FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

FusionGeneSummary

leaf

FusionProtFeature

leaf

FusionGeneSequence

leaf

FusionGenePPI

leaf

RelatedDrugs

leaf

RelatedDiseases

Fusion gene ID: 8003

FusionGeneSummary for COL6A3_PICALM

check button Fusion gene summary
Fusion gene informationFusion gene name: COL6A3_PICALM
Fusion gene ID: 8003
HgeneTgene
Gene symbol

COL6A3

PICALM

Gene ID

1293

8301

Gene namecollagen type VI alpha 3 chainphosphatidylinositol binding clathrin assembly protein
SynonymsBTHLM1|DYT27|UCMD1CALM|CLTH|LAP
Cytomap

2q37.3

11q14.2

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-3(VI) chaincollagen VI, alpha-3 polypeptidecollagen, type VI, alpha 3phosphatidylinositol-binding clathrin assembly proteinclathrin assembly lymphoid myeloid leukemia protein
Modification date2018052320180523
UniProtAcc

P12111

Q13492

Ensembl transtripts involved in fusion geneENST00000347401, ENST00000353578, 
ENST00000295550, ENST00000472056, 
ENST00000409809, ENST00000346358, 
ENST00000392004, ENST00000392003, 
ENST00000473258, 
ENST00000532317, 
ENST00000526033, ENST00000393346, 
ENST00000528398, ENST00000356360, 
ENST00000528411, 
Fusion gene scores* DoF score8 X 8 X 2=1287 X 12 X 4=336
# samples 1014
** MAII scorelog2(10/128*10)=-0.356143810225275
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(14/336*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COL6A3 [Title/Abstract] AND PICALM [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
TgenePICALM

GO:0006898

receptor-mediated endocytosis

10436022

TgenePICALM

GO:0032880

regulation of protein localization

10436022

TgenePICALM

GO:0045893

positive regulation of transcription, DNA-templated

11425879

TgenePICALM

GO:0048261

negative regulation of receptor-mediated endocytosis

10436022


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
ChiTaRS3.1DA556762COL6A3chr2

238305369

-PICALMchr11

85695019

-
* 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
Frame-shitENST00000347401ENST00000532317COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000347401ENST00000526033COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000347401ENST00000393346COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000347401ENST00000528398COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000347401ENST00000356360COL6A3chr2

238305369

-PICALMchr11

85695019

-
5CDS-intronENST00000347401ENST00000528411COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000353578ENST00000532317COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000353578ENST00000526033COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000353578ENST00000393346COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000353578ENST00000528398COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000353578ENST00000356360COL6A3chr2

238305369

-PICALMchr11

85695019

-
5CDS-intronENST00000353578ENST00000528411COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000295550ENST00000532317COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000295550ENST00000526033COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000295550ENST00000393346COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000295550ENST00000528398COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000295550ENST00000356360COL6A3chr2

238305369

-PICALMchr11

85695019

-
5CDS-intronENST00000295550ENST00000528411COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000472056ENST00000532317COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000472056ENST00000526033COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000472056ENST00000393346COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000472056ENST00000528398COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000472056ENST00000356360COL6A3chr2

238305369

-PICALMchr11

85695019

-
5CDS-intronENST00000472056ENST00000528411COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000409809ENST00000532317COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000409809ENST00000526033COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000409809ENST00000393346COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000409809ENST00000528398COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000409809ENST00000356360COL6A3chr2

238305369

-PICALMchr11

85695019

-
5CDS-intronENST00000409809ENST00000528411COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000346358ENST00000532317COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000346358ENST00000526033COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000346358ENST00000393346COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000346358ENST00000528398COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000346358ENST00000356360COL6A3chr2

238305369

-PICALMchr11

85695019

-
5CDS-intronENST00000346358ENST00000528411COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000392004ENST00000532317COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000392004ENST00000526033COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000392004ENST00000393346COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000392004ENST00000528398COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000392004ENST00000356360COL6A3chr2

238305369

-PICALMchr11

85695019

-
5CDS-intronENST00000392004ENST00000528411COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000392003ENST00000532317COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000392003ENST00000526033COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000392003ENST00000393346COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000392003ENST00000528398COL6A3chr2

238305369

-PICALMchr11

85695019

-
Frame-shitENST00000392003ENST00000356360COL6A3chr2

238305369

-PICALMchr11

85695019

-
5CDS-intronENST00000392003ENST00000528411COL6A3chr2

238305369

-PICALMchr11

85695019

-
intron-3CDSENST00000473258ENST00000532317COL6A3chr2

238305369

-PICALMchr11

85695019

-
intron-3CDSENST00000473258ENST00000526033COL6A3chr2

238305369

-PICALMchr11

85695019

-
intron-3CDSENST00000473258ENST00000393346COL6A3chr2

238305369

-PICALMchr11

85695019

-
intron-3CDSENST00000473258ENST00000528398COL6A3chr2

238305369

-PICALMchr11

85695019

-
intron-3CDSENST00000473258ENST00000356360COL6A3chr2

238305369

-PICALMchr11

85695019

-
intron-intronENST00000473258ENST00000528411COL6A3chr2

238305369

-PICALMchr11

85695019

-

Top

FusionProtFeatures for COL6A3_PICALM


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
COL6A3

P12111

PICALM

Q13492

Assembly protein recruiting clathrin and adapter proteincomplex 2 (AP2) to cell membranes at sites of coated-pit formationand clathrin-vesicle assembly. May be required to determine theamount of membrane to be recycled, possibly by regulating the sizeof the clathrin cage. Involved in AP2-dependent clathrin-mediatedendocytosis at the neuromuscular junction.{ECO:0000269|PubMed:10436022}.

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


Top

FusionGeneSequence for COL6A3_PICALM


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).

Top

FusionGenePPI for COL6A3_PICALM


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
COL6A3GANPICALMPLCG1, CLTC, ITSN1, AP2A1, HIP1R, LAMTOR3, EEF1A1, SEC24D, DNM2, EGFR, FLOT1, SEC24C, ATP6V1E1, ILF3, HNRNPDL, SH3GLB2, ABCC2, ATP6V1F, CD55, SIRT1, FN1, VCAM1, ITGA4, PELI2, KLHL20, SLC25A41, ITLN1, ATF6B, SLC25A32, SOX2, FAM64A, CYP1A1, HNRNPA1, UNK, NTRK1, C14orf166, CARS, CPPED1, HNRNPD, ILVBL, ITGB1, LPP, PAPOLA, DDX1, EWSR1, FERMT2, FUS, ILK, NPLOC4, PFKM, PTPRF, VCL, PXN, STXBP1, TRIM25, UNC13D, XPO1, AP2B1, AP2M1, CLTA, CLTB, DAB2, EPS15, GAK, MYO6, PIK3C2A, SEC13, CLTCL1, CAPZA2, DBN1, MYH9, LIMA1, GTSE1, ANLN, MYO19, MYO18A, CLINT1, SEC16A, TNRC6A, BMP2K, MICAL3, DENND1A, WNK1, PRRC2B, STON2, FCHO2, MCM2, SNW1, CDC5L, SMURF1, CDH1, STAMBPL1, RALBP1, SNRNP27, DLST


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


Top

RelatedDrugs for COL6A3_PICALM


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

Top

RelatedDiseases for COL6A3_PICALM


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL6A3C1834674Bethlem myopathy4CTD_human;ORPHANET;UNIPROT
HgeneCOL6A3C0000786Spontaneous abortion1CTD_human
HgeneCOL6A3C0410179Scleroatonic muscular dystrophy1CTD_human;ORPHANET;UNIPROT
HgeneCOL6A3C4225336DYSTONIA 271ORPHANET;UNIPROT
TgenePICALMC0002395Alzheimer's Disease2CTD_human