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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:CAP1-CHEK1 (FusionGDB2 ID:12857)

Fusion Gene Summary for CAP1-CHEK1

check button Fusion gene summary
Fusion gene informationFusion gene name: CAP1-CHEK1
Fusion gene ID: 12857
HgeneTgene
Gene symbol

CAP1

CHEK1

Gene ID

10487

1111

Gene namecyclase associated actin cytoskeleton regulatory protein 1checkpoint kinase 1
SynonymsCAP|CAP1-PENCHK1
Cytomap

1p34.2

11q24.2

Type of geneprotein-codingprotein-coding
Descriptionadenylyl cyclase-associated protein 1CAP, adenylate cyclase-associated protein 1adenylate cyclase associated protein 1testis secretory sperm-binding protein Li 218pserine/threonine-protein kinase Chk1CHK1 checkpoint homologCheckpoint, S. pombe, homolog of, 1Chk1-Scell cycle checkpoint kinase
Modification date2020031320200313
UniProtAcc

Q01518

O14757

Ensembl transtripts involved in fusion geneENST00000372797, ENST00000372802, 
ENST00000372792, ENST00000372798, 
ENST00000340450, ENST00000372805, 
ENST00000479759, 		ENST00000438015, 
ENST00000427383, ENST00000428830, 
ENST00000532449, ENST00000544373, 
ENST00000534070, ENST00000524737, 
ENST00000278916, 
Fusion gene scores* DoF score16 X 13 X 7=14563 X 3 X 3=27
# samples 193
** MAII scorelog2(19/1456*10)=-2.93793903186775
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CAP1 [Title/Abstract] AND CHEK1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCAP1(40525801)-CHEK1(125514000), # samples:1
Anticipated loss of major functional domain due to fusion event.CAP1-CHEK1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CAP1-CHEK1 seems lost the major protein functional domain in Tgene partner, which is a kinase due to the frame-shifted ORF.
CAP1-CHEK1 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
CAP1-CHEK1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CAP1-CHEK1 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
* 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
TgeneCHEK1

GO:0000077

DNA damage checkpoint

16963448

TgeneCHEK1

GO:0006915

apoptotic process

23028632

TgeneCHEK1

GO:0006975

DNA damage induced protein phosphorylation

16963448

TgeneCHEK1

GO:0010569

regulation of double-strand break repair via homologous recombination

15665856

TgeneCHEK1

GO:0018107

peptidyl-threonine phosphorylation

15665856

TgeneCHEK1

GO:0045787

positive regulation of cell cycle

26296656

TgeneCHEK1

GO:0045839

negative regulation of mitotic nuclear division

15311285

TgeneCHEK1

GO:0046602

regulation of mitotic centrosome separation

15311285


check buttonFusion gene breakpoints across CAP1 (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 CHEK1 (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/ACS190866CAP1chr1

40525801

+CHEK1chr11

125514000

+


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Fusion Gene ORF analysis for CAP1-CHEK1

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
Frame-shiftENST00000372797ENST00000438015CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372797ENST00000427383CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372797ENST00000428830CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372797ENST00000532449CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372797ENST00000544373CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372797ENST00000534070CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372797ENST00000524737CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372797ENST00000278916CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372802ENST00000438015CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372802ENST00000427383CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372802ENST00000428830CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372802ENST00000532449CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372802ENST00000544373CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372802ENST00000534070CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372802ENST00000524737CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372802ENST00000278916CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372792ENST00000438015CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372792ENST00000427383CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372792ENST00000428830CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372792ENST00000532449CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372792ENST00000544373CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372792ENST00000534070CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372792ENST00000524737CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372792ENST00000278916CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372798ENST00000438015CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372798ENST00000427383CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372798ENST00000428830CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372798ENST00000532449CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372798ENST00000544373CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372798ENST00000534070CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372798ENST00000524737CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372798ENST00000278916CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000340450ENST00000438015CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000340450ENST00000427383CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000340450ENST00000428830CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000340450ENST00000532449CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000340450ENST00000544373CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000340450ENST00000534070CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000340450ENST00000524737CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000340450ENST00000278916CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372805ENST00000438015CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372805ENST00000427383CAP1chr1

40525801

+CHEK1chr11

125514000

+
Frame-shiftENST00000372805ENST00000428830CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372805ENST00000532449CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372805ENST00000544373CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372805ENST00000534070CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372805ENST00000524737CAP1chr1

40525801

+CHEK1chr11

125514000

+
5CDS-3UTRENST00000372805ENST00000278916CAP1chr1

40525801

+CHEK1chr11

125514000

+
intron-3CDSENST00000479759ENST00000438015CAP1chr1

40525801

+CHEK1chr11

125514000

+
intron-3CDSENST00000479759ENST00000427383CAP1chr1

40525801

+CHEK1chr11

125514000

+
intron-3CDSENST00000479759ENST00000428830CAP1chr1

40525801

+CHEK1chr11

125514000

+
intron-3UTRENST00000479759ENST00000532449CAP1chr1

40525801

+CHEK1chr11

125514000

+
intron-3UTRENST00000479759ENST00000544373CAP1chr1

40525801

+CHEK1chr11

125514000

+
intron-3UTRENST00000479759ENST00000534070CAP1chr1

40525801

+CHEK1chr11

125514000

+
intron-3UTRENST00000479759ENST00000524737CAP1chr1

40525801

+CHEK1chr11

125514000

+
intron-3UTRENST00000479759ENST00000278916CAP1chr1

40525801

+CHEK1chr11

125514000

+

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 CAP1-CHEK1


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 CAP1-CHEK1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CAP1

Q01518

CHEK1

O14757

FUNCTION: Directly regulates filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localization and the establishment of cell polarity.FUNCTION: Serine/threonine-protein kinase which is required for checkpoint-mediated cell cycle arrest and activation of DNA repair in response to the presence of DNA damage or unreplicated DNA (PubMed:11535615, PubMed:12446774, PubMed:12399544, PubMed:14559997, PubMed:14988723, PubMed:15311285, PubMed:15665856, PubMed:15650047). May also negatively regulate cell cycle progression during unperturbed cell cycles (PubMed:11535615, PubMed:12446774, PubMed:12399544, PubMed:14559997, PubMed:14988723, PubMed:15311285, PubMed:15665856, PubMed:15650047). This regulation is achieved by a number of mechanisms that together help to preserve the integrity of the genome (PubMed:11535615, PubMed:12446774, PubMed:12399544, PubMed:14559997, PubMed:14988723, PubMed:15311285, PubMed:15665856, PubMed:15650047). Recognizes the substrate consensus sequence [R-X-X-S/T] (PubMed:11535615, PubMed:12446774, PubMed:12399544, PubMed:14559997, PubMed:14988723, PubMed:15311285, PubMed:15665856, PubMed:15650047). Binds to and phosphorylates CDC25A, CDC25B and CDC25C (PubMed:9278511, PubMed:12676583, PubMed:14681206, PubMed:12676925, PubMed:12759351, PubMed:19734889, PubMed:14559997). Phosphorylation of CDC25A at 'Ser-178' and 'Thr-507' and phosphorylation of CDC25C at 'Ser-216' creates binding sites for 14-3-3 proteins which inhibit CDC25A and CDC25C (PubMed:9278511). Phosphorylation of CDC25A at 'Ser-76', 'Ser-124', 'Ser-178', 'Ser-279' and 'Ser-293' promotes proteolysis of CDC25A (PubMed:9278511, PubMed:12676583, PubMed:14681206, PubMed:12676925, PubMed:12759351, PubMed:19734889). Phosphorylation of CDC25A at 'Ser-76' primes the protein for subsequent phosphorylation at 'Ser-79', 'Ser-82' and 'Ser-88' by NEK11, which is required for polyubiquitination and degradation of CDCD25A (PubMed:9278511, PubMed:19734889, PubMed:20090422). Inhibition of CDC25 leads to increased inhibitory tyrosine phosphorylation of CDK-cyclin complexes and blocks cell cycle progression (PubMed:9278511). Also phosphorylates NEK6 (PubMed:18728393). Binds to and phosphorylates RAD51 at 'Thr-309', which promotes the release of RAD51 from BRCA2 and enhances the association of RAD51 with chromatin, thereby promoting DNA repair by homologous recombination (PubMed:15665856). Phosphorylates multiple sites within the C-terminus of TP53, which promotes activation of TP53 by acetylation and promotes cell cycle arrest and suppression of cellular proliferation (PubMed:10673501, PubMed:15659650, PubMed:16511572). Also promotes repair of DNA cross-links through phosphorylation of FANCE (PubMed:17296736). Binds to and phosphorylates TLK1 at 'Ser-743', which prevents the TLK1-dependent phosphorylation of the chromatin assembly factor ASF1A (PubMed:12660173, PubMed:12955071). This may enhance chromatin assembly both in the presence or absence of DNA damage (PubMed:12660173, PubMed:12955071). May also play a role in replication fork maintenance through regulation of PCNA (PubMed:18451105). May regulate the transcription of genes that regulate cell-cycle progression through the phosphorylation of histones (By similarity). Phosphorylates histone H3.1 (to form H3T11ph), which leads to epigenetic inhibition of a subset of genes (By similarity). May also phosphorylate RB1 to promote its interaction with the E2F family of transcription factors and subsequent cell cycle arrest (PubMed:17380128). Phosphorylates SPRTN, promoting SPRTN recruitment to chromatin (PubMed:31316063). Reduces replication stress and activates the G2/M checkpoint, by phosphorylating and inactivating PABIR1/FAM122A and promoting the serine/threonine-protein phosphatase 2A-mediated dephosphorylation and stabilization of WEE1 levels and activity (PubMed:33108758). {ECO:0000250|UniProtKB:O35280, ECO:0000269|PubMed:10673501, ECO:0000269|PubMed:11535615, ECO:0000269|PubMed:12399544, ECO:0000269|PubMed:12446774, ECO:0000269|PubMed:12660173, ECO:0000269|PubMed:12676583, ECO:0000269|PubMed:12676925, ECO:0000269|PubMed:12759351, ECO:0000269|PubMed:12955071, ECO:0000269|PubMed:14559997, ECO:0000269|PubMed:14681206, ECO:0000269|PubMed:14988723, ECO:0000269|PubMed:15311285, ECO:0000269|PubMed:15650047, ECO:0000269|PubMed:15659650, ECO:0000269|PubMed:15665856, ECO:0000269|PubMed:16511572, ECO:0000269|PubMed:17296736, ECO:0000269|PubMed:17380128, ECO:0000269|PubMed:18451105, ECO:0000269|PubMed:18728393, ECO:0000269|PubMed:19734889, ECO:0000269|PubMed:20090422, ECO:0000269|PubMed:31316063, ECO:0000269|PubMed:33108758, ECO:0000269|PubMed:9278511}.; FUNCTION: [Isoform 2]: Endogenous repressor of isoform 1, interacts with, and antagonizes CHK1 to promote the S to G2/M phase transition. {ECO:0000269|PubMed:22184239}.

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 CAP1-CHEK1


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 CAP1-CHEK1


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 CAP1-CHEK1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneCHEK1O14757DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgeneCHEK1O14757DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational

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Related Diseases for CAP1-CHEK1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCAP1C0001787Osteoporosis, Age-Related1CTD_human
HgeneCAP1C0019193Hepatitis, Toxic1CTD_human
HgeneCAP1C0029456Osteoporosis1CTD_human
HgeneCAP1C0029459Osteoporosis, Senile1CTD_human
HgeneCAP1C0751406Post-Traumatic Osteoporosis1CTD_human
HgeneCAP1C0860207Drug-Induced Liver Disease1CTD_human
HgeneCAP1C1262760Hepatitis, Drug-Induced1CTD_human
HgeneCAP1C3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneCAP1C4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneCAP1C4279912Chemically-Induced Liver Toxicity1CTD_human
TgeneCHEK1C0006142Malignant neoplasm of breast1CTD_human
TgeneCHEK1C0032578Polyploidy1CTD_human
TgeneCHEK1C0036341Schizophrenia1PSYGENET
TgeneCHEK1C0678222Breast Carcinoma1CTD_human
TgeneCHEK1C1257931Mammary Neoplasms, Human1CTD_human
TgeneCHEK1C1458155Mammary Neoplasms1CTD_human
TgeneCHEK1C4704874Mammary Carcinoma, Human1CTD_human