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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: 19363

FusionGeneSummary for LAMA3_SNRPD1

check button Fusion gene summary
Fusion gene informationFusion gene name: LAMA3_SNRPD1
Fusion gene ID: 19363
HgeneTgene
Gene symbol

LAMA3

SNRPD1

Gene ID

3910

6633

Gene namelaminin subunit alpha 4small nuclear ribonucleoprotein D2 polypeptide
SynonymsCMD1JJ|LAMA3|LAMA4*-1SMD2|SNRPD1|Sm-D2
Cytomap

6q21

19q13.32

Type of geneprotein-codingprotein-coding
Descriptionlaminin subunit alpha-4laminin alpha 4 chainlaminin, alpha 4small nuclear ribonucleoprotein Sm D2small nuclear ribonucleoprotein D2 polypeptide 16.5kDasnRNP core protein D2
Modification date2018052220180523
UniProtAcc

Q16787

P62314

Ensembl transtripts involved in fusion geneENST00000313654, ENST00000399516, 
ENST00000269217, ENST00000587184, 
ENST00000588770, 
ENST00000300413, 
ENST00000579618, ENST00000582475, 
Fusion gene scores* DoF score18 X 14 X 9=22684 X 3 X 4=48
# samples 234
** MAII scorelog2(23/2268*10)=-3.30171487399785
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LAMA3 [Title/Abstract] AND SNRPD1 [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
TgeneSNRPD1

GO:0000387

spliceosomal snRNP assembly

18984161


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
TCGALDHNSCTCGA-CV-7104-01ALAMA3chr18

21357583

+SNRPD1chr18

19209023

+
* 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-shitENST00000313654ENST00000300413LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
5CDS-3UTRENST00000313654ENST00000579618LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
5CDS-3UTRENST00000313654ENST00000582475LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
Frame-shitENST00000399516ENST00000300413LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
5CDS-3UTRENST00000399516ENST00000579618LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
5CDS-3UTRENST00000399516ENST00000582475LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
intron-3CDSENST00000269217ENST00000300413LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
intron-3UTRENST00000269217ENST00000579618LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
intron-3UTRENST00000269217ENST00000582475LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
intron-3CDSENST00000587184ENST00000300413LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
intron-3UTRENST00000587184ENST00000579618LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
intron-3UTRENST00000587184ENST00000582475LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
intron-3CDSENST00000588770ENST00000300413LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
intron-3UTRENST00000588770ENST00000579618LAMA3chr18

21357583

+SNRPD1chr18

19209023

+
intron-3UTRENST00000588770ENST00000582475LAMA3chr18

21357583

+SNRPD1chr18

19209023

+

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FusionProtFeatures for LAMA3_SNRPD1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LAMA3

Q16787

SNRPD1

P62314

Core component of the spliceosomal U1, U2, U4 and U5small nuclear ribonucleoproteins (snRNPs), the building blocks ofthe spliceosome. Thereby, plays an important role in the splicingof cellular pre-mRNAs. Most spliceosomal snRNPs contain a commonset of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF andSNRPG that assemble in a heptameric protein ring on the Sm site ofthe small nuclear RNA to form the core snRNP. May act as a chargedprotein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts withRNA. {ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:23333303}.

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 LAMA3_SNRPD1


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 LAMA3_SNRPD1


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
LAMA3SDC2, APC, SIRT1, TUBG1, TSHR, TAZ, PTPRK, PLG, PLAT, SPINK4, CD44, DEFA1, SCGB2A2, GML, SCGB1D4, SLAMF1SNRPD1LSM8, RNU11, PRMT5, CLNS1A, WDR77, GEMIN5, SMN1, SNRPD2, SF3A2, DDX20, SMN2, CDC5L, SRRM2, RBM39, SREK1, HDGF, ARRB1, ARRB2, HNRNPA1, CUL3, CUL4A, CUL4B, CUL5, CUL2, CUL1, COPS5, COPS6, DCUN1D1, CAND1, NEDD8, SNRPB, SF3B3, SNRPE, SF3A1, SNRPA1, SNRPD3, PRPF8, SNRNP70, LSM2, SF3B1, SF3B2, YBX1, HNRNPU, SF3B5, SF3B6, HNRNPK, PRPF6, SNRNP200, HNRNPM, EFTUD2, U2AF2, HNRNPA2B1, PRPF19, TPR, SART1, DDX5, BCAS2, TOP1, EEF1A1, HSPA5, UCHL3, TRIM28, RPS7, SRP14, SUPT16H, HSP90AB1, PTGES3, APEX1, ESR1, MAGOH, EIF4A3, SMURF1, CTNNB1, FN1, VCAM1, U2AF1, LSM3, IFIT1, IFIT2, IFIT3, IL7R, ITGA4, PAN2, CD81, IGSF8, ICAM1, NPM1, EGFR, SRPK2, SRPK3, PRPF4B, FERMT2, PDHB, SCLY, EIF5, WWOX, ASB1, ASB2, OBSL1, EZH2, SUZ12, EED, RNF2, BLK, DDX23, SNRNP40, SNUPN, MCFD2, PRPF31, RCC2, RUVBL1, SF3A3, DHX9, DPY30, LSM7, LUC7L, LUC7L2, PDCD4, SNRPF, TIA1, TMOD3, USP7, YWHAE, YWHAQ, RNU12, GEMIN7, CRBN, PTPN4, SNRPN, SNRPG, CD2BP2, LSM6, GEMIN2, PRPF3, NCL, CYLD, AAR2, EAPP, TSSC4, HEY1, LMNA


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 LAMA3_SNRPD1


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 LAMA3_SNRPD1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLAMA3C0027339Nail Diseases1CTD_human
HgeneLAMA3C0037299Skin Ulcer1CTD_human;HPO
HgeneLAMA3C0079301Junctional Epidermolysis Bullosa1CTD_human
HgeneLAMA3C1328355Laryngoonychocutaneous syndrome1CTD_human;ORPHANET