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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:CLPTM1-KIAA1671 (FusionGDB2 ID:HG1209TG85379)

Fusion Gene Summary for CLPTM1-KIAA1671

check button Fusion gene summary
Fusion gene informationFusion gene name: CLPTM1-KIAA1671
Fusion gene ID: hg1209tg85379
HgeneTgene
Gene symbol

CLPTM1

KIAA1671

Gene ID

1209

85379

Gene nameCLPTM1 regulator of GABA type A receptor forward traffickingKIAA1671
Synonyms--
Cytomap('CLPTM1')('KIAA1671')

19q13.32

22q11.23

Type of geneprotein-codingprotein-coding
Descriptioncleft lip and palate transmembrane protein 1CLPTM1, transmembrane proteincleft lip and palate associated transmembrane protein 1uncharacterized protein KIAA1671CTA-221G9.5
Modification date2020031320200313
UniProtAcc

O96005

Q9BY89

Ensembl transtripts involved in fusion geneENST00000337392, ENST00000541297, 
ENST00000546079, ENST00000589158, 
Fusion gene scores* DoF score16 X 12 X 8=153616 X 17 X 6=1632
# samples 2016
** MAII scorelog2(20/1536*10)=-2.94110631094643
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(16/1632*10)=-3.35049724708413
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLPTM1 [Title/Abstract] AND KIAA1671 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLPTM1(45476442)-KIAA1671(25445330), # samples:1
CLPTM1(45476466)-KIAA1671(25447996), # samples:1
CLPTM1(45476965)-KIAA1671(25448011), # 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


check button Fusion gene information
* 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
ChimerDB4ACCTCGA-OR-A5J1-01ACLPTM1chr19

45476442

+KIAA1671chr22

25445330

-
ChimerDB4ACCTCGA-OR-A5J1-01ACLPTM1chr19

45476466

+KIAA1671chr22

25447996

-
ChimerDB4ACCTCGA-OR-A5J1-01ACLPTM1chr19

45476965

+KIAA1671chr22

25448011

-


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Fusion Gene ORF analysis for CLPTM1-KIAA1671

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
5CDS-intronENST00000337392ENST00000358431CLPTM1chr19

45476442

+KIAA1671chr22

25445330

-
5CDS-intronENST00000337392ENST00000358431CLPTM1chr19

45476466

+KIAA1671chr22

25447996

-
5CDS-intronENST00000337392ENST00000401395CLPTM1chr19

45476442

+KIAA1671chr22

25445330

-
5CDS-intronENST00000337392ENST00000401395CLPTM1chr19

45476466

+KIAA1671chr22

25447996

-
5CDS-intronENST00000337392ENST00000406486CLPTM1chr19

45476442

+KIAA1671chr22

25445330

-
5CDS-intronENST00000337392ENST00000406486CLPTM1chr19

45476466

+KIAA1671chr22

25447996

-
5CDS-intronENST00000541297ENST00000358431CLPTM1chr19

45476442

+KIAA1671chr22

25445330

-
5CDS-intronENST00000541297ENST00000358431CLPTM1chr19

45476466

+KIAA1671chr22

25447996

-
5CDS-intronENST00000541297ENST00000401395CLPTM1chr19

45476442

+KIAA1671chr22

25445330

-
5CDS-intronENST00000541297ENST00000401395CLPTM1chr19

45476466

+KIAA1671chr22

25447996

-
5CDS-intronENST00000541297ENST00000406486CLPTM1chr19

45476442

+KIAA1671chr22

25445330

-
5CDS-intronENST00000541297ENST00000406486CLPTM1chr19

45476466

+KIAA1671chr22

25447996

-
5CDS-intronENST00000546079ENST00000358431CLPTM1chr19

45476466

+KIAA1671chr22

25447996

-
5CDS-intronENST00000546079ENST00000401395CLPTM1chr19

45476466

+KIAA1671chr22

25447996

-
5CDS-intronENST00000546079ENST00000406486CLPTM1chr19

45476466

+KIAA1671chr22

25447996

-
5UTR-intronENST00000546079ENST00000358431CLPTM1chr19

45476442

+KIAA1671chr22

25445330

-
5UTR-intronENST00000546079ENST00000401395CLPTM1chr19

45476442

+KIAA1671chr22

25445330

-
5UTR-intronENST00000546079ENST00000406486CLPTM1chr19

45476442

+KIAA1671chr22

25445330

-
intron-intronENST00000337392ENST00000358431CLPTM1chr19

45476965

+KIAA1671chr22

25448011

-
intron-intronENST00000337392ENST00000401395CLPTM1chr19

45476965

+KIAA1671chr22

25448011

-
intron-intronENST00000337392ENST00000406486CLPTM1chr19

45476965

+KIAA1671chr22

25448011

-
intron-intronENST00000541297ENST00000358431CLPTM1chr19

45476965

+KIAA1671chr22

25448011

-
intron-intronENST00000541297ENST00000401395CLPTM1chr19

45476965

+KIAA1671chr22

25448011

-
intron-intronENST00000541297ENST00000406486CLPTM1chr19

45476965

+KIAA1671chr22

25448011

-
intron-intronENST00000546079ENST00000358431CLPTM1chr19

45476965

+KIAA1671chr22

25448011

-
intron-intronENST00000546079ENST00000401395CLPTM1chr19

45476965

+KIAA1671chr22

25448011

-
intron-intronENST00000546079ENST00000406486CLPTM1chr19

45476965

+KIAA1671chr22

25448011

-
intron-intronENST00000589158ENST00000358431CLPTM1chr19

45476442

+KIAA1671chr22

25445330

-
intron-intronENST00000589158ENST00000358431CLPTM1chr19

45476466

+KIAA1671chr22

25447996

-
intron-intronENST00000589158ENST00000358431CLPTM1chr19

45476965

+KIAA1671chr22

25448011

-
intron-intronENST00000589158ENST00000401395CLPTM1chr19

45476442

+KIAA1671chr22

25445330

-
intron-intronENST00000589158ENST00000401395CLPTM1chr19

45476466

+KIAA1671chr22

25447996

-
intron-intronENST00000589158ENST00000401395CLPTM1chr19

45476965

+KIAA1671chr22

25448011

-
intron-intronENST00000589158ENST00000406486CLPTM1chr19

45476442

+KIAA1671chr22

25445330

-
intron-intronENST00000589158ENST00000406486CLPTM1chr19

45476466

+KIAA1671chr22

25447996

-
intron-intronENST00000589158ENST00000406486CLPTM1chr19

45476965

+KIAA1671chr22

25448011

-

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 CLPTM1-KIAA1671


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)


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Fusion Protein Features for CLPTM1-KIAA1671


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/:45476442/:25445330)
- 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
CLPTM1

O96005

KIAA1671

Q9BY89

FUNCTION: May play a role in T-cell development. {ECO:0000250}.

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 CLPTM1-KIAA1671


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 CLPTM1-KIAA1671


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 CLPTM1-KIAA1671


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 CLPTM1-KIAA1671


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCLPTM1C0030297Pancreatic Neoplasm1CTD_human
HgeneCLPTM1C0346647Malignant neoplasm of pancreas1CTD_human