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

LMBRD1 Gene

protein-coding   GIFtS: 52
GCID: GC06M070385

LMBR1 domain containing 1

(Previous name: chromosome 6 open reading frame 209 )
(Previous symbol: C6orf209)
 Explore 14 diseases affiliated with
LMBRD1 via our new
 Human Malady Compendium 
Biological research products
for LMBRD1
    

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

Aliases
LMBR1 Domain Containing 11 2     CblF1
C6orf2091 2 3     Chromosome 6 Open Reading Frame 2091
NESI2 3 5     MAHCF2
Nuclear Export Signal-Interacting Protein2 3     Hepatitis Delta Antigen-L Interacting Protein2
HDAg-L-Interacting Protein NESI2 3     Liver Regeneration P-53 Related Protein2
LMBD12 5     Probable Lysosomal Cobalamin Transporter2
FLJ112401     LMBR1 Domain-Containing Protein 13
BA810I22.11     

External Ids:    HGNC: 230381   Entrez Gene: 557882   Ensembl: ENSG000001682167   OMIM: 6126255   UniProtKB: Q9NUN53   

Export aliases for LMBRD1 gene to outside databases

Previous GC identifers: GC06M070443 GC06M067576


(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 LMBRD1:
This gene encodes a lysosomal membrane protein that may be involved in the transport and metabolism of cobalamin. This
protein also interacts with the large form of the hepatitis delta antigen and may be required for the
nucleocytoplasmic shuttling of the hepatitis delta virus. Mutations in this gene are associated with the vitamin B12
metabolism disorder termed, homocystinuria-megaloblastic anemia complementation type F.(provided by RefSeq, Oct 2009)

UniProtKB/Swiss-Prot: LMBD1_HUMAN, Q9NUN5
Function: Probable lysosomal cobalamin transporter. Required to export cobalamin from lysosomes allowing its conversion
to cofactors. Isoform 3 may play a role in the assembly of hepatitis delta virus (HDV)

Gene Wiki entry for LMBRD1


(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_000006.11  NC_018917.1  NT_007299.13  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the LMBRD1 gene promoter:
         HOXA9   HOXA9B   SREBP-1c   SREBP-1b   SREBP-1a   IRF-7A   Meis-1a   Pax-4a   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLMBRD1 promoter sequence
   Search SABiosciences Chromatin IP Primers for LMBRD1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat LMBRD1


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

Entrez Gene cytogenetic band: 6q13   Ensembl cytogenetic band:  6q13   HGNC cytogenetic band: 6q13

LMBRD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LMBRD1 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M070385:  view genomic region     (about GC identifiers)

Start:
70,385,641 bp from pter      End:
70,507,049 bp from pter
Size:
121,409 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: LMBD1_HUMAN, Q9NUN5 (See protein sequence)
Recommended Name: Probable lysosomal cobalamin transporter  
Size: 540 amino acids; 61389 Da
Subunit: Isoform 3 interacts with Hepatitis delta virus NES(HDAg-L)
Subcellular location: Lysosome membrane; Multi-pass membrane protein
Sequence caution: Sequence=AAK26247.1; Type=Frameshift; Positions=137;
Secondary accessions: A8K204 E1P531 Q5VUN6 Q86Y70 Q96FW4 Q9BY56 Q9NZD6
Alternative splicing: 4 isoforms:  Q9NUN5-1   Q9NUN5-2   Q9NUN5-3   Q9NUN5-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for LMBRD1: NX_Q9NUN5

Post-translational modifications:

  • N-glycosylated1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9NUN5

  • LMBRD1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_060838.3  
    ENSEMBL proteins: 
     ENSP00000359609   ENSP00000359602   ENSP00000433385  

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    Uscn Proteins for LMBRD1

    Gene Ontology (GO): 2 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--


    LMBRD1 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

    LMBRD1 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR006876 LMBR1-like_membr_prot

    Graphical View of Domain Structure for InterPro Entry Q9NUN5

    ProtoNet protein and cluster: Q9NUN5

    UniProtKB/Swiss-Prot: LMBD1_HUMAN, Q9NUN5
    Similarity: Belongs to the LIMR family. LMBRD1 subfamily


    (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: LMBD1_HUMAN, Q9NUN5
    Function: Probable lysosomal cobalamin transporter. Required to export cobalamin from lysosomes allowing its conversion
    to cofactors. Isoform 3 may play a role in the assembly of hepatitis delta virus (HDV)

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    hsa-miR-1299
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    Inhib. RNA
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0031419cobalamin binding IEA--


    LMBRD1 for ontologies           About GeneDecksing



    (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
    1Vitamin digestion and absorption
    Vitamin digestion and absorption1.00

    Pathway sources
    See GeneCards unified pathways
    Show all pathways



    1         Kegg Pathway  (Kegg details for LMBRD1):
        Vitamin digestion and absorption


    LMBRD1 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for LMBRD1

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for LMBRD1 (ENSP000003596094) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006810transport IEA--
    GO:0019048virus-host interaction IEA--
    GO:0044419interspecies interaction between organisms ----


    LMBRD1 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
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for LMBRD1
    Search CenterWatch for drugs/clinical trials and news about LMBRD1 / LMBD1 

    (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,
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    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 LMBRD1 gene: 
    NM_018368.3  

    Unigene Clusters for LMBRD1:

    LMBR1 domain containing 1
    Hs.271643  [show with all ESTs], Hs.736005  [show with all ESTs]
    Unigene Representative Sequences: AB074281, AK021916
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000370577(uc010kal.3 uc003pfa.3 uc003pfb.3) ENST00000370570(uc003pez.3)
    ENST00000472827

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    Inhib. RNA
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    Additional cDNA sequence: AK021916.1 

    20 DOTS entries:

    DT.100037108  DT.100788689  DT.416652  DT.101977488  DT.91650685  DT.100719931  DT.92022767  DT.95225381 
    DT.100788684  DT.100788690  DT.121358132  DT.40131423  DT.121358112  DT.121358159  DT.121358059  DT.121358096 
    DT.121358101  DT.433274  DT.92443785  DT.92443791 

    24/242 AceView cDNA sequences (see all 242):

    CD679602 BG565225 CA388735 AK002102 AI766639 AI031904 NM_018368 BI711177 
    AF113224 CF265153 BQ439774 BU838454 CA943518 CR612672 AA043189 CR618396 
    AL560287 AI241774 AA721753 BU072102 BQ286780 CR595980 AW827132 BE895637 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for LMBRD1    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17a · 17b
    SP1:                    -                                                                                                   
    SP2:                                                                                                                        
    SP3:                    -           -     -                                         -                                       


    ECgene alternative splicing isoforms for LMBRD1

    (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

    LMBRD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTATGTAAAT

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

    About this image
    See LMBRD1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for LMBRD1

    SOURCE GeneReport for Unigene clusters: Hs.271643 Hs.736005

    UniProtKB/Swiss-Prot: LMBD1_HUMAN, Q9NUN5
    Tissue specificity: Isoform 3 is expressed in liver

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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 chordates.

    Orthologs for LMBRD1 gene from 5/20 species (see all 20)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lmbrd11 , 5 LMBR1 domain containing 11, 5 85.86(n)1
    93.64(a)1
      1 (10.18 cM)5
    684211  NM_026719.21  NP_080995.21 
     246785445 
    chicken
    (Gallus gallus)
    Aves LMBRD11 LMBR1 domain containing 1 77.99(n)
    82.93(a)
      421874  NM_001006413.1  NP_001006413.1 
    lizard
    (Anolis carolinensis)
    Reptilia LMBRD16
    --
    81(a)
    1 ↔ 1
    1(167033067-167114105)
    African clawed frog
    (Xenopus laevis)
    Amphibia LOC3984682 hypothetical protein LOC398468 78.9(n)    BC054294.1 
    zebrafish
    (Danio rerio)
    Actinopterygii CK026834.12   -- 72.96(n)    CK026834.1 


    ENSEMBL Gene Tree for LMBRD1 (if available)
    TreeFam Gene Tree for LMBRD1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (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

    10/2033 NCBI SNPs in LMBRD1 are shown (see all 2033    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs768703861,2
    C,--67577303(+) GAACTC/TGTGAA 2 K E mis10--------
    rs1133704071,2
    C,--67577482(+) AACTTT/AGGTCT 1 -- int11Minor allele frequency- A:0.50NA 2
    rs32140221,2
    C,F,H,--67577483(+) acttaG/Agtctc 1 -- int14Minor allele frequency- A:0.01NS EA 418
    rs455273391,2
    --67577496(+) TCCAAA/GGCCCA 1 -- int10--------
    rs777930181,2
    F,--67579574(+) AAACAT/CAAAAT 1 -- int11Minor allele frequency- C:0.07WA 118
    rs1999676671,2
    C--67579843(+) TAAAAA/CAAAAA 1 -- int10--------
    rs94548681,2
    C,F,H,--67580718(+) GAGAAC/AAATTG 1 -- int120Minor allele frequency- A:0.07EA NA NS WA 2532
    rs783138991,2
    C,F,--67581227(+) ACAGAG/AGCTGA 1 -- int11Minor allele frequency- A:0.03WA 118
    rs69019411,2
    C,F,H,--67581874(+) CAAAAG/TAAAAT 1 -- int15Minor allele frequency- T:0.01NS EA WA 420
    rs126618421,2
    H--67581953(+) GGGGGA/GGGGGG 1 -- int1 trp30--------

    HapMap Linkage Disequilibrium report for LMBRD1 (70385641 - 70507049 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for LMBRD1
         1 CNV: 59358
         1 Indel: 47153
    Human Gene Mutation Database (HGMD): LMBRD1

    Locus Specific Mutation Databases (LSDB): LMBRD1

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

    LMBRD1 for disorders           About GeneDecksing

    OMIM gene information: 612625   
    OMIM disorders: 277380  
    UniProtKB/Swiss-Prot: LMBD1_HUMAN, Q9NUN5
  • Defects in LMBRD1 are the cause of methylmalonic aciduria and homocystinuria type cblF (MMAHCF) [MIM:277380].
  • A disorder of cobalamin metabolism characterized by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and
    methylcobalamin (MeCbl). It is due to accumulation of free cobalamin in lysosomes, thus hindering its conversion to
    cofactors. Clinical features include developmental delay, stomatitis, glossitis, seizures and methylmalonic aciduria
    responsive to vitamin B12

    14 diseases for LMBRD1:    About MalaCards
    megaloblastic anemia    cblf    homocystinuria    homocystinuria-megaloblastic anemia
    hepatitis    methylmalonic aciduria and homocystinuria    methylmalonic aciduria and homocystinuria type cblf    disorders of intracellular cobalamin metabolism
    anemia    bile reflux    glossitis    metabolic disorders
    stomatitis    malaria

    1 disease from the University of Copenhagen DISEASES database for LMBRD1:
    Tyrosinemia type I
    GeneTests: LMBRD1
    Disorders of Intracellular Cobalamin Metabolism


    Export disorders for LMBRD1 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 LMBRD1 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with LMBRD1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of a putative lysosomal cobalamin exporter altered in the cblF defect of vitamin B12 metabolism. (PubMed id 19136951)1, 2, 3 Rutsch F.... Nuernberg P. (2009)
    2. Novel nuclear export signal-interacting protein, NESI, critical for the assembly of hepatitis delta virus. (PubMed id 15956556)1, 2 Wang Y.-H.... Chang M.-F. (2005)
    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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    5. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
    6. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PubMed id 11042152)1, 2 Zhang Q.-H.... Chen Z. (2000)
    7. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    8. Novel splice site mutations and a large deletion in t hree patients with the cblF inborn error of vitamin B12 metabolism. (PubMed id 21303734)1 Miousse I.R....Rosenblatt D.S. (2011)
    9. LMBRD1: the gene for the cblF defect of vitamin Ba88a88 m etabolism. (PubMed id 20446115)1 Rutsch F....Fowler B. (2011)
    10. Global identification of modular cullin-RING ligase su bstrates. (PubMed id 21963094)1 Emanuele M.J....Elledge S.J. (2011)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 55788 HGNC: 23038 AceView: C6orf209 Ensembl:ENSG00000168216 euGenes: HUgn55788
    ECgene: LMBRD1 Kegg: 55788 H-InvDB: LMBRD1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for LMBRD1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for LMBRD1 gene:
    Search GeneIP for patents involving LMBRD1

    GeneCards and IP:
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