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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:KIF3A-PDLIM4

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: KIF3A-PDLIM4
	FusionPDB ID: 42689
	FusionGDB2.0 ID: 42689
		Hgene	Tgene
	Gene symbol	KIF3A	PDLIM4
	Gene ID	11127	8572
	Gene name	kinesin family member 3A	PDZ and LIM domain 4
	Synonyms	FLA10\|KLP-20	RIL
	Cytomap	5q31.1	5q31.1
	Type of gene	protein-coding	protein-coding
	Description	kinesin-like protein KIF3Akinesin family protein 3Amicrotubule plus end-directed kinesin motor 3A	PDZ and LIM domain protein 4LIM domain proteinLIM protein RILenigma homologreversion-induced LIM protein
	Modification date	20200313	20200313
	UniProtAcc	Q9Y496	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000378735, ENST00000378746, ENST00000403231, ENST00000487055,	ENST00000484620, ENST00000253754, ENST00000379018,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	5 X 5 X 2=50	4 X 2 X 4=32
	# samples	5	4
	** MAII score	log2(5/50*10)=0	log2(4/32*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)	PubMed: KIF3A [Title/Abstract] AND PDLIM4 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	KIF3A(132073106)-PDLIM4(131598302), # samples:2
Anticipated loss of major functional domain due to fusion event.	KIF3A-PDLIM4 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. KIF3A-PDLIM4 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. KIF3A-PDLIM4 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. KIF3A-PDLIM4 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
Tgene	PDLIM4	GO:0031532	actin cytoskeleton reorganization	21636573

Fusion gene breakpoints across KIF3A (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 PDLIM4 (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	STAD	TCGA-HU-8238-01A	KIF3A	chr5	132073106	-	PDLIM4	chr5	131598302	+

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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)
ENST00000378746	KIF3A	chr5	132073106	-	ENST00000253754	PDLIM4	chr5	131598302	+	2350	225	138	1124	328
ENST00000378746	KIF3A	chr5	132073106	-	ENST00000379018	PDLIM4	chr5	131598302	+	1110	225	138	872	244
ENST00000378735	KIF3A	chr5	132073106	-	ENST00000253754	PDLIM4	chr5	131598302	+	2284	159	72	1058	328
ENST00000378735	KIF3A	chr5	132073106	-	ENST00000379018	PDLIM4	chr5	131598302	+	1044	159	72	806	244
ENST00000403231	KIF3A	chr5	132073106	-	ENST00000253754	PDLIM4	chr5	131598302	+	2131	6	0	905	301
ENST00000403231	KIF3A	chr5	132073106	-	ENST00000379018	PDLIM4	chr5	131598302	+	891	6	0	653	217

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
ENST00000378746	ENST00000253754	KIF3A	chr5	132073106	-	PDLIM4	chr5	131598302	+	0.09395748	0.9060425
ENST00000378746	ENST00000379018	KIF3A	chr5	132073106	-	PDLIM4	chr5	131598302	+	0.16878004	0.83122
ENST00000378735	ENST00000253754	KIF3A	chr5	132073106	-	PDLIM4	chr5	131598302	+	0.084945954	0.9150541
ENST00000378735	ENST00000379018	KIF3A	chr5	132073106	-	PDLIM4	chr5	131598302	+	0.11432276	0.8856773
ENST00000403231	ENST00000253754	KIF3A	chr5	132073106	-	PDLIM4	chr5	131598302	+	0.08316314	0.91683686
ENST00000403231	ENST00000379018	KIF3A	chr5	132073106	-	PDLIM4	chr5	131598302	+	0.08575824	0.9142418

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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

>42689_42689_1_KIF3A-PDLIM4_KIF3A_chr5_132073106_ENST00000378735_PDLIM4_chr5_131598302_ENST00000253754_length(amino acids)=328AA_BP=29
MAILSAHPVSLGCTPGGDVRRAREGAKMPVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSVSRPEGRSWPSAP
DDSKAQAHRIHIDPEIQDGSPTTSRRPSGTGTGPEDGRPSLGSPYGQPPRFPVPHNGSSEATLPAQMSTLHVSPPPSADPARGLPRSRDC
RVDLGSEVYRMLREPAEPVAAEPKQSGSFRYLQGMLEAGEGGDWPGPGGPRNLKPTASKLGAPLSGLQGLPECTRCGHGIVGTIVKARDK

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

>42689_42689_2_KIF3A-PDLIM4_KIF3A_chr5_132073106_ENST00000378735_PDLIM4_chr5_131598302_ENST00000379018_length(amino acids)=244AA_BP=29
MAILSAHPVSLGCTPGGDVRRAREGAKMPVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSVSRPEGRSWPSAP
DDSKAQAHRIHIDPEIQDGSPTTSRRPSGTGTGPEDGRPSLGSPYGQPPRFPVPHNGSSEATLPAQMSTLHVSPPPSADPARGLPRSRDC

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

>42689_42689_3_KIF3A-PDLIM4_KIF3A_chr5_132073106_ENST00000378746_PDLIM4_chr5_131598302_ENST00000253754_length(amino acids)=328AA_BP=29
MAILSAHPVSLGCTPGGDVRRAREGAKMPVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSVSRPEGRSWPSAP
DDSKAQAHRIHIDPEIQDGSPTTSRRPSGTGTGPEDGRPSLGSPYGQPPRFPVPHNGSSEATLPAQMSTLHVSPPPSADPARGLPRSRDC
RVDLGSEVYRMLREPAEPVAAEPKQSGSFRYLQGMLEAGEGGDWPGPGGPRNLKPTASKLGAPLSGLQGLPECTRCGHGIVGTIVKARDK

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

>42689_42689_4_KIF3A-PDLIM4_KIF3A_chr5_132073106_ENST00000378746_PDLIM4_chr5_131598302_ENST00000379018_length(amino acids)=244AA_BP=29
MAILSAHPVSLGCTPGGDVRRAREGAKMPVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSVSRPEGRSWPSAP
DDSKAQAHRIHIDPEIQDGSPTTSRRPSGTGTGPEDGRPSLGSPYGQPPRFPVPHNGSSEATLPAQMSTLHVSPPPSADPARGLPRSRDC

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

>42689_42689_5_KIF3A-PDLIM4_KIF3A_chr5_132073106_ENST00000403231_PDLIM4_chr5_131598302_ENST00000253754_length(amino acids)=301AA_BP=2
MPVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSVSRPEGRSWPSAPDDSKAQAHRIHIDPEIQDGSPTTSRRP
SGTGTGPEDGRPSLGSPYGQPPRFPVPHNGSSEATLPAQMSTLHVSPPPSADPARGLPRSRDCRVDLGSEVYRMLREPAEPVAAEPKQSG
SFRYLQGMLEAGEGGDWPGPGGPRNLKPTASKLGAPLSGLQGLPECTRCGHGIVGTIVKARDKLYHPECFMCSDCGLNLKQRGYFFLDER

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

>42689_42689_6_KIF3A-PDLIM4_KIF3A_chr5_132073106_ENST00000403231_PDLIM4_chr5_131598302_ENST00000379018_length(amino acids)=217AA_BP=2
MPVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSVSRPEGRSWPSAPDDSKAQAHRIHIDPEIQDGSPTTSRRP
SGTGTGPEDGRPSLGSPYGQPPRFPVPHNGSSEATLPAQMSTLHVSPPPSADPARGLPRSRDCRVDLGSEVYRMLREPAEPVAAEPKQSG

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

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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/chr5:132073106/chr5:131598302)
- 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
KIF3A Q9Y496	.
FUNCTION: Microtubule-based anterograde translocator for membranous organelles. Plus end-directed microtubule sliding activity in vitro. Plays a role in primary cilia formation. Plays a role in centriole cohesion and subdistal appendage organization and function. Regulates the formation of the subdistal appendage via recruitment of DCTN1 to the centriole. Also required for ciliary basal feet formation and microtubule anchoring to mother centriole. {ECO:0000250\|UniProtKB:P28741}.	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

PDLIM4

chr5:132073106

chr5:131598302

ENST00000253754

253_312

31.0

331.0

Domain

LIM zinc-binding

Tgene

PDLIM4

chr5:132073106

chr5:131598302

ENST00000379018

253_312

31.0

247.0

Domain

LIM zinc-binding

- 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

KIF3A

chr5:132073106

chr5:131598302

ENST00000378746

355_590

2.0

700.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

KIF3A

chr5:132073106

chr5:131598302

ENST00000378746

14_345

2.0

700.0

Domain

Kinesin motor

Hgene

KIF3A

chr5:132073106

chr5:131598302

ENST00000378746

100_107

2.0

700.0

Nucleotide binding

ATP

Hgene

KIF3A

chr5:132073106

chr5:131598302

ENST00000378746

697_699

2.0

700.0

Region

Note=Globular

Tgene

PDLIM4

chr5:132073106

chr5:131598302

ENST00000253754

1_84

31.0

331.0

Domain

PDZ

Tgene

PDLIM4

chr5:132073106

chr5:131598302

ENST00000379018

1_84

31.0

247.0

Domain

PDZ

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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
KIF3A
PDLIM4

- 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 KIF3A-PDLIM4

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 KIF3A-PDLIM4

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