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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:PRIM2-COL21A1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PRIM2-COL21A1
	FusionPDB ID: 68590
	FusionGDB2.0 ID: 68590
		Hgene	Tgene
	Gene symbol	PRIM2	COL21A1
	Gene ID	5558	81578
	Gene name	DNA primase subunit 2	collagen type XXI alpha 1 chain
	Synonyms	PRIM2A\|p58	COLA1L\|FP633
	Cytomap	6p11.2	6p12.1\|6p12.3-p11.2
	Type of gene	protein-coding	protein-coding
	Description	DNA primase large subunitDNA primase 58 kDa subunitprimase (DNA) subunit 2primase, DNA, polypeptide 2 (58kDa)	collagen alpha-1(XXI) chainalpha 1 chain-like collagencollagen, type XXI, alpha 1
	Modification date	20200313	20200320
	UniProtAcc	.	Q96P44
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000389488, ENST00000607273,	ENST00000244728, ENST00000370808, ENST00000370819, ENST00000535941, ENST00000467045,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	9 X 6 X 6=324	8 X 7 X 6=336
	# samples	10	10
	** MAII score	log2(10/324*10)=-1.6959938131099 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/336*10)=-1.74846123300404 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PRIM2 [Title/Abstract] AND COL21A1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PRIM2(57246966)-COL21A1(55929420), # samples:3
Anticipated loss of major functional domain due to fusion event.	PRIM2-COL21A1 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. PRIM2-COL21A1 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. PRIM2-COL21A1 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. PRIM2-COL21A1 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.

* 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 PRIM2 (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 COL21A1 (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	BRCA	TCGA-BH-A0BL-01A	PRIM2	chr6	57246966	+	COL21A1	chr6	55929420	-
ChimerDB4	BRCA	TCGA-BH-A0BL	PRIM2	chr6	57246966	+	COL21A1	chr6	55929420	-

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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)
ENST00000607273	PRIM2	chr6	57246966	+	ENST00000244728	COL21A1	chr6	55929420	-	2594	780	48	1526	492
ENST00000607273	PRIM2	chr6	57246966	+	ENST00000370819	COL21A1	chr6	55929420	-	2594	780	48	1526	492
ENST00000607273	PRIM2	chr6	57246966	+	ENST00000535941	COL21A1	chr6	55929420	-	2593	780	48	1526	492
ENST00000607273	PRIM2	chr6	57246966	+	ENST00000370808	COL21A1	chr6	55929420	-	2491	780	48	1424	458

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
ENST00000607273	ENST00000244728	PRIM2	chr6	57246966	+	COL21A1	chr6	55929420	-	0.000152323	0.99984765
ENST00000607273	ENST00000370819	PRIM2	chr6	57246966	+	COL21A1	chr6	55929420	-	0.000152323	0.99984765
ENST00000607273	ENST00000535941	PRIM2	chr6	57246966	+	COL21A1	chr6	55929420	-	0.000151232	0.9998487
ENST00000607273	ENST00000370808	PRIM2	chr6	57246966	+	COL21A1	chr6	55929420	-	0.000145453	0.99985456

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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

>68590_68590_1_PRIM2-COL21A1_PRIM2_chr6_57246966_ENST00000607273_COL21A1_chr6_55929420_ENST00000244728_length(amino acids)=492AA_BP=242
MCFPEFEFLQVTKMEFSGRKWRKLRLAGDQRNASYPHCLQFYLQPPSENISLIEFENLAIDRVKLLKSVENLGVSYVKGTEQYQSKLESE
LRKLKFSYRENLEDEYEPRRRDHISHFILRLAYCQSEELRRWFIQQEMDLLRFRFSILPKDKIQDFLKDSQLQFEAISDEEKTLREQEIV
ASSPSLSGLKLGFESIYKIPFADALDLFRGRKVYLEDGFAYVPLKDIVAIILNEFRAKLSKALAGQKGENGRQGIPGQQGIQGHHGAKGE
RGEKGEPGVRGAIGSKGESGVDGLMGPAGPKGQPGDPGPQGPPGLDGKPGREFSEQFIRQVCTDVIRAQLPVLLQSGRIRNCDHCLSQHG
SPGIPGPPGPIGPEGPRGLPGLPGRDGVPGLVGVPGRPGVRGLKGLPGRNGEKGSQGFGYPGEQGPPGPPGPEGPPGISKEGPPGDPGLP

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

>68590_68590_2_PRIM2-COL21A1_PRIM2_chr6_57246966_ENST00000607273_COL21A1_chr6_55929420_ENST00000370808_length(amino acids)=458AA_BP=242
MCFPEFEFLQVTKMEFSGRKWRKLRLAGDQRNASYPHCLQFYLQPPSENISLIEFENLAIDRVKLLKSVENLGVSYVKGTEQYQSKLESE
LRKLKFSYRENLEDEYEPRRRDHISHFILRLAYCQSEELRRWFIQQEMDLLRFRFSILPKDKIQDFLKDSQLQFEAISDEEKTLREQEIV
ASSPSLSGLKLGFESIYKIPFADALDLFRGRKVYLEDGFAYVPLKDIVAIILNEFRAKLSKALAGQKGENGRQGIPGQQGIQGHHGAKGE
RGEKGEPGVRGAIGSKGESGVDGLMGPAGPKGQPGDPGPQGPPGLDGKPGREFSEQFIRQVCTDVIRGPEGPRGLPGLPGRDGVPGLVGV
PGRPGVRGLKGLPGRNGEKGSQGFGYPGEQGPPGPPGPEGPPGISKEGPPGDPGLPGKDGDHGKPGIQGQPGPPGICDPSLCFSVIARRD

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

>68590_68590_3_PRIM2-COL21A1_PRIM2_chr6_57246966_ENST00000607273_COL21A1_chr6_55929420_ENST00000370819_length(amino acids)=492AA_BP=242
MCFPEFEFLQVTKMEFSGRKWRKLRLAGDQRNASYPHCLQFYLQPPSENISLIEFENLAIDRVKLLKSVENLGVSYVKGTEQYQSKLESE
LRKLKFSYRENLEDEYEPRRRDHISHFILRLAYCQSEELRRWFIQQEMDLLRFRFSILPKDKIQDFLKDSQLQFEAISDEEKTLREQEIV
ASSPSLSGLKLGFESIYKIPFADALDLFRGRKVYLEDGFAYVPLKDIVAIILNEFRAKLSKALAGQKGENGRQGIPGQQGIQGHHGAKGE
RGEKGEPGVRGAIGSKGESGVDGLMGPAGPKGQPGDPGPQGPPGLDGKPGREFSEQFIRQVCTDVIRAQLPVLLQSGRIRNCDHCLSQHG
SPGIPGPPGPIGPEGPRGLPGLPGRDGVPGLVGVPGRPGVRGLKGLPGRNGEKGSQGFGYPGEQGPPGPPGPEGPPGISKEGPPGDPGLP

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

>68590_68590_4_PRIM2-COL21A1_PRIM2_chr6_57246966_ENST00000607273_COL21A1_chr6_55929420_ENST00000535941_length(amino acids)=492AA_BP=242
MCFPEFEFLQVTKMEFSGRKWRKLRLAGDQRNASYPHCLQFYLQPPSENISLIEFENLAIDRVKLLKSVENLGVSYVKGTEQYQSKLESE
LRKLKFSYRENLEDEYEPRRRDHISHFILRLAYCQSEELRRWFIQQEMDLLRFRFSILPKDKIQDFLKDSQLQFEAISDEEKTLREQEIV
ASSPSLSGLKLGFESIYKIPFADALDLFRGRKVYLEDGFAYVPLKDIVAIILNEFRAKLSKALAGQKGENGRQGIPGQQGIQGHHGAKGE
RGEKGEPGVRGAIGSKGESGVDGLMGPAGPKGQPGDPGPQGPPGLDGKPGREFSEQFIRQVCTDVIRAQLPVLLQSGRIRNCDHCLSQHG
SPGIPGPPGPIGPEGPRGLPGLPGRDGVPGLVGVPGRPGVRGLKGLPGRNGEKGSQGFGYPGEQGPPGPPGPEGPPGISKEGPPGDPGLP

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

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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/chr6:57246966/chr6:55929420)
- 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
.	COL21A1 Q96P44
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

COL21A1

chr6:57246966

chr6:55929420

ENST00000244728

734_787

709.0

958.0

Domain

Note=Collagen-like 5

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000244728

825_882

709.0

958.0

Domain

Note=Collagen-like 6

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000244728

884_934

709.0

958.0

Domain

Note=Collagen-like 7

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370808

230_412

109.0

324.0

Domain

Note=Laminin G-like

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370808

448_500

109.0

324.0

Domain

Note=Collagen-like 1

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370808

501_542

109.0

324.0

Domain

Note=Collagen-like 2

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370808

543_594

109.0

324.0

Domain

Note=Collagen-like 3

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370808

681_733

109.0

324.0

Domain

Note=Collagen-like 4

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370808

734_787

109.0

324.0

Domain

Note=Collagen-like 5

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370808

825_882

109.0

324.0

Domain

Note=Collagen-like 6

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370808

884_934

109.0

324.0

Domain

Note=Collagen-like 7

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370819

734_787

706.0

955.0

Domain

Note=Collagen-like 5

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370819

825_882

706.0

955.0

Domain

Note=Collagen-like 6

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370819

884_934

706.0

955.0

Domain

Note=Collagen-like 7

- 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

COL21A1

chr6:57246966

chr6:55929420

ENST00000244728

230_412

709.0

958.0

Domain

Note=Laminin G-like

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000244728

37_211

709.0

958.0

Domain

VWFA

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000244728

448_500

709.0

958.0

Domain

Note=Collagen-like 1

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000244728

501_542

709.0

958.0

Domain

Note=Collagen-like 2

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000244728

543_594

709.0

958.0

Domain

Note=Collagen-like 3

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000244728

681_733

709.0

958.0

Domain

Note=Collagen-like 4

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370808

37_211

109.0

324.0

Domain

VWFA

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370819

230_412

706.0

955.0

Domain

Note=Laminin G-like

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370819

37_211

706.0

955.0

Domain

VWFA

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370819

448_500

706.0

955.0

Domain

Note=Collagen-like 1

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370819

501_542

706.0

955.0

Domain

Note=Collagen-like 2

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370819

543_594

706.0

955.0

Domain

Note=Collagen-like 3

Tgene

COL21A1

chr6:57246966

chr6:55929420

ENST00000370819

681_733

706.0

955.0

Domain

Note=Collagen-like 4

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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 >>>1036_PRIM2_57246966_COL21A1_55929420_1036_PRIM2_57246966_COL21A1_55929420_ranked_0.pdb	PRIM2	57246966	57246966	ENST00000370808	COL21A1	chr6	55929420	-	MCFPEFEFLQVTKMEFSGRKWRKLRLAGDQRNASYPHCLQFYLQPPSENISLIEFENLAIDRVKLLKSVENLGVSYVKGTEQYQSKLESE LRKLKFSYRENLEDEYEPRRRDHISHFILRLAYCQSEELRRWFIQQEMDLLRFRFSILPKDKIQDFLKDSQLQFEAISDEEKTLREQEIV ASSPSLSGLKLGFESIYKIPFADALDLFRGRKVYLEDGFAYVPLKDIVAIILNEFRAKLSKALAGQKGENGRQGIPGQQGIQGHHGAKGE RGEKGEPGVRGAIGSKGESGVDGLMGPAGPKGQPGDPGPQGPPGLDGKPGREFSEQFIRQVCTDVIRAQLPVLLQSGRIRNCDHCLSQHG SPGIPGPPGPIGPEGPRGLPGLPGRDGVPGLVGVPGRPGVRGLKGLPGRNGEKGSQGFGYPGEQGPPGPPGPEGPPGISKEGPPGDPGLP	492

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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.

PRIM2_pLDDT.png

COL21A1_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
PRIM2
COL21A1

- 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 PRIM2-COL21A1

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 PRIM2-COL21A1

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