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Aliases for LMBRD1 Gene

Aliases for LMBRD1 Gene

  • LMBR1 Domain Containing 1 2 3 5
  • Nuclear Export Signal-Interacting Protein 3 4
  • HDAg-L-Interacting Protein NESI 3 4
  • C6orf209 3 4
  • NESI 3 4
  • Hepatitis Delta Antigen-L Interacting Protein 3
  • Probable Lysosomal Cobalamin Transporter 3
  • Liver Regeneration P-53 Related Protein 3
  • Chromosome 6 Open Reading Frame 209 2
  • LMBR1 Domain-Containing Protein 1 4
  • LMBD1 3
  • MAHCF 3

External Ids for LMBRD1 Gene

Previous HGNC Symbols for LMBRD1 Gene

  • C6orf209

Previous GeneCards Identifiers for LMBRD1 Gene

  • GC06M070443
  • GC06M067576
  • GC06M070385

Summaries for LMBRD1 Gene

Entrez Gene Summary for LMBRD1 Gene

  • 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]

GeneCards Summary for LMBRD1 Gene

LMBRD1 (LMBR1 Domain Containing 1) is a Protein Coding gene. Diseases associated with LMBRD1 include Methylmalonic Aciduria And Homocystinuria, Cblf Type and Cblf. Among its related pathways are Vitamin digestion and absorption and Metabolism of water-soluble vitamins and cofactors. GO annotations related to this gene include insulin receptor binding and cobalamin binding.

UniProtKB/Swiss-Prot for LMBRD1 Gene

  • 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 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LMBRD1 Gene

Genomics for LMBRD1 Gene

Regulatory Elements for LMBRD1 Gene

Enhancers for LMBRD1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G069756 0.9 dbSUPER 17.7 +36.6 36632 7.8 HDAC1 ATF1 TBL1XR1 ARNT CHAMP1 TCF12 GATA2 ELK1 SCRT2 CREM LMBRD1 GAPDHP42 COL19A1 GC06M069784
GH06G069770 0.4 dbSUPER 12.6 +24.8 24782 2.9 ZNF24 LMBRD1 GAPDHP42 GC06M069784
GH06G069774 0.3 FANTOM5 12.6 +23.0 23014 0.2 LMBRD1 GC06M069784 GAPDHP42
GH06G069795 1.3 ENCODE dbSUPER 0.7 +0.6 561 3.0 HDGF PKNOX1 FOXA2 ARID4B SIN3A YY1 SLC30A9 ZNF766 CBX5 ZNF143 GAPDHP42 LMBRD1 GC06M069784
GH06G069812 1.3 Ensembl ENCODE dbSUPER 0.4 -17.4 -17442 5.2 CTCF PKNOX1 ZSCAN4 YY1 CTBP1 GATA3 CBX5 EED RELB IKZF2 COL19A1 LMBRD1 GC06P069860
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LMBRD1 on UCSC Golden Path with GeneCards custom track

Promoters for LMBRD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000198623 857 1801 HDGF PKNOX1 FOXA2 ARID4B SIN3A YY1 SLC30A9 ZNF766 CBX5 ZNF143

Genomic Location for LMBRD1 Gene

Chromosome:
6
Start:
69,675,749 bp from pter
End:
69,797,157 bp from pter
Size:
121,409 bases
Orientation:
Minus strand

Genomic View for LMBRD1 Gene

Genes around LMBRD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LMBRD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LMBRD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LMBRD1 Gene

Proteins for LMBRD1 Gene

  • Protein details for LMBRD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NUN5-LMBD1_HUMAN
    Recommended name:
    Probable lysosomal cobalamin transporter
    Protein Accession:
    Q9NUN5
    Secondary Accessions:
    • A8K204
    • E1P531
    • Q5VUN6
    • Q86Y70
    • Q96FW4
    • Q9BY56
    • Q9NZD6

    Protein attributes for LMBRD1 Gene

    Size:
    540 amino acids
    Molecular mass:
    61389 Da
    Quaternary structure:
    • Isoform 3 interacts with Hepatitis delta virus NES(HDAg-L).
    SequenceCaution:
    • Sequence=AAK26247.1; Type=Frameshift; Positions=137; Evidence={ECO:0000305};

    Alternative splice isoforms for LMBRD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LMBRD1 Gene

Post-translational modifications for LMBRD1 Gene

  • N-glycosylated.
  • Glycosylation at posLast=7878, Asn88, posLast=170170, Asn347, posLast=448448, and Asn457
  • Modification sites at PhosphoSitePlus

Other Protein References for LMBRD1 Gene

No data available for DME Specific Peptides for LMBRD1 Gene

Domains & Families for LMBRD1 Gene

Protein Domains for LMBRD1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LMBRD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NUN5

UniProtKB/Swiss-Prot:

LMBD1_HUMAN :
  • Belongs to the LIMR family. LMBRD1 subfamily.
Family:
  • Belongs to the LIMR family. LMBRD1 subfamily.
genes like me logo Genes that share domains with LMBRD1: view

No data available for Gene Families for LMBRD1 Gene

Function for LMBRD1 Gene

Molecular function for LMBRD1 Gene

UniProtKB/Swiss-Prot 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 Ontology (GO) - Molecular Function for LMBRD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005158 insulin receptor binding IEA --
GO:0015235 cobalamin transporter activity TAS --
GO:0031419 cobalamin binding IEA --
genes like me logo Genes that share ontologies with LMBRD1: view
genes like me logo Genes that share phenotypes with LMBRD1: view

Human Phenotype Ontology for LMBRD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LMBRD1 Gene

MGI Knock Outs for LMBRD1:

Animal Model Products

CRISPR Products

miRNA for LMBRD1 Gene

miRTarBase miRNAs that target LMBRD1

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for LMBRD1 Gene

Localization for LMBRD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LMBRD1 Gene

Lysosome membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LMBRD1 gene
Compartment Confidence
lysosome 5
plasma membrane 4
cytosol 1

Gene Ontology (GO) - Cellular Components for LMBRD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane TAS --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IDA,IEA 19946888
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LMBRD1: view

Pathways & Interactions for LMBRD1 Gene

genes like me logo Genes that share pathways with LMBRD1: view

Interacting Proteins for LMBRD1 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000359609%0d%0a9606.ENSP00000319690%0d%0a
Selected Interacting proteins: ENSP00000359609 Q9NUN5-LMBD1_HUMAN for LMBRD1 Gene via STRING IID

Gene Ontology (GO) - Biological Process for LMBRD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0009235 cobalamin metabolic process TAS --
GO:0015889 cobalamin transport IEA --
GO:0016032 viral process IEA --
GO:0038016 insulin receptor internalization IEA --
genes like me logo Genes that share ontologies with LMBRD1: view

No data available for SIGNOR curated interactions for LMBRD1 Gene

Transcripts for LMBRD1 Gene

Unigene Clusters for LMBRD1 Gene

LMBR1 domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LMBRD1 Gene

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

Relevant External Links for LMBRD1 Gene

GeneLoc Exon Structure for
LMBRD1
ECgene alternative splicing isoforms for
LMBRD1

Expression for LMBRD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LMBRD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LMBRD1 Gene

This gene is overexpressed in Amniocyte (13.8), Skin (7.5), and Spinal cord (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LMBRD1 Gene



Protein tissue co-expression partners for LMBRD1 Gene

NURSA nuclear receptor signaling pathways regulating expression of LMBRD1 Gene:

LMBRD1

SOURCE GeneReport for Unigene cluster for LMBRD1 Gene:

Hs.271643

mRNA Expression by UniProt/SwissProt for LMBRD1 Gene:

Q9NUN5-LMBD1_HUMAN
Tissue specificity: Isoform 3 is expressed in liver.

Evidence on tissue expression from TISSUES for LMBRD1 Gene

  • Nervous system(4.9)
  • Heart(4.3)
  • Bone marrow(4.2)
  • Blood(2.3)
  • Skin(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LMBRD1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • outer ear
  • skull
  • tongue
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • kidney
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • red blood cell
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with LMBRD1: view

Primer Products

No data available for mRNA differential expression in normal tissues for LMBRD1 Gene

Orthologs for LMBRD1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for LMBRD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LMBRD1 34 35
  • 99.69 (n)
dog
(Canis familiaris)
Mammalia LMBRD1 34 35
  • 93.96 (n)
cow
(Bos Taurus)
Mammalia LMBRD1 34 35
  • 91.89 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 90 (a)
OneToMany
-- 35
  • 82 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia LMBRD1 35
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lmbrd1 34 16 35
  • 85.76 (n)
rat
(Rattus norvegicus)
Mammalia Lmbrd1 34
  • 85.45 (n)
chicken
(Gallus gallus)
Aves LMBRD1 34 35
  • 77.78 (n)
lizard
(Anolis carolinensis)
Reptilia LMBRD1 35
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lmbrd1 34
  • 73.92 (n)
Str.13023 34
African clawed frog
(Xenopus laevis)
Amphibia LOC398468 34
zebrafish
(Danio rerio)
Actinopterygii lmbrd1 34 35
  • 67.62 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU02100 34
  • 41.41 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 35 (a)
OneToOne
Species where no ortholog for LMBRD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LMBRD1 Gene

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

Paralogs for LMBRD1 Gene

No data available for Paralogs for LMBRD1 Gene

Variants for LMBRD1 Gene

Sequence variations from dbSNP and Humsavar for LMBRD1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs749272546 Pathogenic 69,701,470(+) ATATT(-/C)AGTGG reference, frameshift-variant
rs112053239 Likely benign 69,797,131(+) GCCCT(C/G)GCTGG upstream-variant-2KB, utr-variant-5-prime
rs114726590 Likely benign 69,701,878(+) TGTCT(A/G)CTGTA intron-variant
rs202207965 Likely benign 69,701,547(+) AAACT(-/A/AA)AAAAA splice-acceptor-variant
rs2305837 Likely benign 69,713,847(+) AATAA(A/G)GTACC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LMBRD1 Gene

Variant ID Type Subtype PubMed ID
esv2038631 CNV deletion 18987734
esv2732253 CNV deletion 23290073
esv3451372 CNV duplication 20981092
esv3609422 CNV loss 21293372
esv999346 CNV deletion 20482838
nsv474410 CNV novel sequence insertion 20440878
nsv819863 CNV loss 19587683
nsv830682 CNV loss 17160897
nsv970139 CNV duplication 23825009
nsv970140 CNV duplication 23825009

Variation tolerance for LMBRD1 Gene

Residual Variation Intolerance Score: 33% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.75; 89.41% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LMBRD1 Gene

Human Gene Mutation Database (HGMD)
LMBRD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LMBRD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LMBRD1 Gene

Disorders for LMBRD1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for LMBRD1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
methylmalonic aciduria and homocystinuria, cblf type
  • methylmalonic aciduria and homocystinuria type cblf
cblf
  • methylmalonic aciduria and homocystinuria, cblf type
hepatitis
  • hepatitis a
disorders of intracellular cobalamin metabolism
transcobalamin ii deficiency
  • tcn2 deficiency
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

LMBD1_HUMAN
  • 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. {ECO:0000269 PubMed:19136951}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for LMBRD1

Genetic Association Database (GAD)
LMBRD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LMBRD1
genes like me logo Genes that share disorders with LMBRD1: view

No data available for Genatlas for LMBRD1 Gene

Publications for LMBRD1 Gene

  1. Identification of a putative lysosomal cobalamin exporter altered in the cblF defect of vitamin B12 metabolism. (PMID: 19136951) Rutsch F. … Nuernberg P. (Nat. Genet. 2009) 2 3 4 64
  2. Translocation of the ABC transporter ABCD4 from the endoplasmic reticulum to lysosomes requires the escort protein LMBD1. (PMID: 27456980) Kawaguchi K. … Imanaka T. (Sci Rep 2016) 2 3 64
  3. Novel nuclear export signal-interacting protein, NESI, critical for the assembly of hepatitis delta virus. (PMID: 15956556) Wang Y.-H. … Chang M.-F. (J. Virol. 2005) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for LMBRD1 Gene

Sources for LMBRD1 Gene

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