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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:FAM219A-PAX5

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: FAM219A-PAX5
	FusionPDB ID: 28934
	FusionGDB2.0 ID: 28934
		Hgene	Tgene
	Gene symbol	FAM219A	PAX5
	Gene ID	203259	5079
	Gene name	family with sequence similarity 219 member A	paired box 5
	Synonyms	C9orf25	ALL3\|BSAP
	Cytomap	9p13.3	9p13.2
	Type of gene	protein-coding	protein-coding
	Description	protein FAM219Auncharacterized protein C9orf25	paired box protein Pax-5B-cell lineage specific activatorpaired box homeotic gene 5paired domain gene 5transcription factor PAX 5
	Modification date	20200313	20200313
	UniProtAcc	Q8IW50	Q02548
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000297620, ENST00000379078, ENST00000379084, ENST00000379087, ENST00000379089, ENST00000445726, ENST00000379080, ENST00000379081,	ENST00000377847, ENST00000377852, ENST00000377853, ENST00000414447, ENST00000446742, ENST00000520154, ENST00000520281, ENST00000522003, ENST00000523145, ENST00000523241, ENST00000358127,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 6 X 4=168	8 X 7 X 6=336
	# samples	8	9
	** MAII score	log2(8/168*10)=-1.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/336*10)=-1.90046432644909 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: FAM219A [Title/Abstract] AND PAX5 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	FAM219A(34458202)-PAX5(36923481), # samples:3
Anticipated loss of major functional domain due to fusion event.	FAM219A-PAX5 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. FAM219A-PAX5 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 FAM219A (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 PAX5 (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-A7-A13D-01A	FAM219A	chr9	34458202	-	PAX5	chr9	36923481	-

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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)
ENST00000379087	FAM219A	chr9	34458202	-	ENST00000358127	PAX5	chr9	36923481	-	8030	349	4869	4171	232
ENST00000379084	FAM219A	chr9	34458202	-	ENST00000358127	PAX5	chr9	36923481	-	8030	349	4869	4171	232
ENST00000379089	FAM219A	chr9	34458202	-	ENST00000358127	PAX5	chr9	36923481	-	8030	349	4869	4171	232
ENST00000445726	FAM219A	chr9	34458202	-	ENST00000358127	PAX5	chr9	36923481	-	8048	367	4887	4189	232
ENST00000297620	FAM219A	chr9	34458202	-	ENST00000358127	PAX5	chr9	36923481	-	8048	367	4887	4189	232
ENST00000379078	FAM219A	chr9	34458202	-	ENST00000358127	PAX5	chr9	36923481	-	8030	349	4869	4171	232

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
ENST00000379087	ENST00000358127	FAM219A	chr9	34458202	-	PAX5	chr9	36923481	-	0.016647343	0.98335266
ENST00000379084	ENST00000358127	FAM219A	chr9	34458202	-	PAX5	chr9	36923481	-	0.016647343	0.98335266
ENST00000379089	ENST00000358127	FAM219A	chr9	34458202	-	PAX5	chr9	36923481	-	0.016647343	0.98335266
ENST00000445726	ENST00000358127	FAM219A	chr9	34458202	-	PAX5	chr9	36923481	-	0.016881024	0.98311895
ENST00000297620	ENST00000358127	FAM219A	chr9	34458202	-	PAX5	chr9	36923481	-	0.016881024	0.98311895
ENST00000379078	ENST00000358127	FAM219A	chr9	34458202	-	PAX5	chr9	36923481	-	0.016647343	0.98335266

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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

>28934_28934_1_FAM219A-PAX5_FAM219A_chr9_34458202_ENST00000297620_PAX5_chr9_36923481_ENST00000358127_length(amino acids)=232AA_BP=
MTGIGAHRLVPSGSSLAHGHFSLGRQKILQVFILECHSGGQAHFWASRALLHRTVWCAARVARLHHPVHPGSSSFRGLEIVICVSRGCGH
PGGPGLGTPAYCHSQAWSLFQSAKAKKGKWGTAHDLGTWTPGVRAGPMSRPGQGLWHGLELTLIPSEPQGQLGKSLDETSEALLWIWSKT

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

>28934_28934_2_FAM219A-PAX5_FAM219A_chr9_34458202_ENST00000379078_PAX5_chr9_36923481_ENST00000358127_length(amino acids)=232AA_BP=
MTGIGAHRLVPSGSSLAHGHFSLGRQKILQVFILECHSGGQAHFWASRALLHRTVWCAARVARLHHPVHPGSSSFRGLEIVICVSRGCGH
PGGPGLGTPAYCHSQAWSLFQSAKAKKGKWGTAHDLGTWTPGVRAGPMSRPGQGLWHGLELTLIPSEPQGQLGKSLDETSEALLWIWSKT

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

>28934_28934_3_FAM219A-PAX5_FAM219A_chr9_34458202_ENST00000379084_PAX5_chr9_36923481_ENST00000358127_length(amino acids)=232AA_BP=
MTGIGAHRLVPSGSSLAHGHFSLGRQKILQVFILECHSGGQAHFWASRALLHRTVWCAARVARLHHPVHPGSSSFRGLEIVICVSRGCGH
PGGPGLGTPAYCHSQAWSLFQSAKAKKGKWGTAHDLGTWTPGVRAGPMSRPGQGLWHGLELTLIPSEPQGQLGKSLDETSEALLWIWSKT

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

>28934_28934_4_FAM219A-PAX5_FAM219A_chr9_34458202_ENST00000379087_PAX5_chr9_36923481_ENST00000358127_length(amino acids)=232AA_BP=
MTGIGAHRLVPSGSSLAHGHFSLGRQKILQVFILECHSGGQAHFWASRALLHRTVWCAARVARLHHPVHPGSSSFRGLEIVICVSRGCGH
PGGPGLGTPAYCHSQAWSLFQSAKAKKGKWGTAHDLGTWTPGVRAGPMSRPGQGLWHGLELTLIPSEPQGQLGKSLDETSEALLWIWSKT

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

>28934_28934_5_FAM219A-PAX5_FAM219A_chr9_34458202_ENST00000379089_PAX5_chr9_36923481_ENST00000358127_length(amino acids)=232AA_BP=
MTGIGAHRLVPSGSSLAHGHFSLGRQKILQVFILECHSGGQAHFWASRALLHRTVWCAARVARLHHPVHPGSSSFRGLEIVICVSRGCGH
PGGPGLGTPAYCHSQAWSLFQSAKAKKGKWGTAHDLGTWTPGVRAGPMSRPGQGLWHGLELTLIPSEPQGQLGKSLDETSEALLWIWSKT

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

>28934_28934_6_FAM219A-PAX5_FAM219A_chr9_34458202_ENST00000445726_PAX5_chr9_36923481_ENST00000358127_length(amino acids)=232AA_BP=
MTGIGAHRLVPSGSSLAHGHFSLGRQKILQVFILECHSGGQAHFWASRALLHRTVWCAARVARLHHPVHPGSSSFRGLEIVICVSRGCGH
PGGPGLGTPAYCHSQAWSLFQSAKAKKGKWGTAHDLGTWTPGVRAGPMSRPGQGLWHGLELTLIPSEPQGQLGKSLDETSEALLWIWSKT

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

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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/chr9:34458202/chr9:36923481)
- 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
FAM219A Q8IW50	PAX5 Q02548
	FUNCTION: Transcription factor that plays an essential role in commitment of lymphoid progenitors to the B-lymphocyte lineage (PubMed:10811620, PubMed:27181361). Fulfills a dual role by repressing B-lineage inappropriate genes and simultaneously activating B-lineage-specific genes (PubMed:10811620, PubMed:27181361). In turn, regulates cell adhesion and migration, induces V(H)-to-D(H)J(H) recombination, facilitates pre-B-cell receptor signaling and promotes development to the mature B-cell stage (PubMed:32612238). Repression of the cohesin-release factor WAPL causes global changes of the chromosomal architecture in pro-B cells to facilitate the generation of a diverse antibody repertoire (PubMed:32612238). {ECO:0000269\|PubMed:10811620, ECO:0000269\|PubMed:27181361, ECO:0000269\|PubMed:32612238}.; FUNCTION: (Microbial infection) Plays an essential role in the maintenance of Epstein-Barr virus genome copy number within the host cell by promoting EBNA1/oriP-dependent binding and transcription (PubMed:31941781). Participates also in the inhibition of lytic EBV reactivation by modulating viral BZLF1 activity (PubMed:23678172). {ECO:0000269\|PubMed:23678172, ECO:0000269\|PubMed:31941781}.

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

- 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

PAX5

chr9:34458202

chr9:36923481

ENST00000358127

16_142

260.0

392.0

DNA binding

Paired

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000377847

16_142

260.0

329.0

DNA binding

Paired

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000377852

16_142

260.0

358.0

DNA binding

Paired

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000377853

16_142

260.0

363.0

DNA binding

Paired

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000414447

16_142

217.0

349.0

DNA binding

Paired

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000446742

16_142

194.0

292.0

DNA binding

Paired

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000520281

16_142

217.0

320.0

DNA binding

Paired

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000358127

19_75

260.0

392.0

Region

PAI subdomain

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000358127

94_142

260.0

392.0

Region

RED subdomain

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000377847

19_75

260.0

329.0

Region

PAI subdomain

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000377847

94_142

260.0

329.0

Region

RED subdomain

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000377852

19_75

260.0

358.0

Region

PAI subdomain

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000377852

94_142

260.0

358.0

Region

RED subdomain

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000377853

19_75

260.0

363.0

Region

PAI subdomain

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000377853

94_142

260.0

363.0

Region

RED subdomain

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000414447

19_75

217.0

349.0

Region

PAI subdomain

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000414447

94_142

217.0

349.0

Region

RED subdomain

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000446742

19_75

194.0

292.0

Region

PAI subdomain

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000446742

94_142

194.0

292.0

Region

RED subdomain

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000520281

19_75

217.0

320.0

Region

PAI subdomain

Tgene

PAX5

chr9:34458202

chr9:36923481

ENST00000520281

94_142

217.0

320.0

Region

RED subdomain

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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
PAX5	TLE4, DAXX, RUNX1, MYB, ID3, EP300, TBP, RB1, MAPK1, KAT2B, CDKN1B, UBE3A, RAD52, HMGB3, HOXC8, MAPK9, NFYC, FBLN1, GRHL2, DTX2, CSNK2A1, UBE2I, CCNC, BCAS2, C1orf109, GNG13, ZMYM5, SEC14L4, RNF144B, OSGIN1, CIB3, SAE1, STAC, TLK2, HMBOX1, NGLY1, NEIL2, LONRF1, LDLRAP1, LARP4, UBXN7, ACOT12, CKS1B, KLHL38, HGS, CXorf38, KRTAP10-8, PNMA5, KRTAP9-3, UBXN2B, CDK3, BKRF1, HIST1H3A, PAX8, KLHL14,

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
FAM219A
PAX5

- 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 FAM219A-PAX5

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 FAM219A-PAX5

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
Tgene	PAX5	C0006413	Burkitt Lymphoma	4	ORPHANET
Tgene	PAX5	C1292769	Precursor B-cell lymphoblastic leukemia	4	ORPHANET
Tgene	PAX5	C0023485	Precursor B-Cell Lymphoblastic Leukemia-Lymphoma	2	CTD_human
Tgene	PAX5	C1961102	Precursor Cell Lymphoblastic Leukemia Lymphoma	2	CGI;CTD_human;UNIPROT
Tgene	PAX5	C0023452	Childhood Acute Lymphoblastic Leukemia	1	CTD_human
Tgene	PAX5	C0023453	L2 Acute Lymphoblastic Leukemia	1	CTD_human
Tgene	PAX5	C1535926	Neurodevelopmental Disorders	1	CTD_human