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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:CLEC16A-GRIN2A (FusionGDB2 ID:17075)

Fusion Gene Summary for CLEC16A-GRIN2A

check button Fusion gene summary
Fusion gene informationFusion gene name: CLEC16A-GRIN2A
Fusion gene ID: 17075
HgeneTgene
Gene symbol

CLEC16A

GRIN2A

Gene ID

23274

2903

Gene nameC-type lectin domain containing 16Aglutamate ionotropic receptor NMDA type subunit 2A
SynonymsGop-1|KIAA0350EPND|FESD|GluN2A|LKS|NMDAR2A|NR2A
Cytomap

16p13.13

16p13.2

Type of geneprotein-codingprotein-coding
Descriptionprotein CLEC16AC-type lectin domain family 16 member Aglutamate 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 2A
Modification date2020031320200313
UniProtAcc

Q2KHT3

Q12879

Ensembl transtripts involved in fusion geneENST00000465491, ENST00000409552, 
ENST00000409790, ENST00000381822, 
ENST00000396573, ENST00000562109, 
ENST00000330684, ENST00000396575, 
ENST00000404927, ENST00000535259, 
ENST00000566670, 
Fusion gene scores* DoF score13 X 9 X 9=10538 X 7 X 5=280
# samples 168
** MAII scorelog2(16/1053*10)=-2.71836162613835
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/280*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLEC16A [Title/Abstract] AND GRIN2A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLEC16A(11154879)-GRIN2A(10032408), # samples:2
Anticipated loss of major functional domain due to fusion event.CLEC16A-GRIN2A seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
CLEC16A-GRIN2A seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
CLEC16A-GRIN2A seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CLEC16A-GRIN2A seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgeneGRIN2A

GO:0045471

response to ethanol

18445116

TgeneGRIN2A

GO:0097553

calcium ion transmembrane import into cytosol

26875626


check buttonFusion gene breakpoints across CLEC16A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across GRIN2A (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4BRCATCGA-S3-AA0Z-01ACLEC16Achr16

11154879

-GRIN2Achr16

10032408

-
ChimerDB4BRCATCGA-S3-AA0Z-01ACLEC16Achr16

11154879

+GRIN2Achr16

10032408

-


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Fusion Gene ORF analysis for CLEC16A-GRIN2A

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
3UTR-3CDSENST00000465491ENST00000396573CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
3UTR-3CDSENST00000465491ENST00000562109CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
3UTR-5UTRENST00000465491ENST00000330684CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
3UTR-5UTRENST00000465491ENST00000396575CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
3UTR-5UTRENST00000465491ENST00000404927CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
3UTR-5UTRENST00000465491ENST00000535259CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
3UTR-5UTRENST00000465491ENST00000566670CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
5CDS-5UTRENST00000409552ENST00000330684CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
5CDS-5UTRENST00000409552ENST00000396575CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
5CDS-5UTRENST00000409552ENST00000404927CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
5CDS-5UTRENST00000409552ENST00000535259CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
5CDS-5UTRENST00000409552ENST00000566670CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
5CDS-5UTRENST00000409790ENST00000330684CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
5CDS-5UTRENST00000409790ENST00000396575CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
5CDS-5UTRENST00000409790ENST00000404927CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
5CDS-5UTRENST00000409790ENST00000535259CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
5CDS-5UTRENST00000409790ENST00000566670CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
Frame-shiftENST00000409552ENST00000396573CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
Frame-shiftENST00000409552ENST00000562109CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
Frame-shiftENST00000409790ENST00000396573CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
Frame-shiftENST00000409790ENST00000562109CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
intron-3CDSENST00000381822ENST00000396573CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
intron-3CDSENST00000381822ENST00000562109CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
intron-5UTRENST00000381822ENST00000330684CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
intron-5UTRENST00000381822ENST00000396575CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
intron-5UTRENST00000381822ENST00000404927CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
intron-5UTRENST00000381822ENST00000535259CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-
intron-5UTRENST00000381822ENST00000566670CLEC16Achr16

11154879

+GRIN2Achr16

10032408

-

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 CLEC16A-GRIN2A


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for CLEC16A-GRIN2A


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/:11154879/:10032408)
- 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
CLEC16A

Q2KHT3

GRIN2A

Q12879

FUNCTION: Regulator of mitophagy through the upstream regulation of the RNF41/NRDP1-PRKN pathway. Mitophagy is a selective form of autophagy necessary for mitochondrial quality control. The RNF41/NRDP1-PRKN pathway regulates autophagosome-lysosome fusion during late mitophagy. May protect RNF41/NRDP1 from proteosomal degradation, RNF41/NRDP1 which regulates proteosomal degradation of PRKN. Plays a key role in beta cells functions by regulating mitophagy/autophagy and mitochondrial health. {ECO:0000269|PubMed:24949970}.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}.

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 CLEC16A-GRIN2A


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 CLEC16A-GRIN2A


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 CLEC16A-GRIN2A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for CLEC16A-GRIN2A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource