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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:MTR-TSC22D1 (FusionGDB2 ID:HG4548TG8848)

Fusion Gene Summary for MTR-TSC22D1

check button Fusion gene summary
Fusion gene informationFusion gene name: MTR-TSC22D1
Fusion gene ID: hg4548tg8848
HgeneTgene
Gene symbol

MTR

TSC22D1

Gene ID

4548

8848

Gene name5-methyltetrahydrofolate-homocysteine methyltransferaseTSC22 domain family member 1
SynonymsHMAG|MS|cblGPtg-2|TGFB1I4|TSC22
Cytomap('MTR')('TSC22D1')

1q43

13q14.11

Type of geneprotein-codingprotein-coding
Descriptionmethionine synthase5-methyltetrahydrofolate-homocysteine methyltransferase 1cobalamin-dependent methionine synthasevitamin-B12 dependent methionine synthaseTSC22 domain family protein 1TGFB-stimulated clone 22 homologTGFbeta-stimulated clone 22cerebral protein 2regulatory protein TSC-22transcriptional regulator TSC-22transforming growth factor beta-1-induced transcript 4 proteintransforming growth fac
Modification date2020031320200313
UniProtAcc

Q99707

.
Ensembl transtripts involved in fusion geneENST00000366577, ENST00000418145, 
ENST00000470570, ENST00000535889, 
Fusion gene scores* DoF score6 X 6 X 3=10824 X 20 X 7=3360
# samples 728
** MAII scorelog2(7/108*10)=-0.625604485218502
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(28/3360*10)=-3.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MTR [Title/Abstract] AND TSC22D1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMTR(237034799)-TSC22D1(45007664), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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


check button Fusion gene information
* 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


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Fusion Gene ORF analysis for MTR-TSC22D1

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

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

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Fusion Genomic Features for MTR-TSC22D1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for MTR-TSC22D1


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/:237034799/:45007664)
- 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
MTR

Q99707

.
FUNCTION: Catalyzes the transfer of a methyl group from methylcob(III)alamin (MeCbl) to homocysteine, yielding enzyme-bound cob(I)alamin and methionine in the cytosol (PubMed:27771510). MeCbl is an active form of cobalamin (vitamin B12) used as a cofactor for methionine biosynthesis. Cob(I)alamin form is regenerated to MeCbl by a transfer of a methyl group from 5-methyltetrahydrofolate (PubMed:27771510). The processing of cobalamin in the cytosol occurs in a multiprotein complex composed of at least MMACHC, MMADHC, MTRR (methionine synthase reductase) and MTR which may contribute to shuttle safely and efficiently cobalamin towards MTR in order to produce methionine (PubMed:27771510). {ECO:0000269|PubMed:27771510, ECO:0000303|PubMed:27771510}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for MTR-TSC22D1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for MTR-TSC22D1


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 (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for MTR-TSC22D1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneMTRQ99707DB00200HydroxocobalaminCofactorSmall moleculeApproved
HgeneMTRQ99707DB11590ThimerosalAntagonistSmall moleculeApproved
HgeneMTRQ99707DB03614MecobalaminCofactorSmall moleculeApproved|Investigational
HgeneMTRQ99707DB00115CyanocobalaminCofactorSmall moleculeApproved|Nutraceutical
HgeneMTRQ99707DB00134MethionineProduct ofSmall moleculeApproved|Nutraceutical

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Related Diseases for MTR-TSC22D1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMTRC1855128Methylcobalamin Deficiency, CblG Type5CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneMTRC0011570Mental Depression2PSYGENET
HgeneMTRC0011581Depressive disorder2PSYGENET
HgeneMTRC0013221Drug toxicity2CTD_human
HgeneMTRC0041755Adverse reaction to drug2CTD_human
HgeneMTRC0001969Alcoholic Intoxication1PSYGENET
HgeneMTRC0005586Bipolar Disorder1PSYGENET
HgeneMTRC0006142Malignant neoplasm of breast1CTD_human
HgeneMTRC0008924Cleft upper lip1CTD_human
HgeneMTRC0008925Cleft Palate1CTD_human
HgeneMTRC0017178Gastrointestinal Diseases1CTD_human
HgeneMTRC0018939Hematological Disease1CTD_human
HgeneMTRC0021364Male infertility1CTD_human
HgeneMTRC0024299Lymphoma1CTD_human
HgeneMTRC0024301Lymphoma, Follicular1CTD_human
HgeneMTRC0036341Schizophrenia1PSYGENET
HgeneMTRC0036572Seizures1GENOMICS_ENGLAND
HgeneMTRC0079745Lymphoma, Large-Cell, Follicular1CTD_human
HgeneMTRC0079758Lymphoma, Mixed-Cell, Follicular1CTD_human
HgeneMTRC0079765Lymphoma, Small Cleaved-Cell, Follicular1CTD_human
HgeneMTRC0162429Malnutrition1CTD_human
HgeneMTRC0268611Arakawa syndrome 21GENOMICS_ENGLAND
HgeneMTRC0270612Leukoencephalopathy1CTD_human
HgeneMTRC0559031Functional Gastrointestinal Disorders1CTD_human
HgeneMTRC0588008Severe depression1PSYGENET
HgeneMTRC0678222Breast Carcinoma1CTD_human
HgeneMTRC0848676Subfertility, Male1CTD_human
HgeneMTRC0917731Male sterility1CTD_human
HgeneMTRC1257931Mammary Neoplasms, Human1CTD_human
HgeneMTRC1458155Mammary Neoplasms1CTD_human
HgeneMTRC1565321Cholera Infantum1CTD_human
HgeneMTRC1837218Cleft palate, isolated1CTD_human
HgeneMTRC1858991Childhood Ataxia with Central Nervous System Hypomyelinization1CTD_human
HgeneMTRC1866558Neural tube defect, folate-sensitive1CTD_human;GENOMICS_ENGLAND
HgeneMTRC1956130Lymphoma, Follicular, Grade 11CTD_human
HgeneMTRC1956131Lymphoma, Follicular, Grade 31CTD_human
HgeneMTRC1956132Lymphoma, Follicular, Grade 21CTD_human
HgeneMTRC4704874Mammary Carcinoma, Human1CTD_human
TgeneC0019207Hepatoma, Morris2CTD_human
TgeneC0019208Hepatoma, Novikoff2CTD_human
TgeneC0023904Liver Neoplasms, Experimental2CTD_human
TgeneC0086404Experimental Hepatoma2CTD_human
TgeneC0007097Carcinoma1CTD_human
TgeneC0007621Neoplastic Cell Transformation1CTD_human
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0024667Animal Mammary Neoplasms1CTD_human
TgeneC0024668Mammary Neoplasms, Experimental1CTD_human
TgeneC0205696Anaplastic carcinoma1CTD_human
TgeneC0205697Carcinoma, Spindle-Cell1CTD_human
TgeneC0205698Undifferentiated carcinoma1CTD_human
TgeneC0205699Carcinomatosis1CTD_human
TgeneC1257925Mammary Carcinoma, Animal1CTD_human