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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:PELI2-GPHN

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PELI2-GPHN
	FusionPDB ID: 64252
	FusionGDB2.0 ID: 64252
		Hgene	Tgene
	Gene symbol	PELI2	GPHN
	Gene ID	57161	10243
	Gene name	pellino E3 ubiquitin protein ligase family member 2	gephyrin
	Synonyms	-	GEPH\|GPH\|GPHRYN\|HKPX1\|MOCODC
	Cytomap	14q22.3	14q23.3-q24.1
	Type of gene	protein-coding	protein-coding
	Description	E3 ubiquitin-protein ligase pellino homolog 2RING-type E3 ubiquitin transferase pellino homolog 2pellino homolog 2pellino-2protein pellino homolog 2	gephyrin
	Modification date	20200313	20200313
	UniProtAcc	.	Q9NQX3
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000267460,	ENST00000544752, ENST00000305960, ENST00000315266, ENST00000459628, ENST00000478722, ENST00000543237,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	9 X 5 X 6=270	42 X 51 X 15=32130
	# samples	10	62
	** MAII score	log2(10/270*10)=-1.43295940727611 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(62/32130*10)=-5.69550895508454 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PELI2 [Title/Abstract] AND GPHN [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PELI2(56645182)-GPHN(67490350), # samples:3
Anticipated loss of major functional domain due to fusion event.	PELI2-GPHN 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. PELI2-GPHN 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. PELI2-GPHN 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. PELI2-GPHN 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
Hgene	PELI2	GO:0001934	positive regulation of protein phosphorylation	12804775
Hgene	PELI2	GO:0043410	positive regulation of MAPK cascade	12804775
Tgene	GPHN	GO:0032324	molybdopterin cofactor biosynthetic process	26613940
Tgene	GPHN	GO:0097112	gamma-aminobutyric acid receptor clustering	26613940

Fusion gene breakpoints across PELI2 (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 GPHN (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	SKCM	TCGA-W3-AA1R-06A	PELI2	chr14	56645182	-	GPHN	chr14	67490350	+
ChimerDB4	SKCM	TCGA-W3-AA1R-06A	PELI2	chr14	56645182	+	GPHN	chr14	67490350	+

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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)

ENST00000267460

PELI2

chr14

56645182

ENST00000315266

GPHN

chr14

67490350

2701

493

286

1839

517

ENST00000267460

PELI2

chr14

56645182

ENST00000478722

GPHN

chr14

67490350

2706

493

286

1839

517

ENST00000267460

PELI2

chr14

56645182

ENST00000459628

GPHN

chr14

67490350

917

493

286

726

146

ENST00000267460

PELI2

chr14

56645182

ENST00000543237

GPHN

chr14

67490350

1926

493

286

1839

517

ENST00000267460

PELI2

chr14

56645182

ENST00000305960

GPHN

chr14

67490350

2100

493

286

1839

517

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
ENST00000267460	ENST00000315266	PELI2	chr14	56645182	+	GPHN	chr14	67490350	+	0.001649991	0.99835
ENST00000267460	ENST00000478722	PELI2	chr14	56645182	+	GPHN	chr14	67490350	+	0.001593082	0.99840695
ENST00000267460	ENST00000459628	PELI2	chr14	56645182	+	GPHN	chr14	67490350	+	0.022658909	0.9773412
ENST00000267460	ENST00000543237	PELI2	chr14	56645182	+	GPHN	chr14	67490350	+	0.004394825	0.9956052
ENST00000267460	ENST00000305960	PELI2	chr14	56645182	+	GPHN	chr14	67490350	+	0.003283365	0.99671656

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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

>64252_64252_1_PELI2-GPHN_PELI2_chr14_56645182_ENST00000267460_GPHN_chr14_67490350_ENST00000305960_length(amino acids)=517AA_BP=69
MFSPGQEEHCAPNKEPVKYGELVVLGYNGALPNGDRGRRKSRFALYKRPKANGVKPSTVHVISTPQASKVQSRCSSKENILRASHSAVDI
TKVARRHRMSPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQP
TQTVMPGQVMRVTTGAPIPCGADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPSEIGLLATVG
VTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEK
DYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKARLSCDVKLDP

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

>64252_64252_2_PELI2-GPHN_PELI2_chr14_56645182_ENST00000267460_GPHN_chr14_67490350_ENST00000315266_length(amino acids)=517AA_BP=69
MFSPGQEEHCAPNKEPVKYGELVVLGYNGALPNGDRGRRKSRFALYKRPKANGVKPSTVHVISTPQASKVQSRCSSKENILRASHSAVDI
TKVARRHRMSPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQP
TQTVMPGQVMRVTTGAPIPCGADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPSEIGLLATVG
VTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEK
DYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKARLSCDVKLDP

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

>64252_64252_3_PELI2-GPHN_PELI2_chr14_56645182_ENST00000267460_GPHN_chr14_67490350_ENST00000459628_length(amino acids)=146AA_BP=69
MFSPGQEEHCAPNKEPVKYGELVVLGYNGALPNGDRGRRKSRFALYKRPKANGVKPSTVHVISTPQASKVQSRCSSKENILRASHSAVDI

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

>64252_64252_4_PELI2-GPHN_PELI2_chr14_56645182_ENST00000267460_GPHN_chr14_67490350_ENST00000478722_length(amino acids)=517AA_BP=69
MFSPGQEEHCAPNKEPVKYGELVVLGYNGALPNGDRGRRKSRFALYKRPKANGVKPSTVHVISTPQASKVQSRCSSKENILRASHSAVDI
TKVARRHRMSPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQP
TQTVMPGQVMRVTTGAPIPCGADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPSEIGLLATVG
VTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEK
DYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKARLSCDVKLDP

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

>64252_64252_5_PELI2-GPHN_PELI2_chr14_56645182_ENST00000267460_GPHN_chr14_67490350_ENST00000543237_length(amino acids)=517AA_BP=69
MFSPGQEEHCAPNKEPVKYGELVVLGYNGALPNGDRGRRKSRFALYKRPKANGVKPSTVHVISTPQASKVQSRCSSKENILRASHSAVDI
TKVARRHRMSPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQP
TQTVMPGQVMRVTTGAPIPCGADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPSEIGLLATVG
VTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEK
DYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKARLSCDVKLDP

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

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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/chr14:56645182/chr14:67490350)
- 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
.	GPHN Q9NQX3
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: Microtubule-associated protein involved in membrane protein-cytoskeleton interactions. It is thought to anchor the inhibitory glycine receptor (GLYR) to subsynaptic microtubules (By similarity). Acts as a major instructive molecule at inhibitory synapses, where it also clusters GABA type A receptors (PubMed:25025157, PubMed:26613940). {ECO:0000250\|UniProtKB:Q03555, ECO:0000269\|PubMed:25025157, ECO:0000269\|PubMed:26613940}.; FUNCTION: Has also a catalytic activity and catalyzes two steps in the biosynthesis of the molybdenum cofactor. In the first step, molybdopterin is adenylated. Subsequently, molybdate is inserted into adenylated molybdopterin and AMP is released. {ECO:0000269\|PubMed:26613940}.

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

GPHN

chr14:56645182

chr14:67490350

ENST00000315266

326_736

288.0

737.0

Region

Note=MPT adenylyltransferase

Tgene

GPHN

chr14:56645182

chr14:67490350

ENST00000478722

326_736

321.0

770.0

Region

Note=MPT adenylyltransferase

- 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

Hgene

PELI2

chr14:56645182

chr14:67490350

ENST00000267460

15_202

69.0

421.0

Domain

Note=FHA%3B atypical

Tgene

GPHN

chr14:56645182

chr14:67490350

ENST00000315266

14_166

288.0

737.0

Region

Note=MPT Mo-transferase

Tgene

GPHN

chr14:56645182

chr14:67490350

ENST00000478722

14_166

321.0

770.0

Region

Note=MPT Mo-transferase

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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
PELI2
GPHN

- 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
Tgene	GPHN	chr14:56645182	chr14:67490350	ENST00000315266		7	22	140_316	288.0	737.0	GABARAP
Tgene	GPHN	chr14:56645182	chr14:67490350	ENST00000478722		8	23	140_316	321.0	770.0	GABARAP

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Related Drugs to PELI2-GPHN

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 PELI2-GPHN

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	GPHN	C1854990	Molybdenum Cofactor Deficiency, Complementation Group C	5	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	GPHN	C0001956	Alcohol Use Disorder	1	CTD_human
Tgene	GPHN	C0001973	Alcoholic Intoxication, Chronic	1	CTD_human
Tgene	GPHN	C0009171	Cocaine Abuse	1	CTD_human
Tgene	GPHN	C0085762	Alcohol abuse	1	CTD_human
Tgene	GPHN	C0236736	Cocaine-Related Disorders	1	CTD_human
Tgene	GPHN	C0543888	Epileptic encephalopathy	1	GENOMICS_ENGLAND
Tgene	GPHN	C0600427	Cocaine Dependence	1	CTD_human