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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:ZNF544-GRIN2D (FusionGDB2 ID:102330)

Fusion Gene Summary for ZNF544-GRIN2D

check button Fusion gene summary
Fusion gene informationFusion gene name: ZNF544-GRIN2D
Fusion gene ID: 102330
HgeneTgene
Gene symbol

ZNF544

GRIN2D

Gene ID

27300

2906

Gene namezinc finger protein 544glutamate ionotropic receptor NMDA type subunit 2D
Synonyms-EB11|EIEE46|GluN2D|NMDAR2D|NR2D
Cytomap

19q13.43

19q13.33

Type of geneprotein-codingprotein-coding
Descriptionzinc finger protein 544glutamate receptor ionotropic, NMDA 2DN-methyl D-aspartate receptor subtype 2DN-methyl-d-aspartate receptor subunit 2Destrogen receptor binding CpG islandglutamate [NMDA] receptor subunit epsilon-4glutamate receptor, ionotropic, N-methyl D-aspartate
Modification date2020031320200313
UniProtAcc.

O15399

Ensembl transtripts involved in fusion geneENST00000596597, ENST00000269829, 
ENST00000333581, ENST00000594384, 
ENST00000595981, ENST00000596652, 
ENST00000596825, ENST00000596929, 
ENST00000599227, ENST00000600044, 
ENST00000600220, ENST00000415203, 
ENST00000599953, 		ENST00000263269, 
Fusion gene scores* DoF score8 X 4 X 6=1925 X 9 X 5=225
# samples 118
** MAII scorelog2(11/192*10)=-0.803602787196497
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/225*10)=-1.49185309632967
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ZNF544 [Title/Abstract] AND GRIN2D [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointZNF544(58741828)-GRIN2D(48907991), # samples:3
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
TgeneGRIN2D

GO:0097553

calcium ion transmembrane import into cytosol

26875626


check buttonFusion gene breakpoints across ZNF544 (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 GRIN2D (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
ChimerDB4SKCMTCGA-D3-A2JE-06AZNF544chr19

58741828

-GRIN2Dchr19

48907991

+
ChimerDB4SKCMTCGA-D3-A2JE-06AZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
ChimerDB4SKCMTCGA-D3-A2JE-06AZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
ChimerDB4SKCMTCGA-D3-A2JEZNF544chr19

58741828

+GRIN2Dchr19

48907990

+


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Fusion Gene ORF analysis for ZNF544-GRIN2D

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-3CDSENST00000596597ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
3UTR-3CDSENST00000596597ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
3UTR-3CDSENST00000596597ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907990

+
5UTR-3CDSENST00000269829ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
5UTR-3CDSENST00000269829ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
5UTR-3CDSENST00000269829ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907990

+
5UTR-3CDSENST00000333581ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
5UTR-3CDSENST00000333581ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
5UTR-3CDSENST00000333581ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907990

+
5UTR-3CDSENST00000594384ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
5UTR-3CDSENST00000594384ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
5UTR-3CDSENST00000594384ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907990

+
5UTR-3CDSENST00000595981ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
5UTR-3CDSENST00000595981ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
5UTR-3CDSENST00000595981ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907990

+
5UTR-3CDSENST00000596652ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
5UTR-3CDSENST00000596652ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
5UTR-3CDSENST00000596652ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907990

+
5UTR-3CDSENST00000596825ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
5UTR-3CDSENST00000596825ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
5UTR-3CDSENST00000596825ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907990

+
5UTR-3CDSENST00000596929ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
5UTR-3CDSENST00000596929ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
5UTR-3CDSENST00000596929ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907990

+
5UTR-3CDSENST00000599227ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
5UTR-3CDSENST00000599227ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
5UTR-3CDSENST00000599227ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907990

+
5UTR-3CDSENST00000600044ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
5UTR-3CDSENST00000600044ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
5UTR-3CDSENST00000600044ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907990

+
5UTR-3CDSENST00000600220ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
5UTR-3CDSENST00000600220ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
5UTR-3CDSENST00000600220ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907990

+
intron-3CDSENST00000415203ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
intron-3CDSENST00000415203ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
intron-3CDSENST00000415203ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907990

+
intron-3CDSENST00000599953ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907991

+
intron-3CDSENST00000599953ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48917248

+
intron-3CDSENST00000599953ENST00000263269ZNF544chr19

58741828

+GRIN2Dchr19

48907990

+

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 ZNF544-GRIN2D


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)
ZNF544chr1958741828+GRIN2Dchr1948907990+1.99E-121
ZNF544chr1958741828+GRIN2Dchr1948907990+1.99E-121
ZNF544chr1958741828+GRIN2Dchr1948917247+2.65E-101
ZNF544chr1958741828+GRIN2Dchr1948907990+1.99E-121
ZNF544chr1958741828+GRIN2Dchr1948907990+1.99E-121
ZNF544chr1958741828+GRIN2Dchr1948917247+2.65E-101

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.
genomic feature of top 1%

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Fusion Protein Features for ZNF544-GRIN2D


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/:58741828/:48907991)
- 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
.GRIN2D

O15399

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}.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:9489750, PubMed:27616483, PubMed:26875626, PubMed:28126851). Sensitivity to glutamate and channel kinetics depend on the subunit composition (PubMed:9489750). {ECO:0000269|PubMed:26875626, ECO:0000269|PubMed:27616483, ECO:0000269|PubMed:28095420, ECO:0000269|PubMed:28126851, ECO:0000269|PubMed:9489750}.

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 ZNF544-GRIN2D


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 ZNF544-GRIN2D


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 ZNF544-GRIN2D


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 ZNF544-GRIN2D


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