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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

LAMP3 Gene

protein-coding   GIFtS: 57
GCID: GC03M182840

lysosomal-associated membrane protein 3

 Explore 28 diseases affiliated with
LAMP3 via our new
 Human Malady Compendium 
Biological research products
for LAMP3
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Lysosomal-Associated Membrane Protein 31 2 3     LAMP-32 3
DCLAMP1 2 3 5     DC LAMP2 3
TSC4031 2 3     DC-Lysosome-Associated Membrane Glycoprotein2 3
CD2081 2     Lysosome-Associated Membrane Glycoprotein 32
DC-LAMP1 2     CD208 Antigen3
LAMP1 2     Protein TSC4033

External Ids:    HGNC: 145821   Entrez Gene: 270742   Ensembl: ENSG000000780817   OMIM: 6058835   UniProtKB: Q9UQV43   

Export aliases for LAMP3 gene to outside databases

Previous GC identifers: GC03M179608 GC03M183695 GC03M184242 GC03M184160 GC03M184322 GC03M180244


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for LAMP3:
Dendritic cells (DCs) are the most potent antigen-presenting cells. Immature DCs efficiently capture antigens and
differentiate into interdigitating dendritic cells (IDCs) in lymphoid tissues that induce primary T-cell responses
(summary by de Saint-Vis et al., 1998 (PubMed 9768752)).(supplied by OMIM, Dec 2010)

UniProtKB/Swiss-Prot: LAMP3_HUMAN, Q9UQV4
Function: May play a role in dendritic cell function and in adaptive immunity

Gene Wiki entry for LAMP3


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000003.11  NC_018914.1  NT_005612.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the LAMP3 gene promoter:
         TBP   Sox5   p53   HNF-1   NCX/Ncx   SEF-1 (1)   ZID   IRF-1   LCR-F1   HNF-1A   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLAMP3 promoter sequence
   Search SABiosciences Chromatin IP Primers for LAMP3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat LAMP3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3q26.3-q27   Ensembl cytogenetic band:  3q27.1   HGNC cytogenetic band: 3q26.3-q27

LAMP3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LAMP3 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M182840:  view genomic region     (about GC identifiers)

Start:
182,840,001 bp from pter      End:
182,881,627 bp from pter
Size:
41,627 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: LAMP3_HUMAN, Q9UQV4 (See protein sequence)
Recommended Name: Lysosome-associated membrane glycoprotein 3 precursor  
Size: 416 amino acids; 44346 Da
Subunit: Monomer
Subcellular location: Lysosome membrane; Single-pass type I membrane protein. Cytoplasmic vesicle membrane; Single-pass
type I membrane protein. Note=During dendritic cell maturation, detected on cytoplasmic vesicles (the MHC II
compartment) that contain MHC II proteins, LAMP1, LAMP2 and LAMP3. Detected on lysosomes in mature dendritic cells
Developmental stage: Up-regulated during dendritic cell maturation
1 PDB 3D structure from and Proteopedia for LAMP3:
4AKM (3D)    
Secondary accessions: D3DNS4 O94781 Q8NEC8

Explore the universe of human proteins at neXtProt for LAMP3: NX_Q9UQV4

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9UQV4

  • LAMP3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_055213.2  
    ENSEMBL proteins: 
     ENSP00000265598   ENSP00000418912   ENSP00000419059   ENSP00000420589  

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    Uscn Proteins for LAMP3

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005765lysosomal membrane IEA--
    GO:0016021integral to membrane IEA--
    GO:0097233alveolar lamellar body membrane IEA--


    LAMP3 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    LAMP3 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR002000 Lysosome-assoc_membr_glycop

    Graphical View of Domain Structure for InterPro Entry Q9UQV4

    ProtoNet protein and cluster: Q9UQV4

    UniProtKB/Swiss-Prot: LAMP3_HUMAN, Q9UQV4
    Similarity: Belongs to the LAMP family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: LAMP3_HUMAN, Q9UQV4
    Function: May play a role in dendritic cell function and in adaptive immunity

    miRNA
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    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LAMP3

    1 GenomeRNAi human phenotype for LAMP3:
     Increased gamma-H2AX phosphory 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Lysosome
    Lysosome1.00

    Pathway sources
    See GeneCards unified pathways
    Show all pathways



    1         Kegg Pathway  (Kegg details for LAMP3):
        Lysosome


    LAMP3 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for LAMP3

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for LAMP3 (Q9UQV42, 3 ENSP000002655984) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ABCA3Q997582, 3, ENSP000003017324MINT-7996593 MINT-7996607 MINT-7996380 I2D: score=1 STRING: ENSP00000301732
    SGTBENSP000003703954STRING: ENSP00000370395
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008283cell proliferation TAS9721848


    LAMP3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    LAMP3 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for LAMP3
    2 Novoseek chemical compound relationships for LAMP3 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    glycogen 5.33 1 16899762 (1)
    histamine 1.58 2 15675967 (2)

    Search CenterWatch for drugs/clinical trials and news about LAMP3 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for LAMP3 gene: 
    NM_014398.3  

    Unigene Cluster for LAMP3:

    Lysosomal-associated membrane protein 3
    Hs.518448  [show with all ESTs]
    Unigene Representative Sequence: NM_014398
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000265598(uc003flh.4) ENST00000466939 ENST00000476015 ENST00000470251
    ENST00000486686

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    Additional cDNA sequence: 

    AB013924.1 AJ005766.1 AK302894.1 AK313172.1 BC032940.2 

    5 DOTS entries:

    DT.312133  DT.100754307  DT.95270377  DT.75135130  DT.95208861 

    24/58 AceView cDNA sequences (see all 58):

    BX116004 BQ013434 AA314075 BQ029162 AA382983 BM985389 BM758382 NM_014398 
    AI304250 T92658 AI285648 AA416838 BF061943 BI822806 AW014530 BM997858 
    H65113 AB013924 BU687869 AA304148 T61471 BM996446 AW274149 BI818999 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for LAMP3    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c · 3d ^ 4 ^ 5 ^ 6 ^ 7
    SP1:                                                                  
    SP2:                                                                  
    SP3:                                                                  
    SP4:              -                                                   


    ECgene alternative splicing isoforms for LAMP3

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    LAMP3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TGTTTCCTTA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    LAMP3 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 2 LifeMap Cells 
    NameCategory
    Definitive endoderm-like cells (A scalable, suspensi...)
    Alveolar type II cells (Derivation of mature...)Lung
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See LAMP3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for LAMP3

    SOURCE GeneReport for Unigene cluster: Hs.518448

    UniProtKB/Swiss-Prot: LAMP3_HUMAN, Q9UQV4
    Tissue specificity: Detected in tonsil interdigitating dendritic cells, in spleen, lymph node, Peyer's patches in the
    small instestine, in thymus medulla and in B cells (at protein level). Expressed in lymphoid organs and dendritic
    cells. Expressed in lung. Up-regulated in carcinomas of the esophagus, colon, rectum, ureter, stomach, breast,
    fallopian tube, thyroid and parotid tissues

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for LAMP3 gene from 5/17 species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lamp31 , 5 lysosomal-associated membrane protein 31, 5 73.02(n)1
    54.46(a)1
      16 (12.17 cM)5
    2397391  NM_177356.31  NP_796330.21 
     196533815 
    chicken
    (Gallus gallus)
    Aves LAMP31 lysosomal-associated membrane protein 3 47.96(n)
    35.82(a)
      424961  NM_001146132.1  NP_001139604.1 
    lizard
    (Anolis carolinensis)
    Reptilia LAMP36
    --
    34(a)
    1 ↔ 1
    3(162317-168189)
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1000030431 lysosome-associated membrane glycoprotein 1-like 48.11(n)
    30.77(a)
      100003043  XM_001342652.3  XP_001342688.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta Lamp16
    Lamp1
    18(a)
    1 → many
    2L(21573389-21577103)


    ENSEMBL Gene Tree for LAMP3 (if available)
    TreeFam Gene Tree for LAMP3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for LAMP3 gene
    LAMP12  CD682  LAMP22  

    LAMP3 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/825 NCBI SNPs in LAMP3 are shown (see all 825    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs6047121,2
    C,A,H,--182839512(-) ACTCCA/GTCTCT 1 -- ds50015Minor allele frequency- G:0.00NA 10
    rs1150395151,2
    --182839619(+) TCCCAG/ACCCTC 1 -- ds50011Minor allele frequency- A:0.01WA 118
    rs1859844301,2
    --182839681(+) ATCTCA/GGCTCC 1 -- ds50010--------
    rs1123369371,2
    --182839766(+) TTAAGC/TAAACT 1 -- ds50011Minor allele frequency- T:0.50CSA 2
    rs788064291,2
    --182839895(+) AATTAT/CAGAAA 1 -- ds50011Minor allele frequency- C:0.01NA 120
    rs123531,2
    --182840022(-) TTTTGT/CAATAA 1 -- ut312Minor allele frequency- C:0.00MN NA 186
    rs23144161,2
    H--182840151(+) CTTGAC/TTAAGA 1 -- ut31 ese33Minor allele frequency- T:0.00EA NS 298
    rs738862311,2
    C,--182840224(+) AAAAAC/ACAGCA 1 -- ut311Minor allele frequency- A:0.50WA 2
    rs1832468011,2
    --182840250(+) GCAGGA/CTGCTC 1 -- ut310--------
    rs1414962751,2
    --182840324(+) GATGGA/GGCTAT 1 -- ut310--------

    HapMap Linkage Disequilibrium report for LAMP3 (182840001 - 182881627 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for LAMP3: --

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    LAMP3 for disorders           About GeneDecksing

    OMIM gene information: 605883    OMIM disorders: --

    20/28 diseases for LAMP3 (see all 28):    About MalaCards
    oculocutaneous albinism    bipolar affective disorder    lupus erythematosus    myocardial infarction
    acute myocardial infarction    systemic lupus erythematosus    albinism    gaucher's disease
    bipolar disorder    rheumatoid arthritis    multiple sclerosis    dermatomyositis
    hemangioma    parkinson's disease    copd    pertussis
    cervical cancer    cervicitis    arthritis    influenza

    5 Novoseek disease relationships for LAMP3 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    necrosis 6.43 1 11104808 (1)
    tumors 5.69 5 11104808 (1), 19244125 (1), 14982840 (1), 17127298 (1)
    lupus erythematosus systemic 1.54 1 7920621 (1)
    aids 0 1 12406887 (1)
    cancer 0 4 16204031 (2), 11485903 (1)

    Human Genome Epidemiology (HuGE) Navigator: LAMP3 (6 documents)

    Export disorders for LAMP3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for LAMP3 gene, integrated from 9 sources (see all 84):
    (articles sorted by number of sources associating them with LAMP3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation and characterization of a novel human lung-specific gene homologous to lysosomal membrane glycoprotein 1 and 2; significantly increased expression in cancers of various tissues. (PubMed id 9721848)1, 2, 3 Ozaki K.... Nakamura Y. (1998)
    2. A novel lysosome-associated membrane glycoprotein, DC-LAMP, induced upon DC maturation, is transiently expressed in MHC class II compartment. (PubMed id 9768752)1, 2, 9 de Saint-Vis B.M.... Lebecque S. (1998)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    4. Overexpression of LAMP3/TSC403/DC-LAMP promotes metastasis in uterine cervical cancer. (PubMed id 16204031)1, 9 Kanao H....Murata Y. (2005)
    5. Increased expression of CD208 (DC-LAMP) in epidermal keratinocytes of psoriatic lesions. (PubMed id 19335688)1, 9 Higaki M....Kawashima M. (2009)
    6. Dendritic cell-lysosomal-associated membrane protein (LAMP) and LAMP-1-HIV-1 gag chimeras have distinct cellular trafficking pathways and prime T and B cell responses to a diverse repertoire of epitopes. (PubMed id 16887987)1, 9 Arruda L.B....Marques E.T. (2006)
    7. Human dendritic cell lysosome-associated membrane protein expressed in lung type II pneumocytes. (PubMed id 15111122)1, 9 Akasaki K....August J.T. (2004)
    8. Crystal structure of the conserved domain of the DC lysosomal associated membrane protein: implications for the lysosomal glycocalyx. (PubMed id 22809326)2 Wilke S.... Bussow K. (2012)
    9. Web-based genome-wide association study identifies tw o novel loci and a substantial genetic component for Parkinson's disease. (PubMed id 21738487)1 Do C.B....Eriksson N. (2011)
    10. Hypoxic regulation and prognostic value of LAMP3 expression in breast cancer. (PubMed id 21319150)1 Nagelkerke A....Span P.N. (2011)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 27074 HGNC: 14582 AceView: LAMP3 Ensembl:ENSG00000078081 euGenes: HUgn27074
    ECgene: LAMP3 Kegg: 27074 H-InvDB: LAMP3

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    NameDescription
    PharmGKB entry for LAMP3 Pharmacogenomics, SNPs, Pathways
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