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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:PUM1-NLRC5 (FusionGDB2 ID:70236)

Fusion Gene Summary for PUM1-NLRC5

check button Fusion gene summary
Fusion gene informationFusion gene name: PUM1-NLRC5
Fusion gene ID: 70236
HgeneTgene
Gene symbol

PUM1

NLRC5

Gene ID

9698

84166

Gene namepumilio RNA binding family member 1NLR family CARD domain containing 5
SynonymsHSPUM|PUMH|PUMH1|PUML1|SCA47CLR16.1|NOD27|NOD4
Cytomap

1p35.2

16q13

Type of geneprotein-codingprotein-coding
Descriptionpumilio homolog 1pumilio-1protein NLRC5NOD-like receptor C5caterpiller protein 16.1nucleotide-binding oligomerization domain protein 4nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5nucleotide-binding oligomerization domains 27
Modification date2020031320200313
UniProtAcc.

Q86WI3

Ensembl transtripts involved in fusion geneENST00000424085, ENST00000257075, 
ENST00000373747, ENST00000426105, 
ENST00000440538, ENST00000373741, 
ENST00000423018, ENST00000373742, 
ENST00000490546, 		ENST00000262510, 
ENST00000436936, ENST00000308149, 
ENST00000543141, ENST00000539144, 
Fusion gene scores* DoF score38 X 31 X 15=176703 X 3 X 2=18
# samples 563
** MAII scorelog2(56/17670*10)=-4.97973140249401
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PUM1 [Title/Abstract] AND NLRC5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNLRC5(57063920)-PUM1(31448407), # samples:1
PUM1(31448407)-NLRC5(57063920), # 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
HgenePUM1

GO:0010608

posttranscriptional regulation of gene expression

25100735

HgenePUM1

GO:0043488

regulation of mRNA stability

26724866

HgenePUM1

GO:0051726

regulation of cell cycle

20818387

HgenePUM1

GO:0051983

regulation of chromosome segregation

26724866

HgenePUM1

GO:1900246

positive regulation of RIG-I signaling pathway

25340845

HgenePUM1

GO:2000637

positive regulation of gene silencing by miRNA

20818387|22345517

TgeneNLRC5

GO:0032088

negative regulation of NF-kappaB transcription factor activity

20434986

TgeneNLRC5

GO:0043549

regulation of kinase activity

20434986

TgeneNLRC5

GO:0045345

positive regulation of MHC class I biosynthetic process

20639463

TgeneNLRC5

GO:0045944

positive regulation of transcription by RNA polymerase II

20639463

TgeneNLRC5

GO:0060335

positive regulation of interferon-gamma-mediated signaling pathway

20061403

TgeneNLRC5

GO:0060339

negative regulation of type I interferon-mediated signaling pathway

20434986

TgeneNLRC5

GO:0060340

positive regulation of type I interferon-mediated signaling pathway

20061403


check buttonFusion gene breakpoints across PUM1 (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 NLRC5 (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
ChiTaRS5.0N/ADB332141PUM1chr1

31448407

+NLRC5chr16

57063920

-


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Fusion Gene ORF analysis for PUM1-NLRC5

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
intron-3CDSENST00000424085ENST00000262510PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000424085ENST00000436936PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000424085ENST00000308149PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000424085ENST00000543141PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000424085ENST00000539144PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000257075ENST00000262510PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000257075ENST00000436936PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000257075ENST00000308149PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000257075ENST00000543141PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000257075ENST00000539144PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000373747ENST00000262510PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000373747ENST00000436936PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000373747ENST00000308149PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000373747ENST00000543141PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000373747ENST00000539144PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000426105ENST00000262510PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000426105ENST00000436936PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000426105ENST00000308149PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000426105ENST00000543141PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000426105ENST00000539144PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000440538ENST00000262510PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000440538ENST00000436936PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000440538ENST00000308149PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000440538ENST00000543141PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000440538ENST00000539144PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000373741ENST00000262510PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000373741ENST00000436936PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000373741ENST00000308149PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000373741ENST00000543141PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000373741ENST00000539144PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000423018ENST00000262510PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000423018ENST00000436936PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000423018ENST00000308149PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000423018ENST00000543141PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000423018ENST00000539144PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000373742ENST00000262510PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000373742ENST00000436936PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000373742ENST00000308149PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000373742ENST00000543141PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000373742ENST00000539144PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000490546ENST00000262510PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000490546ENST00000436936PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-3CDSENST00000490546ENST00000308149PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000490546ENST00000543141PUM1chr1

31448407

+NLRC5chr16

57063920

-
intron-intronENST00000490546ENST00000539144PUM1chr1

31448407

+NLRC5chr16

57063920

-

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 PUM1-NLRC5


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 PUM1-NLRC5


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.NLRC5

Q86WI3

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Probable regulator of the NF-kappa-B and type I interferon signaling pathways. May also regulate the type II interferon signaling pathway. Plays a role in homeostatic control of innate immunity and in antiviral defense mechanisms. {ECO:0000269|PubMed:20061403, ECO:0000269|PubMed:20434986}.

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 PUM1-NLRC5


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 PUM1-NLRC5


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 PUM1-NLRC5


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 PUM1-NLRC5


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePUM1C0004134Ataxia1GENOMICS_ENGLAND
HgenePUM1C0010417Cryptorchidism1GENOMICS_ENGLAND
HgenePUM1C0019193Hepatitis, Toxic1CTD_human
HgenePUM1C0036572Seizures1GENOMICS_ENGLAND
HgenePUM1C0557874Global developmental delay1GENOMICS_ENGLAND
HgenePUM1C0860207Drug-Induced Liver Disease1CTD_human
HgenePUM1C1262760Hepatitis, Drug-Induced1CTD_human
HgenePUM1C3658290Drug-Induced Acute Liver Injury1CTD_human
HgenePUM1C3714756Intellectual Disability1GENOMICS_ENGLAND
HgenePUM1C4025871Abnormality of the face1GENOMICS_ENGLAND
HgenePUM1C4277682Chemical and Drug Induced Liver Injury1CTD_human
HgenePUM1C4279912Chemically-Induced Liver Toxicity1CTD_human
HgenePUM1C4693672SPINOCEREBELLAR ATAXIA 471GENOMICS_ENGLAND;UNIPROT
TgeneNLRC5C0023893Liver Cirrhosis, Experimental1CTD_human