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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 18503

FusionGeneSummary for KDM5C_PTPMT1

check button Fusion gene summary
Fusion gene informationFusion gene name: KDM5C_PTPMT1
Fusion gene ID: 18503
HgeneTgene
Gene symbol

KDM5C

PTPMT1

Gene ID

8242

114971

Gene namelysine demethylase 5Cprotein tyrosine phosphatase, mitochondrial 1
SynonymsDXS1272E|JARID1C|MRX13|MRXJ|MRXSCJ|MRXSJ|SMCX|XE169DUSP23|MOSP|PLIP|PNAS-129
Cytomap

Xp11.22

11p11.2

Type of geneprotein-codingprotein-coding
Descriptionlysine-specific demethylase 5CJmjC domain-containing protein SMCXJumonji, AT rich interactive domain 1C (RBP2-like)Jumonji/ARID domain-containing protein 1CSmcx homolog, X chromosomeSmcy homolog, X-linkedhistone demethylase JARID1Clysine (K)-specifphosphatidylglycerophosphatase and protein-tyrosine phosphatase 1NB4 apoptosis/differentiation related proteinPTEN-like phosphatasephosphoinositide lipid phosphatase
Modification date2018052320180523
UniProtAcc

P41229

Q8WUK0

Ensembl transtripts involved in fusion geneENST00000452825, ENST00000375401, 
ENST00000404049, ENST00000375379, 
ENST00000375383, ENST00000465402, 
ENST00000426530, ENST00000534775, 
ENST00000326656, ENST00000326674, 
ENST00000527079, 
Fusion gene scores* DoF score12 X 12 X 5=7202 X 2 X 2=8
# samples 122
** MAII scorelog2(12/720*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: KDM5C [Title/Abstract] AND PTPMT1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneKDM5C

GO:0034720

histone H3-K4 demethylation

17320160


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1AA434511KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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-3CDSENST00000452825ENST00000426530KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000452825ENST00000534775KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000452825ENST00000326656KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000452825ENST00000326674KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000452825ENST00000527079KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3CDSENST00000375401ENST00000426530KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000375401ENST00000534775KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000375401ENST00000326656KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000375401ENST00000326674KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000375401ENST00000527079KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3CDSENST00000404049ENST00000426530KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000404049ENST00000534775KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000404049ENST00000326656KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000404049ENST00000326674KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000404049ENST00000527079KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3CDSENST00000375379ENST00000426530KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000375379ENST00000534775KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000375379ENST00000326656KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000375379ENST00000326674KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000375379ENST00000527079KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3CDSENST00000375383ENST00000426530KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000375383ENST00000534775KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000375383ENST00000326656KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000375383ENST00000326674KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000375383ENST00000527079KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3CDSENST00000465402ENST00000426530KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000465402ENST00000534775KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000465402ENST00000326656KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000465402ENST00000326674KDM5CchrX

53221566

+PTPMT1chr11

47593062

+
intron-3UTRENST00000465402ENST00000527079KDM5CchrX

53221566

+PTPMT1chr11

47593062

+

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FusionProtFeatures for KDM5C_PTPMT1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
KDM5C

P41229

PTPMT1

Q8WUK0

Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code(PubMed:28262558). Does not demethylate histone H3 'Lys-9', H3'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylatestrimethylated and dimethylated but not monomethylated H3 'Lys-4'.Participates in transcriptional repression of neuronal genes byrecruiting histone deacetylases and REST at neuron-restrictivesilencer elements. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock componentPER2 (By similarity). {ECO:0000250|UniProtKB:P41230,ECO:0000269|PubMed:17320160, ECO:0000269|PubMed:17320161,ECO:0000269|PubMed:17468742, ECO:0000269|PubMed:26645689,ECO:0000269|PubMed:28262558}. Lipid phosphatase which dephosphorylatesphosphatidylglycerophosphate (PGP) to phosphatidylglycerol (PG)(By similarity). PGP is an essential intermediate in thebiosynthetic pathway of cardiolipin, a mitochondrial-specificphospholipid regulating the membrane integrity and activities ofthe organelle (By similarity). Has also been shown to displayphosphatase activity toward phosphoprotein substrates,specifically mediates dephosphorylation of mitochondrial proteins,thereby playing an essential role in ATP production (Bysimilarity). Has probably a preference for proteins phosphorylatedon Ser and/or Thr residues compared to proteins phosphorylated onTyr residues (By similarity). Probably involved in regulation ofinsulin secretion in pancreatic beta cells (By similarity). Mayprevent intrinsic apoptosis, probably by regulating mitochondrialmembrane integrity (PubMed:24709986).{ECO:0000250|UniProtKB:P0C089, ECO:0000250|UniProtKB:Q66GT5,ECO:0000269|PubMed:24709986}.

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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FusionGeneSequence for KDM5C_PTPMT1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for KDM5C_PTPMT1


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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RelatedDrugs for KDM5C_PTPMT1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for KDM5C_PTPMT1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKDM5CC1845243MENTAL RETARDATION, X-LINKED, SYNDROMIC, CLAES-JENSEN TYPE4CTD_human;ORPHANET;UNIPROT
HgeneKDM5CC0004352Autistic Disorder1CTD_human
HgeneKDM5CC0007134Renal Cell Carcinoma1CTD_human
HgeneKDM5CC3714756Intellectual Disability1CTD_human