBR3, USP2, FAM19A3, FCGRT, ZNF408, PRG3, DLK2, TYW3, MGAT4C, DEFA1, UST, EGFL6, WNT7A | CALR | CD40, ELF3, EPB41, LRP1, PLAT, MBL2, PDIA3, CANX, PRF1, FGB, APP, CD1D, APOB, TAPBP, VWF, AR, F5, NR3C1, TF, SLC6A4, NKX2-1, SLC2A1, H2AFX, PSMA3, LRIF1, SMARCB1, MAPK6, TAP1, ELAVL1, SIRT7, CDK2, GRK5, KCNH2, PRKCSH, GANAB, KRT17, HSP90B1, P4HB, HLA-E, LPL, ATF2, MTNR1A, ITGA3, HLA-A, CALR, CLN5, SOX2, SLC27A2, UPF2, PARK2, AARSD1, ACTR2, ANP32B, ARPC1B, ARPC3, ARPC1A, ARPC5, EEF2K, LPP, RPA3, SH3GLB1, NSUN2, PFDN5, PRKACA, RPA1, SH3GL1, THG1L, TPD52L2, LGR4, HUWE1, CUL7, SUZ12, RNF2, EGFR, INHA, NTM, HSPB1, ATP5B, CALU, EEF2, ENO1, ENO2, ENO3, EZR, HNRNPU, HSP90AB1, MATR3, MSN, PTGES3, RCN1, RDX, TKT, TPT1, VCP, WDR1, YWHAE, MAPRE3, NACA2, PCNA, NTRK1, KRAS, TSHR, PLP1, EWSR1, TCTN3, CNTRL, TCTN1, PPME1, F8, B2M, UBE3A, MCM2, RNY3, RNY1, RNY4, TRIM21, U2AF2, CDC73, HYPK, PTPRN, ACP5, DUSP13, SFRP4, WNT7A, CHI3L1, BMP4, PTPN22, PTPRO, TCTN2, EDEM3, HLA-B, TRIM25 |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for LDLR_CALR |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Hgene | LDLR | P01130 | DB00707 | Porfimer sodium | Low-density lipoprotein receptor | small molecule | approved|investigational |
| Tgene | CALR | P27797 | DB00031 | Tenecteplase | Calreticulin | biotech | approved |
| Tgene | CALR | P27797 | DB11093 | Calcium Citrate | Calreticulin | small molecule | approved |
| Tgene | CALR | P27797 | DB11348 | Calcium Phosphate | Calreticulin | small molecule | approved |
| Tgene | CALR | P27797 | DB00025 | Antihemophilic factor, human recombinant | Calreticulin | biotech | approved|investigational |
| Tgene | CALR | P27797 | DB01065 | Melatonin | Calreticulin | small molecule | approved|nutraceutical|vet_approved |
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RelatedDiseases for LDLR_CALR |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | LDLR | C0745103 | Hyperlipoproteinemia Type IIa | 32 | CTD_human;ORPHANET;UNIPROT |
| Hgene | LDLR | C0020445 | Hypercholesterolemia, Familial | 6 | CTD_human;HPO |
| Hgene | LDLR | C0004153 | Atherosclerosis | 4 | CTD_human |
| Hgene | LDLR | C0020443 | Hypercholesterolemia | 4 | CTD_human;HPO |
| Hgene | LDLR | C0400966 | Non-alcoholic Fatty Liver Disease | 3 | CTD_human |
| Hgene | LDLR | C0020473 | Hyperlipidemia | 2 | CTD_human;HPO |
| Hgene | LDLR | C1956346 | Coronary Artery Disease | 2 | CTD_human |
| Hgene | LDLR | C0010068 | Coronary heart disease | 1 | CTD_human |
| Hgene | LDLR | C0015695 | Fatty Liver | 1 | CTD_human |
| Hgene | LDLR | C0020507 | Hyperplasia | 1 | CTD_human |
| Hgene | LDLR | C0028754 | Obesity | 1 | CTD_human |
| Hgene | LDLR | C0034362 | Q Fever | 1 | CTD_human |
| Hgene | LDLR | C0085762 | Alcohol abuse | 1 | PSYGENET |
| Hgene | LDLR | C0242339 | Dyslipidemias | 1 | CTD_human |
| Hgene | LDLR | C1862939 | AMYOTROPHIC LATERAL SCLEROSIS 1 | 1 | CTD_human |
| Tgene | CALR | C0033975 | Psychotic Disorders | 2 | PSYGENET |
| Tgene | CALR | C0036337 | Schizoaffective Disorder | 2 | PSYGENET |
| Tgene | CALR | C0349204 | Nonorganic psychosis | 2 | PSYGENET |
| Tgene | CALR | C0005586 | Bipolar Disorder | 1 | PSYGENET |
| Tgene | CALR | C0009404 | Colorectal Neoplasms | 1 | CTD_human |
| Tgene | CALR | C0025205 | Melanoma, Experimental | 1 | CTD_human |
| Tgene | CALR | C0027626 | Neoplasm Invasiveness | 1 | CTD_human |
| Tgene | CALR | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
| Tgene | CALR | C0033937 | Psychoses, Drug | 1 | PSYGENET |
| Tgene | CALR | C0036349 | Paranoid Schizophrenia | 1 | PSYGENET |
| Tgene | CALR | C0036939 | Shared Paranoid Disorder | 1 | PSYGENET |
| Tgene | CALR | C0151744 | Myocardial Ischemia | 1 | CTD_human |
| Tgene | CALR | C0279626 | Squamous cell carcinoma of esophagus | 1 | CTD_human |
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