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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:METTL21A-PLEKHM3 (FusionGDB2 ID:52763)

Fusion Gene Summary for METTL21A-PLEKHM3

check button Fusion gene summary
Fusion gene informationFusion gene name: METTL21A-PLEKHM3
Fusion gene ID: 52763
HgeneTgene
Gene symbol

METTL21A

PLEKHM3

Gene ID

151194

389072

Gene namemethyltransferase like 21Apleckstrin homology domain containing M3
SynonymsFAM119A|HCA557b|HSPA-KMTDAPR|PLEKHM1L
Cytomap

2q33.3

2q33.3

Type of geneprotein-codingprotein-coding
Descriptionprotein N-lysine methyltransferase METTL21AHSPA lysine methyltransferasefamily with sequence similarity 119, member Aheat shock protein 70kDa lysine (K) methyltransferasehepatocellular carcinoma-associated antigen 557bmethyltransferase-like protein 2pleckstrin homology domain-containing family M member 3PH domain-containing family M member 3differentiation associated protein
Modification date2020032820200313
UniProtAcc

Q8WXB1

.
Ensembl transtripts involved in fusion geneENST00000432416, ENST00000458426, 
ENST00000425132, ENST00000477919, 
ENST00000411432, ENST00000448007, 
ENST00000272839, ENST00000448823, 
ENST00000406927, ENST00000426075, 
ENST00000442521, 		ENST00000427836, 
ENST00000389247, ENST00000457206, 
Fusion gene scores* DoF score5 X 4 X 3=607 X 4 X 5=140
# samples 56
** MAII scorelog2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/140*10)=-1.22239242133645
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: METTL21A [Title/Abstract] AND PLEKHM3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMETTL21A(208486530)-PLEKHM3(208693220), # 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
HgeneMETTL21A

GO:0006479

protein methylation

22948820|23349634

HgeneMETTL21A

GO:0018022

peptidyl-lysine methylation

23921388

HgeneMETTL21A

GO:0043462

regulation of ATPase activity

23921388


check buttonFusion gene breakpoints across METTL21A (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 PLEKHM3 (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
ChimerDB4LUADTCGA-55-6969-01AMETTL21Achr2

208486530

-PLEKHM3chr2

208693220

-


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Fusion Gene ORF analysis for METTL21A-PLEKHM3

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
Frame-shiftENST00000432416ENST00000427836METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000432416ENST00000389247METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000432416ENST00000457206METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
Frame-shiftENST00000458426ENST00000427836METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000458426ENST00000389247METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000458426ENST00000457206METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
In-frameENST00000425132ENST00000427836METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000425132ENST00000389247METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000425132ENST00000457206METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
intron-3CDSENST00000477919ENST00000427836METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
intron-intronENST00000477919ENST00000389247METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
intron-intronENST00000477919ENST00000457206METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
Frame-shiftENST00000411432ENST00000427836METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000411432ENST00000389247METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000411432ENST00000457206METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
In-frameENST00000448007ENST00000427836METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000448007ENST00000389247METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000448007ENST00000457206METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
Frame-shiftENST00000272839ENST00000427836METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000272839ENST00000389247METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000272839ENST00000457206METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
intron-3CDSENST00000448823ENST00000427836METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
intron-intronENST00000448823ENST00000389247METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
intron-intronENST00000448823ENST00000457206METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
In-frameENST00000406927ENST00000427836METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000406927ENST00000389247METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000406927ENST00000457206METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
Frame-shiftENST00000426075ENST00000427836METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000426075ENST00000389247METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000426075ENST00000457206METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
Frame-shiftENST00000442521ENST00000427836METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000442521ENST00000389247METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-
5CDS-intronENST00000442521ENST00000457206METTL21Achr2

208486530

-PLEKHM3chr2

208693220

-

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)
ENST00000425132METTL21Achr2208486530-ENST00000427836PLEKHM3chr2208693220-597403117518133
ENST00000448007METTL21Achr2208486530-ENST00000427836PLEKHM3chr2208693220-62443096545149
ENST00000406927METTL21Achr2208486530-ENST00000427836PLEKHM3chr2208693220-596402116517133

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
ENST00000425132ENST00000427836METTL21Achr2208486530-PLEKHM3chr2208693220-0.0248874180.9751126
ENST00000448007ENST00000427836METTL21Achr2208486530-PLEKHM3chr2208693220-0.017061080.9829389
ENST00000406927ENST00000427836METTL21Achr2208486530-PLEKHM3chr2208693220-0.0252767760.97472316

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Fusion Genomic Features for METTL21A-PLEKHM3


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 METTL21A-PLEKHM3


check button Go to

FGviewer for the breakpoints of chr2:208486530-chr2:208693220

.
- 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
METTL21A

Q8WXB1

.
FUNCTION: Protein-lysine methyltransferase that selectively trimethylates residues in heat shock protein 70 (HSP70) family members. Contributes to the in vivo trimethylation of Lys residues in HSPA1 and HSPA8. In vitro methylates 'Lys-561' in HSPA1, 'Lys-564' in HSPA2, 'Lys-585' in HSPA5, 'Lys-563' in HSPA6 and 'Lys-561' in HSPA8. {ECO:0000269|PubMed:22948820, ECO:0000269|PubMed:23349634, ECO:0000269|PubMed:23921388}.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.

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
HgeneMETTL21Achr2:208486530chr2:208693220ENST00000406927-3473_7586.33333333333333219.0RegionS-adenosyl-L-methionine binding
HgeneMETTL21Achr2:208486530chr2:208693220ENST00000411432-3473_7586.33333333333333219.0RegionS-adenosyl-L-methionine binding
HgeneMETTL21Achr2:208486530chr2:208693220ENST00000425132-3473_7586.3333333333333391.0RegionS-adenosyl-L-methionine binding
HgeneMETTL21Achr2:208486530chr2:208693220ENST00000426075-2373_7586.33333333333333219.0RegionS-adenosyl-L-methionine binding
HgeneMETTL21Achr2:208486530chr2:208693220ENST00000442521-3473_7586.33333333333333219.0RegionS-adenosyl-L-methionine binding
HgeneMETTL21Achr2:208486530chr2:208693220ENST00000448007-3473_7586.33333333333333219.0RegionS-adenosyl-L-methionine binding
HgeneMETTL21Achr2:208486530chr2:208693220ENST00000458426-3473_7586.3333333333333391.0RegionS-adenosyl-L-methionine binding
TgenePLEKHM3chr2:208486530chr2:208693220ENST0000038924708169_1750718.0Compositional biasNote=Poly-Gln
TgenePLEKHM3chr2:208486530chr2:208693220ENST0000038924708211_3080718.0DomainPH 1
TgenePLEKHM3chr2:208486530chr2:208693220ENST0000038924708361_4560718.0DomainPH 2
TgenePLEKHM3chr2:208486530chr2:208693220ENST0000038924708669_7220718.0Zinc fingerNote=Phorbol-ester/DAG-type

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgenePLEKHM3chr2:208486530chr2:208693220ENST0000042783668169_175702.6666666666666762.0Compositional biasNote=Poly-Gln
TgenePLEKHM3chr2:208486530chr2:208693220ENST0000042783668211_308702.6666666666666762.0DomainPH 1
TgenePLEKHM3chr2:208486530chr2:208693220ENST0000042783668361_456702.6666666666666762.0DomainPH 2
TgenePLEKHM3chr2:208486530chr2:208693220ENST0000042783668669_722702.6666666666666762.0Zinc fingerNote=Phorbol-ester/DAG-type


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Fusion Gene Sequence for METTL21A-PLEKHM3


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.
>In-frame_ENST00000425132_ENST00000427836_TCGA-55-6969-01A_METTL21A_chr2_208486530_-_PLEKHM3_chr2_208693220_length(transcript)=597nt_BP=403nt
CGGGCCGGGGCCGCCCGCCCCCGCGTCGCGGGCTCTTTAAGGCCGGCGGTTTTCGCAGCCAGCCCGGGGCGGGGAAAGCGGAGCGCGCGC
TCCACGCGGGACCGCCTCCCGGGCCGTCTGAGCAGAGGGCGGGGTGCAGGCGGAATGGCCCTCGTGCCCTATGAGGAGACCACGGAATTT
GGGTTGCAGAAATTCCACAAGCCTCTTGCAACTTTTTCCTTTGCAAACCACACGATCCAGATCCGGCAGGACTGGAGACACCTGGGAGTC
GCAGCGGTGGTTTGGGATGCGGCCATCGTTCTTTCCACATACCTGGAGATGGGAGCTGTGGAGCTCAGGGGCCGCTCTGCCGTGGAGCTG
GGTGCTGGCACGGGGCTGGTGGGCATAGTGGCTGCCCTGCTGGGTGTGAAAGCTGTGGAGCCGTTTTCCATTCTGAATGCAAAGAAAAGT
CTGTCCCCTGCCCGAGGTGTGTTCGCCGAGAGCTGCAGAAGAAGCAGAAGTCTTTCTGGCAGAGACTGAACATGGACGAGAGTCTAGAGG

>In-frame_ENST00000425132_ENST00000427836_TCGA-55-6969-01A_METTL21A_chr2_208486530_-_PLEKHM3_chr2_208693220_length(amino acids)=133AA_start in transcript=117_stop in transcript=518
MSRGRGAGGMALVPYEETTEFGLQKFHKPLATFSFANHTIQIRQDWRHLGVAAVVWDAAIVLSTYLEMGAVELRGRSAVELGAGTGLVGI

--------------------------------------------------------------
>In-frame_ENST00000448007_ENST00000427836_TCGA-55-6969-01A_METTL21A_chr2_208486530_-_PLEKHM3_chr2_208693220_length(transcript)=624nt_BP=430nt
CCAGTGTCGCTCACTTCCAGGGTCGGGGAGACGGAACTGCGGCGACCATGTATTTCTGGTTTATCAAACCGCTAACACCCAGTCTAAGGG
CAGGTTCTGTCCCATTGTTATCACTATCGAAGCAGCCGATGGAGGAGGGGAGGTCTGAGCAGAGGGCGGGGTGCAGGCGGAATGGCCCTC
GTGCCCTATGAGGAGACCACGGAATTTGGGTTGCAGAAATTCCACAAGCCTCTTGCAACTTTTTCCTTTGCAAACCACACGATCCAGATC
CGGCAGGACTGGAGACACCTGGGAGTCGCAGCGGTGGTTTGGGATGCGGCCATCGTTCTTTCCACATACCTGGAGATGGGAGCTGTGGAG
CTCAGGGGCCGCTCTGCCGTGGAGCTGGGTGCTGGCACGGGGCTGGTGGGCATAGTGGCTGCCCTGCTGGGTGTGAAAGCTGTGGAGCCG
TTTTCCATTCTGAATGCAAAGAAAAGTCTGTCCCCTGCCCGAGGTGTGTTCGCCGAGAGCTGCAGAAGAAGCAGAAGTCTTTCTGGCAGA

>In-frame_ENST00000448007_ENST00000427836_TCGA-55-6969-01A_METTL21A_chr2_208486530_-_PLEKHM3_chr2_208693220_length(amino acids)=149AA_start in transcript=96_stop in transcript=545
MSHCYHYRSSRWRRGGLSRGRGAGGMALVPYEETTEFGLQKFHKPLATFSFANHTIQIRQDWRHLGVAAVVWDAAIVLSTYLEMGAVELR

--------------------------------------------------------------
>In-frame_ENST00000406927_ENST00000427836_TCGA-55-6969-01A_METTL21A_chr2_208486530_-_PLEKHM3_chr2_208693220_length(transcript)=596nt_BP=402nt
GGGCCGGGGCCGCCCGCCCCCGCGTCGCGGGCTCTTTAAGGCCGGCGGTTTTCGCAGCCAGCCCGGGGCGGGGAAAGCGGAGCGCGCGCT
CCACGCGGGACCGCCTCCCGGGCCGTCTGAGCAGAGGGCGGGGTGCAGGCGGAATGGCCCTCGTGCCCTATGAGGAGACCACGGAATTTG
GGTTGCAGAAATTCCACAAGCCTCTTGCAACTTTTTCCTTTGCAAACCACACGATCCAGATCCGGCAGGACTGGAGACACCTGGGAGTCG
CAGCGGTGGTTTGGGATGCGGCCATCGTTCTTTCCACATACCTGGAGATGGGAGCTGTGGAGCTCAGGGGCCGCTCTGCCGTGGAGCTGG
GTGCTGGCACGGGGCTGGTGGGCATAGTGGCTGCCCTGCTGGGTGTGAAAGCTGTGGAGCCGTTTTCCATTCTGAATGCAAAGAAAAGTC
TGTCCCCTGCCCGAGGTGTGTTCGCCGAGAGCTGCAGAAGAAGCAGAAGTCTTTCTGGCAGAGACTGAACATGGACGAGAGTCTAGAGGA

>In-frame_ENST00000406927_ENST00000427836_TCGA-55-6969-01A_METTL21A_chr2_208486530_-_PLEKHM3_chr2_208693220_length(amino acids)=133AA_start in transcript=116_stop in transcript=517
MSRGRGAGGMALVPYEETTEFGLQKFHKPLATFSFANHTIQIRQDWRHLGVAAVVWDAAIVLSTYLEMGAVELRGRSAVELGAGTGLVGI

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

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Fusion Gene PPI Analysis for METTL21A-PLEKHM3


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 METTL21A-PLEKHM3


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 METTL21A-PLEKHM3


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