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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:MRPL21-SHANK2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: MRPL21-SHANK2
	FusionPDB ID: 54952
	FusionGDB2.0 ID: 54952
		Hgene	Tgene
	Gene symbol	MRPL21	SHANK2
	Gene ID	219927	22941
	Gene name	mitochondrial ribosomal protein L21	SH3 and multiple ankyrin repeat domains 2
	Synonyms	L21mt\|MRP-L21	AUTS17\|CORTBP1\|CTTNBP1\|ProSAP1\|SHANK\|SPANK-3
	Cytomap	11q13.3	11q13.3-q13.4
	Type of gene	protein-coding	protein-coding
	Description	39S ribosomal protein L21, mitochondrialmitochondrial large ribosomal subunit protein bL21m	SH3 and multiple ankyrin repeat domains protein 2GKAP/SAPAP interacting proteincortactin SH3 domain-binding proteincortactin-binding protein 1proline-rich synapse associated protein 1
	Modification date	20200313	20200326
	UniProtAcc	Q7Z2W9	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000362034, ENST00000450904, ENST00000567045,	ENST00000357171, ENST00000409530, ENST00000449116, ENST00000468619, ENST00000409161, ENST00000449833, ENST00000338508, ENST00000423696,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	12 X 14 X 10=1680	36 X 29 X 10=10440
	# samples	17	47
	** MAII score	log2(17/1680*10)=-3.30485458152842 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(47/10440*10)=-4.47331714489225 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: MRPL21 [Title/Abstract] AND SHANK2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	MRPL21(68660358)-SHANK2(70319544), # samples:3
Anticipated loss of major functional domain due to fusion event.	MRPL21-SHANK2 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. MRPL21-SHANK2 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. MRPL21-SHANK2 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. MRPL21-SHANK2 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. MRPL21-SHANK2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. MRPL21-SHANK2 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner

Gene

GO ID

GO term

PubMed ID

Fusion gene breakpoints across MRPL21 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across SHANK2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	HNSC	TCGA-F7-7848-01A	MRPL21	chr11	68660358	-	SHANK2	chr11	70319544	-
ChimerDB4	HNSC	TCGA-F7-7848	MRPL21	chr11	68660357	-	SHANK2	chr11	70319544	-
ChimerDB4	HNSC	TCGA-F7-7848	MRPL21	chr11	68660358	-	SHANK2	chr11	70319544	-

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000450904	MRPL21	chr11	68660358	-	ENST00000449833	SHANK2	chr11	70319544	-	6126	542	486	1112	208
ENST00000450904	MRPL21	chr11	68660358	-	ENST00000409161	SHANK2	chr11	70319544	-	4549	542	486	1112	208
ENST00000362034	MRPL21	chr11	68660358	-	ENST00000423696	SHANK2	chr11	70319544	-	4568	563	507	1133	208
ENST00000362034	MRPL21	chr11	68660358	-	ENST00000338508	SHANK2	chr11	70319544	-	4568	563	507	1133	208
ENST00000450904	MRPL21	chr11	68660357	-	ENST00000449833	SHANK2	chr11	70319544	-	6126	542	486	1112	208
ENST00000450904	MRPL21	chr11	68660357	-	ENST00000409161	SHANK2	chr11	70319544	-	4549	542	486	1112	208
ENST00000362034	MRPL21	chr11	68660357	-	ENST00000423696	SHANK2	chr11	70319544	-	4568	563	507	1133	208
ENST00000362034	MRPL21	chr11	68660357	-	ENST00000338508	SHANK2	chr11	70319544	-	4568	563	507	1133	208

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000450904	ENST00000449833	MRPL21	chr11	68660358	-	SHANK2	chr11	70319544	-	0.003661255	0.9963387
ENST00000450904	ENST00000409161	MRPL21	chr11	68660358	-	SHANK2	chr11	70319544	-	0.006076434	0.9939236
ENST00000362034	ENST00000423696	MRPL21	chr11	68660358	-	SHANK2	chr11	70319544	-	0.005637704	0.99436224
ENST00000362034	ENST00000338508	MRPL21	chr11	68660358	-	SHANK2	chr11	70319544	-	0.005637704	0.99436224
ENST00000450904	ENST00000449833	MRPL21	chr11	68660357	-	SHANK2	chr11	70319544	-	0.003661255	0.9963387
ENST00000450904	ENST00000409161	MRPL21	chr11	68660357	-	SHANK2	chr11	70319544	-	0.006076434	0.9939236
ENST00000362034	ENST00000423696	MRPL21	chr11	68660357	-	SHANK2	chr11	70319544	-	0.005637704	0.99436224
ENST00000362034	ENST00000338508	MRPL21	chr11	68660357	-	SHANK2	chr11	70319544	-	0.005637704	0.99436224

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Fusion Amino Acid Sequences

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

>54952_54952_1_MRPL21-SHANK2_MRPL21_chr11_68660357_ENST00000362034_SHANK2_chr11_70319544_ENST00000338508_length(amino acids)=208AA_BP=19
MAKNHYEIQEKEKLQEEKKSPEIMSTISGTRSTTVTFTVRPGTSQPITLQSRPPDYESRTSGTRRAPSPVVSPTEMNKETLPAPLSAATA
SPSPALSDVFSLPSQPPSGDLFGLNPAGRSRSPSPSILQQPISNKPFTTKPVHLWTKPDVADWLESLNLGEHKEAFMDNEIDGSHLPNLQ

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

>54952_54952_2_MRPL21-SHANK2_MRPL21_chr11_68660357_ENST00000362034_SHANK2_chr11_70319544_ENST00000423696_length(amino acids)=208AA_BP=19
MAKNHYEIQEKEKLQEEKKSPEIMSTISGTRSTTVTFTVRPGTSQPITLQSRPPDYESRTSGTRRAPSPVVSPTEMNKETLPAPLSAATA
SPSPALSDVFSLPSQPPSGDLFGLNPAGRSRSPSPSILQQPISNKPFTTKPVHLWTKPDVADWLESLNLGEHKEAFMDNEIDGSHLPNLQ

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

>54952_54952_3_MRPL21-SHANK2_MRPL21_chr11_68660357_ENST00000450904_SHANK2_chr11_70319544_ENST00000409161_length(amino acids)=208AA_BP=19
MAKNHYEIQEKEKLQEEKKSPEIMSTISGTRSTTVTFTVRPGTSQPITLQSRPPDYESRTSGTRRAPSPVVSPTEMNKETLPAPLSAATA
SPSPALSDVFSLPSQPPSGDLFGLNPAGRSRSPSPSILQQPISNKPFTTKPVHLWTKPDVADWLESLNLGEHKEAFMDNEIDGSHLPNLQ

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

>54952_54952_4_MRPL21-SHANK2_MRPL21_chr11_68660357_ENST00000450904_SHANK2_chr11_70319544_ENST00000449833_length(amino acids)=208AA_BP=19
MAKNHYEIQEKEKLQEEKKSPEIMSTISGTRSTTVTFTVRPGTSQPITLQSRPPDYESRTSGTRRAPSPVVSPTEMNKETLPAPLSAATA
SPSPALSDVFSLPSQPPSGDLFGLNPAGRSRSPSPSILQQPISNKPFTTKPVHLWTKPDVADWLESLNLGEHKEAFMDNEIDGSHLPNLQ

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

>54952_54952_5_MRPL21-SHANK2_MRPL21_chr11_68660358_ENST00000362034_SHANK2_chr11_70319544_ENST00000338508_length(amino acids)=208AA_BP=19
MAKNHYEIQEKEKLQEEKKSPEIMSTISGTRSTTVTFTVRPGTSQPITLQSRPPDYESRTSGTRRAPSPVVSPTEMNKETLPAPLSAATA
SPSPALSDVFSLPSQPPSGDLFGLNPAGRSRSPSPSILQQPISNKPFTTKPVHLWTKPDVADWLESLNLGEHKEAFMDNEIDGSHLPNLQ

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

>54952_54952_6_MRPL21-SHANK2_MRPL21_chr11_68660358_ENST00000362034_SHANK2_chr11_70319544_ENST00000423696_length(amino acids)=208AA_BP=19
MAKNHYEIQEKEKLQEEKKSPEIMSTISGTRSTTVTFTVRPGTSQPITLQSRPPDYESRTSGTRRAPSPVVSPTEMNKETLPAPLSAATA
SPSPALSDVFSLPSQPPSGDLFGLNPAGRSRSPSPSILQQPISNKPFTTKPVHLWTKPDVADWLESLNLGEHKEAFMDNEIDGSHLPNLQ

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

>54952_54952_7_MRPL21-SHANK2_MRPL21_chr11_68660358_ENST00000450904_SHANK2_chr11_70319544_ENST00000409161_length(amino acids)=208AA_BP=19
MAKNHYEIQEKEKLQEEKKSPEIMSTISGTRSTTVTFTVRPGTSQPITLQSRPPDYESRTSGTRRAPSPVVSPTEMNKETLPAPLSAATA
SPSPALSDVFSLPSQPPSGDLFGLNPAGRSRSPSPSILQQPISNKPFTTKPVHLWTKPDVADWLESLNLGEHKEAFMDNEIDGSHLPNLQ

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

>54952_54952_8_MRPL21-SHANK2_MRPL21_chr11_68660358_ENST00000450904_SHANK2_chr11_70319544_ENST00000449833_length(amino acids)=208AA_BP=19
MAKNHYEIQEKEKLQEEKKSPEIMSTISGTRSTTVTFTVRPGTSQPITLQSRPPDYESRTSGTRRAPSPVVSPTEMNKETLPAPLSAATA
SPSPALSDVFSLPSQPPSGDLFGLNPAGRSRSPSPSILQQPISNKPFTTKPVHLWTKPDVADWLESLNLGEHKEAFMDNEIDGSHLPNLQ

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

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr11:68660358/chr11:70319544)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
MRPL21 Q7Z2W9	.
	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.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Tgene

SHANK2

chr11:68660357

chr11:70319544

ENST00000423696

1407_1470

1280.6666666666667

1471.0

Domain

SAM

Tgene

SHANK2

chr11:68660357

chr11:70319544

ENST00000449833

1407_1470

1064.6666666666667

1255.0

Domain

SAM

Tgene

SHANK2

chr11:68660358

chr11:70319544

ENST00000423696

1407_1470

1280.6666666666667

1471.0

Domain

SAM

Tgene

SHANK2

chr11:68660358

chr11:70319544

ENST00000449833

1407_1470

1064.6666666666667

1255.0

Domain

SAM

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Tgene

SHANK2

chr11:68660357

chr11:70319544

ENST00000423696

509_535

1280.6666666666667

1471.0

Compositional bias

Note=Pro-rich

Tgene

SHANK2

chr11:68660357

chr11:70319544

ENST00000449833

509_535

1064.6666666666667

1255.0

Compositional bias

Note=Pro-rich

Tgene

SHANK2

chr11:68660358

chr11:70319544

ENST00000423696

509_535

1280.6666666666667

1471.0

Compositional bias

Note=Pro-rich

Tgene

SHANK2

chr11:68660358

chr11:70319544

ENST00000449833

509_535

1064.6666666666667

1255.0

Compositional bias

Note=Pro-rich

Tgene

SHANK2

chr11:68660357

chr11:70319544

ENST00000423696

147_206

1280.6666666666667

1471.0

Domain

SH3

Tgene

SHANK2

chr11:68660357

chr11:70319544

ENST00000423696

247_341

1280.6666666666667

1471.0

Domain

PDZ

Tgene

SHANK2

chr11:68660357

chr11:70319544

ENST00000449833

147_206

1064.6666666666667

1255.0

Domain

SH3

Tgene

SHANK2

chr11:68660357

chr11:70319544

ENST00000449833

247_341

1064.6666666666667

1255.0

Domain

PDZ

Tgene

SHANK2

chr11:68660358

chr11:70319544

ENST00000423696

147_206

1280.6666666666667

1471.0

Domain

SH3

Tgene

SHANK2

chr11:68660358

chr11:70319544

ENST00000423696

247_341

1280.6666666666667

1471.0

Domain

PDZ

Tgene

SHANK2

chr11:68660358

chr11:70319544

ENST00000449833

147_206

1064.6666666666667

1255.0

Domain

SH3

Tgene

SHANK2

chr11:68660358

chr11:70319544

ENST00000449833

247_341

1064.6666666666667

1255.0

Domain

PDZ

Tgene

SHANK2

chr11:68660357

chr11:70319544

ENST00000423696

948_954

1280.6666666666667

1471.0

Motif

SH3-binding

Tgene

SHANK2

chr11:68660357

chr11:70319544

ENST00000449833

948_954

1064.6666666666667

1255.0

Motif

SH3-binding

Tgene

SHANK2

chr11:68660358

chr11:70319544

ENST00000423696

948_954

1280.6666666666667

1471.0

Motif

SH3-binding

Tgene

SHANK2

chr11:68660358

chr11:70319544

ENST00000449833

948_954

1064.6666666666667

1255.0

Motif

SH3-binding

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>300_MRPL21_68660358_SHANK2_70319544_ranked_0.pdb	MRPL21	68660357	68660358	ENST00000338508	SHANK2	chr11	70319544	-	MAKNHYEIQEKEKLQEEKKSPEIMSTISGTRSTTVTFTVRPGTSQPITLQSRPPDYESRTSGTRRAPSPVVSPTEMNKETLPAPLSAATA SPSPALSDVFSLPSQPPSGDLFGLNPAGRSRSPSPSILQQPISNKPFTTKPVHLWTKPDVADWLESLNLGEHKEAFMDNEIDGSHLPNLQ	208

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

MRPL21_pLDDT.png

SHANK2_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
MRPL21
SHANK2

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to MRPL21-SHANK2

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to MRPL21-SHANK2

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source