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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:PITPNM2-KCNAB1 (FusionGDB2 ID:65610)

Fusion Gene Summary for PITPNM2-KCNAB1

check button Fusion gene summary
Fusion gene informationFusion gene name: PITPNM2-KCNAB1
Fusion gene ID: 65610
HgeneTgene
Gene symbol

PITPNM2

KCNAB1

Gene ID

57605

7881

Gene namephosphatidylinositol transfer protein membrane associated 2potassium voltage-gated channel subfamily A member regulatory beta subunit 1
SynonymsNIR-3|NIR3|RDGB2|RDGBA2AKR6A3|KCNA1B|KV-BETA-1|Kvb1.3|hKvBeta3|hKvb3
Cytomap

12q24.31

3q25.31

Type of geneprotein-codingprotein-coding
Descriptionmembrane-associated phosphatidylinositol transfer protein 2PYK2 N-terminal domain-interacting receptor 3retinal degeneration B alpha 2voltage-gated potassium channel subunit beta-1K(+) channel subunit beta-1K+ channel Beta1a chainpotassium channel beta 3 chainpotassium channel beta3 subunitpotassium channel shaker chain beta 1apotassium channel, voltage gated subfamily A regulator
Modification date2020031320200313
UniProtAcc.

Q14722

Ensembl transtripts involved in fusion geneENST00000280562, ENST00000320201, 
ENST00000392428, ENST00000451868, 
ENST00000542749, ENST00000546049, 
ENST00000302490, ENST00000389634, 
ENST00000389636, ENST00000471742, 
ENST00000490337, ENST00000497291, 
Fusion gene scores* DoF score11 X 10 X 7=77013 X 10 X 6=780
# samples 1114
** MAII scorelog2(11/770*10)=-2.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/780*10)=-2.47804729680464
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PITPNM2 [Title/Abstract] AND KCNAB1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPITPNM2(123533127)-KCNAB1(156257933), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgenePITPNM2

GO:0048015

phosphatidylinositol-mediated signaling

10022914

TgeneKCNAB1

GO:1901379

regulation of potassium ion transmembrane transport

7890032


check buttonFusion gene breakpoints across PITPNM2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across KCNAB1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS5.0N/ACF144413PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+


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Fusion Gene ORF analysis for PITPNM2-KCNAB1

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
intron-intronENST00000280562ENST00000302490PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000280562ENST00000389634PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000280562ENST00000389636PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000280562ENST00000471742PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000280562ENST00000490337PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000280562ENST00000497291PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000320201ENST00000302490PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000320201ENST00000389634PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000320201ENST00000389636PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000320201ENST00000471742PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000320201ENST00000490337PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000320201ENST00000497291PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000392428ENST00000302490PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000392428ENST00000389634PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000392428ENST00000389636PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000392428ENST00000471742PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000392428ENST00000490337PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000392428ENST00000497291PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000451868ENST00000302490PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000451868ENST00000389634PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000451868ENST00000389636PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000451868ENST00000471742PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000451868ENST00000490337PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000451868ENST00000497291PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000542749ENST00000302490PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000542749ENST00000389634PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000542749ENST00000389636PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000542749ENST00000471742PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000542749ENST00000490337PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000542749ENST00000497291PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000546049ENST00000302490PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000546049ENST00000389634PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000546049ENST00000389636PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000546049ENST00000471742PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000546049ENST00000490337PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+
intron-intronENST00000546049ENST00000497291PITPNM2chr12

123533127

-KCNAB1chr3

156257933

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for PITPNM2-KCNAB1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for PITPNM2-KCNAB1


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:123533127/:156257933)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.KCNAB1

Q14722

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Cytoplasmic potassium channel subunit that modulates the characteristics of the channel-forming alpha-subunits (PubMed:7499366, PubMed:7603988, PubMed:17156368,PubMed:17540341, PubMed:19713757). Modulates action potentials via its effect on the pore-forming alpha subunits (By similarity). Promotes expression of the pore-forming alpha subunits at the cell membrane, and thereby increases channel activity (By similarity). Mediates closure of delayed rectifier potassium channels by physically obstructing the pore via its N-terminal domain and increases the speed of channel closure for other family members (PubMed:9763623). Promotes the closure of KCNA1, KCNA2 and KCNA5 channels (PubMed:7499366, PubMed:7890032, PubMed:7603988, PubMed:7649300, PubMed:8938711, PubMed:12077175, PubMed:12130714, PubMed:15361858, PubMed:17540341, PubMed:19713757). Accelerates KCNA4 channel closure (PubMed:7890032, PubMed:7649300, PubMed:7890764, PubMed:9763623). Accelerates the closure of heteromeric channels formed by KCNA1 and KCNA4 (PubMed:17156368). Accelerates the closure of heteromeric channels formed by KCNA2, KCNA5 and KCNA6 (By similarity). Isoform KvB1.2 has no effect on KCNA1, KCNA2 or KCNB1 (PubMed:7890032, PubMed:7890764). Enhances KCNB1 and KCNB2 channel activity (By similarity). Binds NADPH; this is required for efficient down-regulation of potassium channel activity (PubMed:17540341). Has NADPH-dependent aldoketoreductase activity (By similarity). Oxidation of the bound NADPH strongly decreases N-type inactivation of potassium channel activity (By similarity). {ECO:0000250|UniProtKB:P63143, ECO:0000250|UniProtKB:P63144, ECO:0000269|PubMed:12077175, ECO:0000269|PubMed:12130714, ECO:0000269|PubMed:15361858, ECO:0000269|PubMed:17156368, ECO:0000269|PubMed:17540341, ECO:0000269|PubMed:19713757, ECO:0000269|PubMed:7499366, ECO:0000269|PubMed:7603988, ECO:0000269|PubMed:7649300, ECO:0000269|PubMed:7890032, ECO:0000269|PubMed:7890764, ECO:0000269|PubMed:8938711, ECO:0000269|PubMed:9763623, ECO:0000305}.

check buttonRetention 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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for PITPNM2-KCNAB1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for PITPNM2-KCNAB1


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for PITPNM2-KCNAB1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for PITPNM2-KCNAB1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource