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Fusion Protein:HNRNPA2B1-CAPN8 |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: HNRNPA2B1-CAPN8 | FusionPDB ID: 37065 | FusionGDB2.0 ID: 37065 | Hgene | Tgene | Gene symbol | HNRNPA2B1 | CAPN8 | Gene ID | 3181 | 388743 |
| Gene name | heterogeneous nuclear ribonucleoprotein A2/B1 | calpain 8 | |
| Synonyms | HNRNPA2|HNRNPB1|HNRPA2|HNRPA2B1|HNRPB1|IBMPFD2|RNPA2|SNRPB1 | nCL-2 | |
| Cytomap | 7p15.2 | 1q41 | |
| Type of gene | protein-coding | protein-coding | |
| Description | heterogeneous nuclear ribonucleoproteins A2/B1HNRNPA2B1/MYC fusionepididymis secretory sperm binding proteinhnRNP A2 / hnRNP B1nuclear ribonucleoprotein particle A2 protein | calpain-8new calpain 2stomach-specific M-type calpain | |
| Modification date | 20200314 | 20200313 | |
| UniProtAcc | P22626 | A6NHC0 | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000354667, ENST00000356674, ENST00000476233, | ENST00000366873, ENST00000366872, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 43 X 37 X 14=22274 | 12 X 2 X 4=96 |
| # samples | 50 | 12 | |
| ** MAII score | log2(50/22274*10)=-5.47728875772656 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(12/96*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: HNRNPA2B1 [Title/Abstract] AND CAPN8 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | HNRNPA2B1(26240192)-CAPN8(223718212), # samples:2 | ||
| Anticipated loss of major functional domain due to fusion event. | HNRNPA2B1-CAPN8 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. HNRNPA2B1-CAPN8 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. HNRNPA2B1-CAPN8 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. HNRNPA2B1-CAPN8 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) |
| 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 |
| Hgene | HNRNPA2B1 | GO:0006397 | mRNA processing | 2557628 |
| Hgene | HNRNPA2B1 | GO:0006406 | mRNA export from nucleus | 10567417 |
| Hgene | HNRNPA2B1 | GO:0031053 | primary miRNA processing | 26321680 |
| Hgene | HNRNPA2B1 | GO:0050658 | RNA transport | 17004321 |
| Hgene | HNRNPA2B1 | GO:1990428 | miRNA transport | 24356509 |
| Fusion gene breakpoints across HNRNPA2B1 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| Fusion gene breakpoints across CAPN8 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Gene Sample Information |
| Fusion gene information from FusionGDB2.0. |
| 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | COAD | TCGA-DM-A1D6-01A | HNRNPA2B1 | chr7 | 26240192 | - | CAPN8 | chr1 | 223718212 | - |
| ChimerDB4 | LUAD | TCGA-49-4494-01A | HNRNPA2B1 | chr7 | 26240192 | - | CAPN8 | chr1 | 223718212 | - |
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Fusion ORF Analysis |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| ENST00000354667 | HNRNPA2B1 | chr7 | 26240192 | - | ENST00000366872 | CAPN8 | chr1 | 223718212 | - | 670 | 175 | 169 | 453 | 94 |
| ENST00000356674 | HNRNPA2B1 | chr7 | 26240192 | - | ENST00000366872 | CAPN8 | chr1 | 223718212 | - | 670 | 175 | 169 | 453 | 94 |
| DeepORF 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. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
| ENST00000354667 | ENST00000366872 | HNRNPA2B1 | chr7 | 26240192 | - | CAPN8 | chr1 | 223718212 | - | 0.02283662 | 0.97716343 |
| ENST00000356674 | ENST00000366872 | HNRNPA2B1 | chr7 | 26240192 | - | CAPN8 | chr1 | 223718212 | - | 0.02283662 | 0.97716343 |
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Fusion Amino Acid Sequences |
| 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 >37065_37065_1_HNRNPA2B1-CAPN8_HNRNPA2B1_chr7_26240192_ENST00000354667_CAPN8_chr1_223718212_ENST00000366872_length(amino acids)=94AA_BP=2 MEEIYWETDYNHSGTIDAHEMRTALRKAGFTLNSQVQQTIALRYACSKLGINFDSFVACMIRLETLFKLFSLLDEDKDGMVQLSLAEWLC -------------------------------------------------------------- >37065_37065_2_HNRNPA2B1-CAPN8_HNRNPA2B1_chr7_26240192_ENST00000356674_CAPN8_chr1_223718212_ENST00000366872_length(amino acids)=94AA_BP=2 MEEIYWETDYNHSGTIDAHEMRTALRKAGFTLNSQVQQTIALRYACSKLGINFDSFVACMIRLETLFKLFSLLDEDKDGMVQLSLAEWLC -------------------------------------------------------------- |
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Fusion Protein Functional Features |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr7:26240192/chr1:223718212) - 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. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| HNRNPA2B1 | CAPN8 |
| FUNCTION: Heterogeneous nuclear ribonucleoprotein (hnRNP) that associates with nascent pre-mRNAs, packaging them into hnRNP particles. The hnRNP particle arrangement on nascent hnRNA is non-random and sequence-dependent and serves to condense and stabilize the transcripts and minimize tangling and knotting. Packaging plays a role in various processes such as transcription, pre-mRNA processing, RNA nuclear export, subcellular location, mRNA translation and stability of mature mRNAs (PubMed:19099192). Forms hnRNP particles with at least 20 other different hnRNP and heterogeneous nuclear RNA in the nucleus. Involved in transport of specific mRNAs to the cytoplasm in oligodendrocytes and neurons: acts by specifically recognizing and binding the A2RE (21 nucleotide hnRNP A2 response element) or the A2RE11 (derivative 11 nucleotide oligonucleotide) sequence motifs present on some mRNAs, and promotes their transport to the cytoplasm (PubMed:10567417). Specifically binds single-stranded telomeric DNA sequences, protecting telomeric DNA repeat against endonuclease digestion (By similarity). Also binds other RNA molecules, such as primary miRNA (pri-miRNAs): acts as a nuclear 'reader' of the N6-methyladenosine (m6A) mark by specifically recognizing and binding a subset of nuclear m6A-containing pri-miRNAs. Binding to m6A-containing pri-miRNAs promotes pri-miRNA processing by enhancing binding of DGCR8 to pri-miRNA transcripts (PubMed:26321680). Involved in miRNA sorting into exosomes following sumoylation, possibly by binding (m6A)-containing pre-miRNAs (PubMed:24356509). Acts as a regulator of efficiency of mRNA splicing, possibly by binding to m6A-containing pre-mRNAs (PubMed:26321680). Plays also a role in the activation of the innate immune response (PubMed:31320558). Mechanistically, senses the presence of viral DNA in the nucleus, homodimerizes and is demethylated by JMJD6 (PubMed:31320558). In turn, translocates to the cytoplasm where it activates the TBK1-IRF3 pathway, leading to interferon alpha/beta production (PubMed:31320558). {ECO:0000250|UniProtKB:A7VJC2, ECO:0000269|PubMed:10567417, ECO:0000269|PubMed:24356509, ECO:0000269|PubMed:26321680, ECO:0000303|PubMed:19099192}.; FUNCTION: (Microbial infection) Involved in the transport of HIV-1 genomic RNA out of the nucleus, to the microtubule organizing center (MTOC), and then from the MTOC to the cytoplasm: acts by specifically recognizing and binding the A2RE (21 nucleotide hnRNP A2 response element) sequence motifs present on HIV-1 genomic RNA, and promotes its transport. {ECO:0000269|PubMed:15294897, ECO:0000269|PubMed:17004321}. | FUNCTION: Calcium-regulated non-lysosomal thiol-protease. Involved in membrane trafficking in the gastric surface mucus cells (pit cells) and may involve the membrane trafficking of mucus cells via interactions with coat protein. Proteolytically cleaves the beta-subunit of coatomer complex (By similarity). {ECO:0000250}. |
| 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. |
| - 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 |
| Tgene | CAPN8 | chr7:26240192 | chr1:223718212 | ENST00000366872 | 15 | 20 | 588_599 | 589.0 | 682.0 | Calcium binding | 1 | |
| Tgene | CAPN8 | chr7:26240192 | chr1:223718212 | ENST00000366872 | 15 | 20 | 618_629 | 589.0 | 682.0 | Calcium binding | 2 | |
| Tgene | CAPN8 | chr7:26240192 | chr1:223718212 | ENST00000366872 | 15 | 20 | 605_640 | 589.0 | 682.0 | Domain | EF-hand 2 | |
| Tgene | CAPN8 | chr7:26240192 | chr1:223718212 | ENST00000366872 | 15 | 20 | 670_703 | 589.0 | 682.0 | Domain | EF-hand 3 |
| - 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 |
| Hgene | HNRNPA2B1 | chr7:26240192 | chr1:223718212 | ENST00000354667 | - | 1 | 12 | 202_353 | 2.0 | 1115.3333333333333 | Compositional bias | Note=Gly-rich |
| Hgene | HNRNPA2B1 | chr7:26240192 | chr1:223718212 | ENST00000356674 | - | 1 | 11 | 202_353 | 2.0 | 439.3333333333333 | Compositional bias | Note=Gly-rich |
| Hgene | HNRNPA2B1 | chr7:26240192 | chr1:223718212 | ENST00000354667 | - | 1 | 12 | 112_191 | 2.0 | 1115.3333333333333 | Domain | RRM 2 |
| Hgene | HNRNPA2B1 | chr7:26240192 | chr1:223718212 | ENST00000354667 | - | 1 | 12 | 21_104 | 2.0 | 1115.3333333333333 | Domain | RRM 1 |
| Hgene | HNRNPA2B1 | chr7:26240192 | chr1:223718212 | ENST00000356674 | - | 1 | 11 | 112_191 | 2.0 | 439.3333333333333 | Domain | RRM 2 |
| Hgene | HNRNPA2B1 | chr7:26240192 | chr1:223718212 | ENST00000356674 | - | 1 | 11 | 21_104 | 2.0 | 439.3333333333333 | Domain | RRM 1 |
| Hgene | HNRNPA2B1 | chr7:26240192 | chr1:223718212 | ENST00000354667 | - | 1 | 12 | 9_15 | 2.0 | 1115.3333333333333 | Motif | Nuclear localization signal |
| Hgene | HNRNPA2B1 | chr7:26240192 | chr1:223718212 | ENST00000356674 | - | 1 | 11 | 9_15 | 2.0 | 439.3333333333333 | Motif | Nuclear localization signal |
| Hgene | HNRNPA2B1 | chr7:26240192 | chr1:223718212 | ENST00000354667 | - | 1 | 12 | 193_353 | 2.0 | 1115.3333333333333 | Region | Low complexity (LC) region |
| Hgene | HNRNPA2B1 | chr7:26240192 | chr1:223718212 | ENST00000354667 | - | 1 | 12 | 308_347 | 2.0 | 1115.3333333333333 | Region | Nuclear targeting sequence |
| Hgene | HNRNPA2B1 | chr7:26240192 | chr1:223718212 | ENST00000356674 | - | 1 | 11 | 193_353 | 2.0 | 439.3333333333333 | Region | Low complexity (LC) region |
| Hgene | HNRNPA2B1 | chr7:26240192 | chr1:223718212 | ENST00000356674 | - | 1 | 11 | 308_347 | 2.0 | 439.3333333333333 | Region | Nuclear targeting sequence |
| Tgene | CAPN8 | chr7:26240192 | chr1:223718212 | ENST00000366872 | 15 | 20 | 45_344 | 589.0 | 682.0 | Domain | Calpain catalytic | |
| Tgene | CAPN8 | chr7:26240192 | chr1:223718212 | ENST00000366872 | 15 | 20 | 575_610 | 589.0 | 682.0 | Domain | EF-hand 1 | |
| Tgene | CAPN8 | chr7:26240192 | chr1:223718212 | ENST00000366872 | 15 | 20 | 356_379 | 589.0 | 682.0 | Region | Note=Domain III |
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Fusion Protein Structures |
| PDB and CIF files of the predicted fusion proteins * Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| Fusion protein PDB link (fusion AA seq ID in FusionPDB) | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | AA seq | Len(AA seq) |
| PDB file >>>19_HNRNPA2B1_26240192_CAPN8_223718212_ranked_0.pdb | HNRNPA2B1 | 26240192 | 26240192 | ENST00000366872 | CAPN8 | chr1 | 223718212 | - | MEEIYWETDYNHSGTIDAHEMRTALRKAGFTLNSQVQQTIALRYACSKLGINFDSFVACMIRLETLFKLFSLLDEDKDGMVQLSLAEWLC | 94 |
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pLDDT score distribution |
| pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
HNRNPA2B1_pLDDT.png  |
CAPN8_pLDDT.png  |
| pLDDT score distribution of the predicted fusion protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
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Ramachandran Plot of Fusion Protein Structure |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide. |
| Fusion AA seq ID in FusionPDB and their Ramachandran plots |
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Fusion Protein-Protein Interaction |
| 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 from validated records (BIOGRID-3.4.160) |
| Gene | PPI interactors |
| Protein-protein interactors based on sequence similarity (STRING) |
| Gene | STRING network |
| HNRNPA2B1 | |
| CAPN8 |
| - Retained interactions in fusion protein (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost interactions due to fusion (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs to HNRNPA2B1-CAPN8 |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to HNRNPA2B1-CAPN8 |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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