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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: 8036

FusionGeneSummary for COMMD1_FARS2

check button Fusion gene summary
Fusion gene informationFusion gene name: COMMD1_FARS2
Fusion gene ID: 8036
HgeneTgene
Gene symbol

COMMD1

FARS2

Gene ID

150684

10667

Gene namecopper metabolism domain containing 1phenylalanyl-tRNA synthetase 2, mitochondrial
SynonymsC2orf5|MURR1COXPD14|FARS1|HSPC320|PheRS|SPG77
Cytomap

2p15

6p25.1

Type of geneprotein-codingprotein-coding
DescriptionCOMM domain-containing protein 1copper metabolism (Murr1) domain containing 1copper metabolism gene MURR1protein Murr1phenylalanine--tRNA ligase, mitochondrialdJ236A3.1 (phenylalanine-tRNA synthetase)dJ520B18.2 (FARS1 (phenylalanine-tRNA synthetase))mitochondrial PHERSphenylalanine tRNA ligase 2, mitochondrialphenylalanine translasephenylalanine-tRNA synthetase 1 (
Modification date2018052320180523
UniProtAcc

Q8N668

O95363

Ensembl transtripts involved in fusion geneENST00000472729, ENST00000311832, 
ENST00000538736, 
ENST00000324331, 
ENST00000274680, 
Fusion gene scores* DoF score3 X 3 X 3=279 X 7 X 7=441
# samples 311
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(11/441*10)=-2.00327513203286
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COMMD1 [Title/Abstract] AND FARS2 [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
HgeneCOMMD1

GO:0031398

positive regulation of protein ubiquitination

17183367|21741370

HgeneCOMMD1

GO:0032088

negative regulation of NF-kappaB transcription factor activity

15799966|16573520

HgeneCOMMD1

GO:0048227

plasma membrane to endosome transport

21741370

HgeneCOMMD1

GO:0055070

copper ion homeostasis

14685266

HgeneCOMMD1

GO:1902306

negative regulation of sodium ion transmembrane transport

14645214

HgeneCOMMD1

GO:2000009

negative regulation of protein localization to cell surface

21741370

TgeneFARS2

GO:0006432

phenylalanyl-tRNA aminoacylation

10329163

TgeneFARS2

GO:0008033

tRNA processing

10329163


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
TCGALDBLCATCGA-GV-A3QI-01ACOMMD1chr2

62228117

+FARS2chr6

5771524

+
* 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
3UTR-3CDSENST00000472729ENST00000324331COMMD1chr2

62228117

+FARS2chr6

5771524

+
3UTR-3CDSENST00000472729ENST00000274680COMMD1chr2

62228117

+FARS2chr6

5771524

+
In-frameENST00000311832ENST00000324331COMMD1chr2

62228117

+FARS2chr6

5771524

+
Frame-shiftENST00000311832ENST00000274680COMMD1chr2

62228117

+FARS2chr6

5771524

+
In-frameENST00000538736ENST00000324331COMMD1chr2

62228117

+FARS2chr6

5771524

+
Frame-shiftENST00000538736ENST00000274680COMMD1chr2

62228117

+FARS2chr6

5771524

+

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FusionProtFeatures for COMMD1_FARS2


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
COMMD1

Q8N668

FARS2

O95363

Proposed scaffold protein that is implicated in diversephysiological processes and whose function may be in part linkedto its ability to regulate ubiquitination of specific cellularproteins. Can modulate activity of cullin-RING E3 ubiquitin ligase(CRL) complexes by displacing CAND1; in vitro promotes CRL E3activity and dissociates CAND1 from CUL1 and CUL2(PubMed:21778237). Promotes ubiquitination of NF-kappa-B subunitRELA and its subsequent proteasomal degradation. Down-regulatesNF-kappa-B activity (PubMed:15799966, PubMed:17183367,PubMed:20048074). Involved in the regulation of membraneexpression and ubiquitination of SLC12A2 (PubMed:23515529).Modulates Na(+) transport in epithelial cells by regulation ofapical cell surface expression of amiloride-sensitive sodiumchannel (ENaC) subunits and by promoting their ubiquitinationpresumably involving NEDD4L. Promotes the localization of SCNN1Dto recycling endosomes (PubMed:14645214, PubMed:20237237,PubMed:21741370). Promotes CFTR cell surface expression throughregulation of its ubiquitination (PubMed:21483833). Down-regulatesSOD1 activity by interfering with its homodimerization(PubMed:20595380). Plays a role in copper ion homeostasis.Involved in copper-dependent ATP7A trafficking between the trans-Golgi network and vesicles in the cell periphery; the function isproposed to depend on its association within the CCC complex andcooperation with the WASH complex on early endosomes(PubMed:25355947). Can bind one copper ion per monomer(PubMed:17309234). May function to facilitate biliary copperexcretion within hepatocytes. Binds to phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) (PubMed:18940794). Involved in theregulation of HIF1A-mediated transcription; competes withARNT/Hif-1-beta for binding to HIF1A resulting in decreased DNAbinding and impaired transcriptional activation by HIF-1(PubMed:20458141). {ECO:0000269|PubMed:14645214,ECO:0000269|PubMed:14685266, ECO:0000269|PubMed:15799966,ECO:0000269|PubMed:16573520, ECO:0000269|PubMed:17183367,ECO:0000269|PubMed:17309234, ECO:0000269|PubMed:20048074,ECO:0000269|PubMed:20237237, ECO:0000269|PubMed:20458141,ECO:0000269|PubMed:20595380, ECO:0000269|PubMed:21483833,ECO:0000269|PubMed:21741370, ECO:0000269|PubMed:21778237,ECO:0000269|PubMed:23515529, ECO:0000269|PubMed:25355947}. Is responsible for the charging of tRNA(Phe) withphenylalanine in mitochondrial translation. To a lesser extent,also catalyzes direct attachment of m-Tyr (an oxidized version ofPhe) to tRNA(Phe), thereby opening the way for delivery of themisacylated tRNA to the ribosome and incorporation of ROS-damagedamino acid into proteins. {ECO:0000269|PubMed:19549855,ECO:0000269|PubMed:22833457}.

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 COMMD1_FARS2


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.
>In-frame_COMMD1_ENST00000311832_chr2_62228117_+_FARS2_ENST00000324331_chr6_5771524_+_200aa
MAAGELEGGKPLSGLLNALAQDTFHGYPGITEELLRSQLYPEVPPEEFRPFLAKMRGILKSIASADMDFNQLEAFLTAQTKKQGGITSDQ
AAVISKFWKSHKTKIRESLMNQSRWNSGLRGLSWRVDGKSQSRHSAQIHTPVAIIELELGKYGQDAQDQPLLPHHVPPHGTDSVPERGQA

>In-frame_COMMD1_ENST00000538736_chr2_62228117_+_FARS2_ENST00000324331_chr6_5771524_+_200aa
MAAGELEGGKPLSGLLNALAQDTFHGYPGITEELLRSQLYPEVPPEEFRPFLAKMRGILKSIASADMDFNQLEAFLTAQTKKQGGITSDQ
AAVISKFWKSHKTKIRESLMNQSRWNSGLRGLSWRVDGKSQSRHSAQIHTPVAIIELELGKYGQDAQDQPLLPHHVPPHGTDSVPERGQA


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_COMMD1_ENST00000311832_chr2_62228117_+_FARS2_ENST00000324331_chr6_5771524_+_601nt
ATGGCGGCGGGCGAGCTTGAGGGTGGCAAACCCCTGAGCGGGCTGCTGAATGCGCTGGCCCAGGACACTTTCCACGGGTACCCCGGCATC
ACAGAGGAGCTGCTACGGAGCCAGCTATATCCAGAGGTGCCACCCGAGGAGTTCCGCCCCTTTCTGGCAAAGATGAGGGGGATTCTTAAG
TCTATTGCGTCTGCAGACATGGATTTCAACCAGCTGGAGGCATTCTTGACTGCTCAAACCAAAAAGCAAGGTGGGATCACATCTGACCAA
GCTGCTGTCATTTCCAAATTCTGGAAGAGCCACAAGACAAAAATCCGTGAGAGCCTCATGAACCAGAGCCGCTGGAATAGCGGGCTTCGG
GGCCTGAGCTGGAGAGTTGATGGCAAGTCTCAGTCAAGGCACTCAGCTCAAATACACACACCTGTTGCCATTATAGAGCTGGAATTAGGC
AAATATGGACAGGACGCACAAGACCAGCCACTGCTACCGCATCACGTACCGCCACATGGAACGGACTCTGTCCCAGAGAGAGGTCAGGCA

>In-frame_COMMD1_ENST00000538736_chr2_62228117_+_FARS2_ENST00000324331_chr6_5771524_+_601nt
ATGGCGGCGGGCGAGCTTGAGGGTGGCAAACCCCTGAGCGGGCTGCTGAATGCGCTGGCCCAGGACACTTTCCACGGGTACCCCGGCATC
ACAGAGGAGCTGCTACGGAGCCAGCTATATCCAGAGGTGCCACCCGAGGAGTTCCGCCCCTTTCTGGCAAAGATGAGGGGGATTCTTAAG
TCTATTGCGTCTGCAGACATGGATTTCAACCAGCTGGAGGCATTCTTGACTGCTCAAACCAAAAAGCAAGGTGGGATCACATCTGACCAA
GCTGCTGTCATTTCCAAATTCTGGAAGAGCCACAAGACAAAAATCCGTGAGAGCCTCATGAACCAGAGCCGCTGGAATAGCGGGCTTCGG
GGCCTGAGCTGGAGAGTTGATGGCAAGTCTCAGTCAAGGCACTCAGCTCAAATACACACACCTGTTGCCATTATAGAGCTGGAATTAGGC
AAATATGGACAGGACGCACAAGACCAGCCACTGCTACCGCATCACGTACCGCCACATGGAACGGACTCTGTCCCAGAGAGAGGTCAGGCA


* Fusion transcript sequences (Full-length transcript).
>In-frame_COMMD1_ENST00000311832_chr2_62228117_+_FARS2_ENST00000324331_chr6_5771524_+_633nt
TCAGCTGTTGCGGGGCGGGGCCTTCGCAGAGCATGGCGGCGGGCGAGCTTGAGGGTGGCAAACCCCTGAGCGGGCTGCTGAATGCGCTGG
CCCAGGACACTTTCCACGGGTACCCCGGCATCACAGAGGAGCTGCTACGGAGCCAGCTATATCCAGAGGTGCCACCCGAGGAGTTCCGCC
CCTTTCTGGCAAAGATGAGGGGGATTCTTAAGTCTATTGCGTCTGCAGACATGGATTTCAACCAGCTGGAGGCATTCTTGACTGCTCAAA
CCAAAAAGCAAGGTGGGATCACATCTGACCAAGCTGCTGTCATTTCCAAATTCTGGAAGAGCCACAAGACAAAAATCCGTGAGAGCCTCA
TGAACCAGAGCCGCTGGAATAGCGGGCTTCGGGGCCTGAGCTGGAGAGTTGATGGCAAGTCTCAGTCAAGGCACTCAGCTCAAATACACA
CACCTGTTGCCATTATAGAGCTGGAATTAGGCAAATATGGACAGGACGCACAAGACCAGCCACTGCTACCGCATCACGTACCGCCACATG
GAACGGACTCTGTCCCAGAGAGAGGTCAGGCACATCCACCAGGCCTTGCAGGAGGCTGCAGTCCAGCTGTTGGGTGTGGAGGGCAGGTTC

>In-frame_COMMD1_ENST00000538736_chr2_62228117_+_FARS2_ENST00000324331_chr6_5771524_+_606nt
AGAGCATGGCGGCGGGCGAGCTTGAGGGTGGCAAACCCCTGAGCGGGCTGCTGAATGCGCTGGCCCAGGACACTTTCCACGGGTACCCCG
GCATCACAGAGGAGCTGCTACGGAGCCAGCTATATCCAGAGGTGCCACCCGAGGAGTTCCGCCCCTTTCTGGCAAAGATGAGGGGGATTC
TTAAGTCTATTGCGTCTGCAGACATGGATTTCAACCAGCTGGAGGCATTCTTGACTGCTCAAACCAAAAAGCAAGGTGGGATCACATCTG
ACCAAGCTGCTGTCATTTCCAAATTCTGGAAGAGCCACAAGACAAAAATCCGTGAGAGCCTCATGAACCAGAGCCGCTGGAATAGCGGGC
TTCGGGGCCTGAGCTGGAGAGTTGATGGCAAGTCTCAGTCAAGGCACTCAGCTCAAATACACACACCTGTTGCCATTATAGAGCTGGAAT
TAGGCAAATATGGACAGGACGCACAAGACCAGCCACTGCTACCGCATCACGTACCGCCACATGGAACGGACTCTGTCCCAGAGAGAGGTC


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FusionGenePPI for COMMD1_FARS2


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
COMMD1NFKBIA, XIAP, SOCS1, CUL2, TCEB1, RELA, CUL1, CUL3, CUL4A, CUL4B, CUL5, CUL7, HIF1A, HSPA4, CLU, CFTR, SCNN1D, KAT2A, AKT1, SGK1, SCNN1B, SPP1, NAIP, BIRC3, CDKN2A, NMRAL1, SOD1, ATP7B, COMMD1, COMMD2, COMMD3, COMMD4, COMMD5, COMMD6, COMMD7, COMMD8, COMMD10, REL, RELB, NFKB1, NFKB2, SCNN1G, ATP7A, BARD1, BRCA1, LIG4, VCP, SLC12A2, CCDC22, BAHCC1, EP300, CCDC93, C16orf62, SCLT1, PARK2, FAM45A, COMMD9, DSCR3, E2F6, TFDP1, BCR, VPS29, VPS33B, STK11IP, TTF2, NFYC, KIF2B, FAM167A, TRIM16L, G6PD, ATAD3C, TBC1D4, RAD21, TRIM25, FAM107AFARS2USP45, G3BP2, ICT1, ISG15, CUL3, RCBTB2, KRT13, KRT31, TRIM27, TADA2A, TFCP2, MKRN3, STX11, CALCOCO2, MID2, IKZF3, APPL1, ADAMTSL4, AGTRAP, TRIM54, HMBOX1, CMTM5, KRT40, KRTAP10-7, KRTAP10-9, KRTAP10-5, KRTAP10-3, NOTCH2NL, ENO1, SHMT2, NXF1, HIST1H1A, ZC3H3, HNRNPA1, GAMT, STAT5A, TOMM40, CHST15, NEDD1, CHCHD2, MRPL38, HIST1H1E, HIST1H1T, ZCRB1


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 COMMD1_FARS2


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 COMMD1_FARS2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOMMD1C0019189Hepatitis, Chronic2CTD_human
HgeneCOMMD1C0020517Hypersensitivity1CTD_human
HgeneCOMMD1C0023890Liver Cirrhosis1CTD_human
HgeneCOMMD1C0041755Adverse reaction to drug1CTD_human
HgeneCOMMD1C1876165Copper-Overload Cirrhosis1CTD_human
TgeneFARS2C3554168COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 142ORPHANET;UNIPROT