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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:KLHL24-CEP89

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: KLHL24-CEP89
FusionPDB ID: 42971
FusionGDB2.0 ID: 42971
HgeneTgene
Gene symbol

KLHL24

CEP89

Gene ID

54800

84902

Gene namekelch like family member 24centrosomal protein 89
SynonymsDRE1|EBSSH|KRIP6CCDC123|CEP123
Cytomap

3q27.1

19q13.11

Type of geneprotein-codingprotein-coding
Descriptionkelch-like protein 24kainate receptor interacting protein for GluR6kelch-like 24centrosomal protein of 89 kDacentrosomal protein 123centrosomal protein 89kDacoiled-coil domain containing 123coiled-coil domain-containing protein 123, mitochondrial
Modification date2020031320200313
UniProtAcc

Q6TFL4

Q96ST8

Ensembl transtripts involved in fusion geneENST idsENST00000242810, ENST00000454652, 
ENST00000476808, ENST00000461813, 
ENST00000590597, ENST00000591863, 
ENST00000305768, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score11 X 11 X 5=60511 X 11 X 7=847
# samples 1415
** MAII scorelog2(14/605*10)=-2.11150831521699
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/847*10)=-2.49739946883632
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: KLHL24 [Title/Abstract] AND CEP89 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KLHL24(183369064)-CEP89(33392318), # samples:2
KLHL24(183381430)-CEP89(33392318), # samples:2
Anticipated loss of major functional domain due to fusion event.KLHL24-CEP89 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.
KLHL24-CEP89 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.
KLHL24-CEP89 seems lost the major protein functional domain in Tgene partner, which is a CGC 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
HgeneKLHL24

GO:0016567

protein ubiquitination

27798626


check buttonFusion gene breakpoints across KLHL24 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across CEP89 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4LUSCTCGA-21-1071-01AKLHL24chr3

183369064

+CEP89chr19

33392318

-
ChimerDB4LUSCTCGA-21-1071-01AKLHL24chr3

183381430

-CEP89chr19

33392318

-
ChimerDB4LUSCTCGA-21-1071KLHL24chr3

183369064

+CEP89chr19

33392318

-
ChimerDB4LUSCTCGA-21-1071KLHL24chr3

183381430

+CEP89chr19

33392318

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000242810KLHL24chr3183369064+ENST00000305768CEP89chr1933392318-222312703502056568
ENST00000454652KLHL24chr3183369064+ENST00000305768CEP89chr1933392318-225913063862092568
ENST00000476808KLHL24chr3183369064+ENST00000305768CEP89chr1933392318-187392001706568

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
ENST00000242810ENST00000305768KLHL24chr3183369064+CEP89chr1933392318-0.0011553280.9988446
ENST00000454652ENST00000305768KLHL24chr3183369064+CEP89chr1933392318-0.0012267930.99877316
ENST00000476808ENST00000305768KLHL24chr3183369064+CEP89chr1933392318-0.0017154930.9982845

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Fusion Amino Acid Sequences


check button 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

>42971_42971_1_KLHL24-CEP89_KLHL24_chr3_183369064_ENST00000242810_CEP89_chr19_33392318_ENST00000305768_length(amino acids)=568AA_BP=306
MVLILGRRLNREDLGVRDSPATKRKVFEMDPKSLTGHEFFDFSSGSSHAENILQIFNEFRDSRLFTDVIICVEGKEFPCHRAVLSACSSY
FRAMFCNDHRESREMLVEINGILAEAMECFLQYVYTGKVKITTENVQYLFETSSLFQISVLRDACAKFLEEQLDPCNCLGIQRFADTHSL
KTLFTKCKNFALQTFEDVSQHEEFLELDKDELIDYICSDELVIGKEEMVFEAVMRWVYRAVDLRRPLLHELLTHVRLPLLHPNYFVQTVE
VDQLIQNSPECYQLLHEARRYHILGNEMMSPRTRPRSQLQKEEEKERAEMEELMEKLTVLQAQKKSLLLEKNSLTEQNKALEAELERAQK
INRKSQKKIEVLKKQVEKAMGNEMSAHQYLANLVGLAENITQERDSLMCLAKCLESEKDGVLNKVIKSNIRLGKLEEKVKGYKKQAALKL
GDISHRLLEQQEDFAGKTAQYRQEMRHLHQVLKDKQEVLDQALQQNREMEGELEVIWESTFRENRRIRELLQDTLTRTGVQDNPRALVAP

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

>42971_42971_2_KLHL24-CEP89_KLHL24_chr3_183369064_ENST00000454652_CEP89_chr19_33392318_ENST00000305768_length(amino acids)=568AA_BP=306
MVLILGRRLNREDLGVRDSPATKRKVFEMDPKSLTGHEFFDFSSGSSHAENILQIFNEFRDSRLFTDVIICVEGKEFPCHRAVLSACSSY
FRAMFCNDHRESREMLVEINGILAEAMECFLQYVYTGKVKITTENVQYLFETSSLFQISVLRDACAKFLEEQLDPCNCLGIQRFADTHSL
KTLFTKCKNFALQTFEDVSQHEEFLELDKDELIDYICSDELVIGKEEMVFEAVMRWVYRAVDLRRPLLHELLTHVRLPLLHPNYFVQTVE
VDQLIQNSPECYQLLHEARRYHILGNEMMSPRTRPRSQLQKEEEKERAEMEELMEKLTVLQAQKKSLLLEKNSLTEQNKALEAELERAQK
INRKSQKKIEVLKKQVEKAMGNEMSAHQYLANLVGLAENITQERDSLMCLAKCLESEKDGVLNKVIKSNIRLGKLEEKVKGYKKQAALKL
GDISHRLLEQQEDFAGKTAQYRQEMRHLHQVLKDKQEVLDQALQQNREMEGELEVIWESTFRENRRIRELLQDTLTRTGVQDNPRALVAP

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

>42971_42971_3_KLHL24-CEP89_KLHL24_chr3_183369064_ENST00000476808_CEP89_chr19_33392318_ENST00000305768_length(amino acids)=568AA_BP=306
MVLILGRRLNREDLGVRDSPATKRKVFEMDPKSLTGHEFFDFSSGSSHAENILQIFNEFRDSRLFTDVIICVEGKEFPCHRAVLSACSSY
FRAMFCNDHRESREMLVEINGILAEAMECFLQYVYTGKVKITTENVQYLFETSSLFQISVLRDACAKFLEEQLDPCNCLGIQRFADTHSL
KTLFTKCKNFALQTFEDVSQHEEFLELDKDELIDYICSDELVIGKEEMVFEAVMRWVYRAVDLRRPLLHELLTHVRLPLLHPNYFVQTVE
VDQLIQNSPECYQLLHEARRYHILGNEMMSPRTRPRSQLQKEEEKERAEMEELMEKLTVLQAQKKSLLLEKNSLTEQNKALEAELERAQK
INRKSQKKIEVLKKQVEKAMGNEMSAHQYLANLVGLAENITQERDSLMCLAKCLESEKDGVLNKVIKSNIRLGKLEEKVKGYKKQAALKL
GDISHRLLEQQEDFAGKTAQYRQEMRHLHQVLKDKQEVLDQALQQNREMEGELEVIWESTFRENRRIRELLQDTLTRTGVQDNPRALVAP

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

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Fusion Protein Functional Features


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/chr3:183369064/chr19:33392318)
- 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
KLHL24

Q6TFL4

CEP89

Q96ST8

FUNCTION: Necessary to maintain the balance between intermediate filament stability and degradation, a process that is essential for skin integrity (PubMed:27889062). As part of the BCR(KLHL24) E3 ubiquitin ligase complex, mediates ubiquitination of KRT14 and controls its levels during keratinocytes differentiation (PubMed:27798626). Specifically reduces kainate receptor-mediated currents in hippocampal neurons, most probably by modulating channel properties (By similarity). {ECO:0000250|UniProtKB:Q56A24, ECO:0000269|PubMed:27798626, ECO:0000269|PubMed:27889062}.FUNCTION: Required for ciliogenesis. Also plays a role in mitochondrial metabolism where it may modulate complex IV activity. {ECO:0000269|PubMed:23348840, ECO:0000269|PubMed:23575228}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneKLHL24chr3:183369064chr19:33392318ENST00000242810+38168_270306.6666666666667601.0DomainNote=BACK
HgeneKLHL24chr3:183369064chr19:33392318ENST00000242810+3866_133306.6666666666667601.0DomainBTB
HgeneKLHL24chr3:183369064chr19:33392318ENST00000454652+49168_270306.6666666666667601.0DomainNote=BACK
HgeneKLHL24chr3:183369064chr19:33392318ENST00000454652+4966_133306.6666666666667601.0DomainBTB
HgeneKLHL24chr3:183369064chr19:33392318ENST00000476808+15168_270306.6666666666667538.0DomainNote=BACK
HgeneKLHL24chr3:183369064chr19:33392318ENST00000476808+1566_133306.6666666666667538.0DomainBTB
TgeneCEP89chr3:183369064chr19:33392318ENST0000059059709234_3330357.0Coiled coilOntology_term=ECO:0000255
TgeneCEP89chr3:183369064chr19:33392318ENST0000059059709369_7190357.0Coiled coilOntology_term=ECO:0000255

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneKLHL24chr3:183369064chr19:33392318ENST00000242810+38314_363306.6666666666667601.0RepeatNote=Kelch 1
HgeneKLHL24chr3:183369064chr19:33392318ENST00000242810+38365_407306.6666666666667601.0RepeatNote=Kelch 2
HgeneKLHL24chr3:183369064chr19:33392318ENST00000242810+38408_454306.6666666666667601.0RepeatNote=Kelch 3
HgeneKLHL24chr3:183369064chr19:33392318ENST00000242810+38456_502306.6666666666667601.0RepeatNote=Kelch 4
HgeneKLHL24chr3:183369064chr19:33392318ENST00000242810+38504_544306.6666666666667601.0RepeatNote=Kelch 5
HgeneKLHL24chr3:183369064chr19:33392318ENST00000242810+38546_592306.6666666666667601.0RepeatNote=Kelch 6
HgeneKLHL24chr3:183369064chr19:33392318ENST00000454652+49314_363306.6666666666667601.0RepeatNote=Kelch 1
HgeneKLHL24chr3:183369064chr19:33392318ENST00000454652+49365_407306.6666666666667601.0RepeatNote=Kelch 2
HgeneKLHL24chr3:183369064chr19:33392318ENST00000454652+49408_454306.6666666666667601.0RepeatNote=Kelch 3
HgeneKLHL24chr3:183369064chr19:33392318ENST00000454652+49456_502306.6666666666667601.0RepeatNote=Kelch 4
HgeneKLHL24chr3:183369064chr19:33392318ENST00000454652+49504_544306.6666666666667601.0RepeatNote=Kelch 5
HgeneKLHL24chr3:183369064chr19:33392318ENST00000454652+49546_592306.6666666666667601.0RepeatNote=Kelch 6
HgeneKLHL24chr3:183369064chr19:33392318ENST00000476808+15314_363306.6666666666667538.0RepeatNote=Kelch 1
HgeneKLHL24chr3:183369064chr19:33392318ENST00000476808+15365_407306.6666666666667538.0RepeatNote=Kelch 2
HgeneKLHL24chr3:183369064chr19:33392318ENST00000476808+15408_454306.6666666666667538.0RepeatNote=Kelch 3
HgeneKLHL24chr3:183369064chr19:33392318ENST00000476808+15456_502306.6666666666667538.0RepeatNote=Kelch 4
HgeneKLHL24chr3:183369064chr19:33392318ENST00000476808+15504_544306.6666666666667538.0RepeatNote=Kelch 5
HgeneKLHL24chr3:183369064chr19:33392318ENST00000476808+15546_592306.6666666666667538.0RepeatNote=Kelch 6
TgeneCEP89chr3:183369064chr19:33392318ENST000003057681319234_333521.6666666666666784.0Coiled coilOntology_term=ECO:0000255
TgeneCEP89chr3:183369064chr19:33392318ENST000003057681319369_719521.6666666666666784.0Coiled coilOntology_term=ECO:0000255


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors
CEP89LATS2, PICK1, PCM1, CEP162, CEP128, ABLIM1, ANKRD26, ANXA1, ATG2B, CEP131, C3orf14, CC2D1A, CCDC138, CCDC14, CCDC66, CCDC77, CCDC85C, CEP170, CEP192, CEP55, CRK, CSPP1, DHX35, DLG5, FGFR1OP, FLII, GPATCH1, HAUS2, HAUS3, HAUS4, HAUS5, HAUS6, HAUS7, HAUS8, KIAA0753, KIF7, LUZP1, MB21D2, MED4, MPHOSPH9, NCS1, NME7, NMT1, OFD1, PIBF1, PLEKHG1, RNF219, SAMD4B, SIRT2, SRBD1, SSX2IP, TCHP, TP53BP2, TXLNG, UNC45A, WDR83, WRAP73, XRN1, YWHAG, YWHAH, ADSL, C2CD3, CEP164, CEP350, CEP72, ERC1, KIAA1671, KIF14, MAP7D3, MARK2, MOB2, MOB4, NAV1, NPHP4, SDCCAG3, SLC25A12, TBC1D2B, TRIM37, TTK, TXLNA, WDR45, TBC1D31, CNTRL, NINL, MYH9, GAR1, CTDSPL, PTPRG, PMF1, HIF1AN, YWHAE, nsp16, nsp2, HSPA12B, PRKACA, C17orf59, C11orf52, CXADR, DIRAS3, EPB41L4A, FLOT1, GJA1, KRAS, KRT8, LCK, LYN, MLLT4, NDC80, OCLN, PARD3, RAB35, RHOB, STX7, ZFPL1, FXR1, VPS33A, RAP1GDS1, MAGEA9, KCTD18, BRK1, MLLT3, WHAMMP3, ZNF263, YWHAQ, MLLT1, CALCOCO2, TOP1MT, YWHAB,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
KLHL24
CEP89all structure


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to KLHL24-CEP89


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to KLHL24-CEP89


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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