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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:GRIN2A-MTHFD1L

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: GRIN2A-MTHFD1L
FusionPDB ID: 34807
FusionGDB2.0 ID: 34807
HgeneTgene
Gene symbol

GRIN2A

MTHFD1L

Gene ID

2903

25902

Gene nameglutamate ionotropic receptor NMDA type subunit 2Amethylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like
SynonymsEPND|FESD|GluN2A|LKS|NMDAR2A|NR2AFTHFSDC1|MTC1THFS|dJ292B18.2
Cytomap

16p13.2

6q25.1

Type of geneprotein-codingprotein-coding
Descriptionglutamate receptor ionotropic, NMDA 2AN-methyl D-aspartate receptor subtype 2AN-methyl-D-aspartate receptor channel, subunit epsilon-1N-methyl-D-aspartate receptor subunit 2Aglutamate receptor, ionotropic, N-methyl D-aspartate 2Amonofunctional C1-tetrahydrofolate synthase, mitochondrial10-formyl-THF synthetaseformyltetrahydrofolate synthetase domain containing 1
Modification date2020031320200313
UniProtAcc

Q12879

Q6UB35

Ensembl transtripts involved in fusion geneENST idsENST00000330684, ENST00000396573, 
ENST00000396575, ENST00000404927, 
ENST00000535259, ENST00000562109, 
ENST00000566670, 		ENST00000367307, 
ENST00000478643, ENST00000367321, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score8 X 7 X 5=28014 X 17 X 13=3094
# samples 727
** MAII scorelog2(7/280*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(27/3094*10)=-3.51844188439821
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: GRIN2A [Title/Abstract] AND MTHFD1L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)GRIN2A(10031816)-MTHFD1L(151413603), # samples:1
Anticipated loss of major functional domain due to fusion event.GRIN2A-MTHFD1L 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.
GRIN2A-MTHFD1L 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.
GRIN2A-MTHFD1L 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.
GRIN2A-MTHFD1L 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.
GRIN2A-MTHFD1L seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
GRIN2A-MTHFD1L seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
GRIN2A-MTHFD1L seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
GRIN2A-MTHFD1L seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
GRIN2A-MTHFD1L seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
GRIN2A-MTHFD1L seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted 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
HgeneGRIN2A

GO:0045471

response to ethanol

18445116

HgeneGRIN2A

GO:0097553

calcium ion transmembrane import into cytosol

26875626

TgeneMTHFD1L

GO:0006760

folic acid-containing compound metabolic process

12937168

TgeneMTHFD1L

GO:0009257

10-formyltetrahydrofolate biosynthetic process

12937168

TgeneMTHFD1L

GO:0015942

formate metabolic process

16171773


check buttonFusion gene breakpoints across GRIN2A (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 MTHFD1L (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
ChimerDB4SARCTCGA-SI-A71O-01AGRIN2Achr16

10031816

-MTHFD1Lchr6

151413603

+


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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)
ENST00000562109GRIN2Achr1610031816-ENST00000367321MTHFD1Lchr6151413603+15111028211031336
ENST00000396575GRIN2Achr1610031816-ENST00000367321MTHFD1Lchr6151413603+1490100701010336

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
ENST00000562109ENST00000367321GRIN2Achr1610031816-MTHFD1Lchr6151413603+0.0018214750.9981785
ENST00000396575ENST00000367321GRIN2Achr1610031816-MTHFD1Lchr6151413603+0.0017146130.99828535

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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

>34807_34807_1_GRIN2A-MTHFD1L_GRIN2A_chr16_10031816_ENST00000396575_MTHFD1L_chr6_151413603_ENST00000367321_length(amino acids)=336AA_BP=
MGRVGYWTLLVLPALLVWRGPAPSAAAEKGPPALNIAVMLGHSHDVTERELRTLWGPEQAAGLPLDVNVVALLMNRTDPKSLITHVCDLM
SGARIHGLVFGDDTDQEAVAQMLDFISSHTFVPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGY
REFISFVKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPK

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

>34807_34807_2_GRIN2A-MTHFD1L_GRIN2A_chr16_10031816_ENST00000562109_MTHFD1L_chr6_151413603_ENST00000367321_length(amino acids)=336AA_BP=
MGRVGYWTLLVLPALLVWRGPAPSAAAEKGPPALNIAVMLGHSHDVTERELRTLWGPEQAAGLPLDVNVVALLMNRTDPKSLITHVCDLM
SGARIHGLVFGDDTDQEAVAQMLDFISSHTFVPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGY
REFISFVKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPK

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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/chr16:10031816/chr6:151413603)
- 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
GRIN2A

Q12879

MTHFD1L

Q6UB35

FUNCTION: Component of NMDA receptor complexes that function as heterotetrameric, ligand-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium. Channel activation requires binding of the neurotransmitter glutamate to the epsilon subunit, glycine binding to the zeta subunit, plus membrane depolarization to eliminate channel inhibition by Mg(2+) (PubMed:8768735, PubMed:26919761, PubMed:26875626, PubMed:28105280). Sensitivity to glutamate and channel kinetics depend on the subunit composition; channels containing GRIN1 and GRIN2A have lower sensitivity to glutamate and faster deactivation kinetics than channels formed by GRIN1 and GRIN2B (PubMed:26919761, PubMed:26875626). Contributes to the slow phase of excitatory postsynaptic current, long-term synaptic potentiation, and learning (By similarity). {ECO:0000250|UniProtKB:P35436, ECO:0000250|UniProtKB:Q00959, ECO:0000269|PubMed:26875626, ECO:0000269|PubMed:26919761, ECO:0000269|PubMed:28105280, ECO:0000269|PubMed:8768735}.FUNCTION: May provide the missing metabolic reaction required to link the mitochondria and the cytoplasm in the mammalian model of one-carbon folate metabolism in embryonic an transformed cells complementing thus the enzymatic activities of MTHFD2. {ECO:0000250, ECO:0000269|PubMed:16171773}.

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
TgeneMTHFD1Lchr16:10031816chr6:151413603ENST000003673070834_420276.0Compositional biasNote=Poly-Gly
TgeneMTHFD1Lchr16:10031816chr6:151413603ENST0000036730708423_4300276.0Nucleotide bindingATP
TgeneMTHFD1Lchr16:10031816chr6:151413603ENST000003673070831_3480276.0RegionNote=Methylenetetrahydrofolate dehydrogenase and cyclohydrolase
TgeneMTHFD1Lchr16:10031816chr6:151413603ENST0000036730708349_9780276.0RegionNote=Formyltetrahydrofolate synthetase

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-313601_620335.66666666666671465.0IntramembraneDiscontinuously helical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-414601_620335.66666666666671465.0IntramembraneDiscontinuously helical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-212601_620335.66666666666671465.0IntramembraneDiscontinuously helical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-314601_620335.66666666666671282.0IntramembraneDiscontinuously helical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-213601_620335.66666666666671282.0IntramembraneDiscontinuously helical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-3131462_1464335.66666666666671465.0MotifPDZ-binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-4141462_1464335.66666666666671465.0MotifPDZ-binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-2121462_1464335.66666666666671465.0MotifPDZ-binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-3141462_1464335.66666666666671282.0MotifPDZ-binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-2131462_1464335.66666666666671282.0MotifPDZ-binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-313511_513335.66666666666671465.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-313599_620335.66666666666671465.0RegionPore-forming
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-313689_690335.66666666666671465.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-313730_731335.66666666666671465.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-414511_513335.66666666666671465.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-414599_620335.66666666666671465.0RegionPore-forming
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-414689_690335.66666666666671465.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-414730_731335.66666666666671465.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-212511_513335.66666666666671465.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-212599_620335.66666666666671465.0RegionPore-forming
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-212689_690335.66666666666671465.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-212730_731335.66666666666671465.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-314511_513335.66666666666671282.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-314599_620335.66666666666671282.0RegionPore-forming
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-314689_690335.66666666666671282.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-314730_731335.66666666666671282.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-213511_513335.66666666666671282.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-213599_620335.66666666666671282.0RegionPore-forming
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-213689_690335.66666666666671282.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-213730_731335.66666666666671282.0RegionGlutamate binding
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-31323_555335.66666666666671465.0Topological domainExtracellular
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-313577_600335.66666666666671465.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-313621_625335.66666666666671465.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-313646_816335.66666666666671465.0Topological domainExtracellular
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-313838_1464335.66666666666671465.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-41423_555335.66666666666671465.0Topological domainExtracellular
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-414577_600335.66666666666671465.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-414621_625335.66666666666671465.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-414646_816335.66666666666671465.0Topological domainExtracellular
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-414838_1464335.66666666666671465.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-21223_555335.66666666666671465.0Topological domainExtracellular
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-212577_600335.66666666666671465.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-212621_625335.66666666666671465.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-212646_816335.66666666666671465.0Topological domainExtracellular
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-212838_1464335.66666666666671465.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-31423_555335.66666666666671282.0Topological domainExtracellular
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-314577_600335.66666666666671282.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-314621_625335.66666666666671282.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-314646_816335.66666666666671282.0Topological domainExtracellular
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-314838_1464335.66666666666671282.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-21323_555335.66666666666671282.0Topological domainExtracellular
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-213577_600335.66666666666671282.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-213621_625335.66666666666671282.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-213646_816335.66666666666671282.0Topological domainExtracellular
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-213838_1464335.66666666666671282.0Topological domainCytoplasmic
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-313556_576335.66666666666671465.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-313626_645335.66666666666671465.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000330684-313817_837335.66666666666671465.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-414556_576335.66666666666671465.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-414626_645335.66666666666671465.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396573-414817_837335.66666666666671465.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-212556_576335.66666666666671465.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-212626_645335.66666666666671465.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000396575-212817_837335.66666666666671465.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-314556_576335.66666666666671282.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-314626_645335.66666666666671282.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000404927-314817_837335.66666666666671282.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-213556_576335.66666666666671282.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-213626_645335.66666666666671282.0TransmembraneHelical
HgeneGRIN2Achr16:10031816chr6:151413603ENST00000562109-213817_837335.66666666666671282.0TransmembraneHelical
TgeneMTHFD1Lchr16:10031816chr6:151413603ENST00000367321252834_42949.0932.6666666666666Compositional biasNote=Poly-Gly
TgeneMTHFD1Lchr16:10031816chr6:151413603ENST000003673212528423_430949.0932.6666666666666Nucleotide bindingATP
TgeneMTHFD1Lchr16:10031816chr6:151413603ENST00000367321252831_348949.0932.6666666666666RegionNote=Methylenetetrahydrofolate dehydrogenase and cyclohydrolase
TgeneMTHFD1Lchr16:10031816chr6:151413603ENST000003673212528349_978949.0932.6666666666666RegionNote=Formyltetrahydrofolate synthetase


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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


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
GRIN2A
MTHFD1L


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 GRIN2A-MTHFD1L


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 GRIN2A-MTHFD1L


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