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LMBRD1 LMBR1 domain containing 1 [ Homo sapiens (human) ]

Gene ID: 55788, updated on 27-Nov-2024

Summary

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Official Symbol
LMBRD1provided by HGNC
Official Full Name
LMBR1 domain containing 1provided by HGNC
Primary source
HGNC:HGNC:23038
See related
Ensembl:ENSG00000168216 MIM:612625; AllianceGenome:HGNC:23038
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NESI; LMBD1; MAHCF; C6orf209
Summary
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]
Expression
Ubiquitous expression in adrenal (RPKM 45.7), kidney (RPKM 42.7) and 25 other tissues See more
Orthologs
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Genomic context

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See LMBRD1 in Genome Data Viewer
Location:
6q13
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (69674010..69797010, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (70854076..70977089, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (70383902..70506902, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901511 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:69404211-69404763 Neighboring gene Sharpr-MPRA regulatory region 12937 Neighboring gene uncharacterized LOC124901492 Neighboring gene adhesion G protein-coupled receptor B3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94316 Neighboring gene Sharpr-MPRA regulatory region 12106 Neighboring gene Sharpr-MPRA regulatory region 1724 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:69890327-69891526 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:69925706-69926680 Neighboring gene Sharpr-MPRA regulatory region 3236 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:70118423-70119622 Neighboring gene NANOG hESC enhancer GRCh37_chr6:70141628-70142137 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:70154657-70155166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:70155167-70155674 Neighboring gene Sharpr-MPRA regulatory region 1352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:70364977-70365478 Neighboring gene MPRA-validated peak5886 silencer Neighboring gene uncharacterized LOC124901337 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:70505853-70506409 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:70506410-70506965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24728 Neighboring gene nucleophosmin 1 pseudogene 37 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 42 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17316 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:70597939-70598122 Neighboring gene NANOG hESC enhancer GRCh37_chr6:70623798-70624319 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:70627263-70628462 Neighboring gene collagen type XIX alpha 1 chain Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:70845103-70845604 Neighboring gene ribosomal protein L37 pseudogene 15 Neighboring gene MPRA-validated peak5887 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24730 Neighboring gene collagen type IX alpha 1 chain

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Novel nuclear export signal-interacting protein, NESI, critical for the assembly of hepatitis delta virus. Wang YH, et al. J Virol, 2005 Jul. PMID 15956556, Free PMC Article
  2. A novel mutation in LMBRD1 causes the cblF defect of vitamin B(12) metabolism in a Turkish patient. Gailus S, et al. J Inherit Metab Dis, 2010 Feb. PMID 20127417
  3. Novel splice site mutations and a large deletion in three patients with the cblF inborn error of vitamin B12 metabolism. Miousse IR, et al. Mol Genet Metab, 2011 Apr. PMID 21303734
  4. Clinical or ATPase domain mutations in ABCD4 disrupt the interaction between the vitamin B(12)-trafficking proteins ABCD4 and LMBD1. Fettelschoss V, et al. J Biol Chem, 2017 Jul 14. PMID 28572511, Free PMC Article
  5. LMBRD1: the gene for the cblF defect of vitamin B₁₂ metabolism. Rutsch F, et al. J Inherit Metab Dis, 2011 Feb. PMID 20446115

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. endogenous ABCD4 was localized to both lysosomes and the ER, and its lysosomal localization was disturbed by knockout of LMBRD1
    Title: Translocation of the ABC transporter ABCD4 from the endoplasmic reticulum to lysosomes requires the escort protein LMBD1.
  2. Data suggest that ABCD4 lysosomal targeting depends on co-expression of and interaction with LMBRD1; mutations in LMBRD1 and ABCD4 that result in cobalamin metabolism disorders cblF and cblJ (or mutations in ATPase domain) disrupt interactions between LMBRD1 and ABCD4. (LMBRD1 = nuclear export signal-interacting protein; ABCD4 = ATP-binding cassette, sub-family D (ALD), member 4)
    Title: Clinical or ATPase domain mutations in ABCD4 disrupt the interaction between the vitamin B(12)-trafficking proteins ABCD4 and LMBD1.
  3. Results propose a model whereby membrane-bound LMBD1 and ABCD4 facilitate the vectorial delivery of lysosomal vitamin B12 to cytoplasmic MMACHC.
    Title: Purification and interaction analyses of two human lysosomal vitamin B12 transporters: LMBD1 and ABCD4.
  4. LMBD1 plays an imperative role in mediating and regulating the endocytosis of the IR.
    Title: LMBD1 protein serves as a specific adaptor for insulin receptor internalization.
  5. These data indicate that by forming complexes with lamin A/C and nucleoporins, NESI facilitates the CRM1-independent nuclear export of large hepatitis delta antigen.
    Title: Nuclear export signal-interacting protein forms complexes with lamin A/C-Nups to mediate the CRM1-independent nuclear export of large hepatitis delta antigen.
  6. novel mutations in LMBRD1 in three patients
    Title: Novel splice site mutations and a large deletion in three patients with the cblF inborn error of vitamin B12 metabolism.
  7. LMBRD1: the gene for the cblF defect of vitamin B metabolism.
    Title: LMBRD1: the gene for the cblF defect of vitamin B₁₂ metabolism.
  8. a LMBRD1 mutation causes the cblF defect of vitamin B(12) metabolism in a Turkish patient [case report]
    Title: A novel mutation in LMBRD1 causes the cblF defect of vitamin B(12) metabolism in a Turkish patient.
  9. LMBRD1 is the gene underlying the cblF defect of cobalamin metabolism and suggests that LMBD1 is a lysosomal membrane exporter for cobalamin.
    Title: Identification of a putative lysosomal cobalamin exporter altered in the cblF defect of vitamin B12 metabolism.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association of lipid-lowering response to statins in combined study populations.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ11240, FLJ11854

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables AP-2 adaptor complex binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables clathrin heavy chain binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables cobalamin binding IEA
Inferred from Electronic Annotation
more info
  
enables insulin receptor binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in clathrin-dependent endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in gastrulation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in insulin receptor internalization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein localization to lysosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein localization to lysosome IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in clathrin-coated endocytic vesicle ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in clathrin-coated vesicle ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
is_active_in lysosomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in lysosomal membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lysosomal membrane TAS
Traceable Author Statement
more info
  
located_in membrane HDA PubMed 
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
lysosomal cobalamin transport escort protein LMBD1
Names
HDAg-L-interacting protein NESI
hepatitis delta antigen-L interacting protein
liver regeneration p-53 related protein
nuclear export signal-interacting protein
probable lysosomal cobalamin transporter

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_016012.2 RefSeqGene

    Range
    74607..197607
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1310

mRNA and Protein(s)

  1. NM_001363722.2 → NP_001350651.1  lysosomal cobalamin transport escort protein LMBD1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' structure, resulting in the use of a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2, 3 and 4 encode the same isoform.
    Source sequence(s)
    AL358133, AL583831, AL590702
    Consensus CDS
    CCDS87415.1
    UniProtKB/TrEMBL
    A0A3B3IT31
    Related
    ENSP00000497302.1, ENST00000648394.1
    Conserved Domains (1) summary
    pfam04791
    Location:28 → 328
    LMBR1; LMBR1-like membrane protein

  2. NM_001367271.1 → NP_001354200.1  lysosomal cobalamin transport escort protein LMBD1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' structure, resulting in the use of a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2, 3 and 4 encode the same isoform.
    Source sequence(s)
    AL358133, AL583831, AL590702
    Consensus CDS
    CCDS87415.1
    UniProtKB/TrEMBL
    A0A3B3IT31
    Related
    ENSP00000497387.1, ENST00000649679.1
    Conserved Domains (1) summary
    pfam04791
    Location:28 → 328
    LMBR1; LMBR1-like membrane protein

  3. NM_001367272.1 → NP_001354201.1  lysosomal cobalamin transport escort protein LMBD1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' structure, resulting in the use of a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2, 3 and 4 encode the same isoform.
    Source sequence(s)
    AK290069, AL358133, AL590702
    Consensus CDS
    CCDS87415.1
    UniProtKB/TrEMBL
    A0A3B3IT31
    Related
    ENSP00000359602.1, ENST00000370570.6
    Conserved Domains (1) summary
    pfam04791
    Location:28 → 328
    LMBR1; LMBR1-like membrane protein

  4. NM_018368.4 → NP_060838.3  lysosomal cobalamin transport escort protein LMBD1 isoform 1

    See identical proteins and their annotated locations for NP_060838.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL358133, AL583831, BC047073, BJ995961, DA028310
    Consensus CDS
    CCDS4969.1
    UniProtKB/Swiss-Prot
    A8K204, E1P531, Q5VUN6, Q86Y70, Q96FW4, Q9BY56, Q9NUN5, Q9NZD6
    UniProtKB/TrEMBL
    A0A3B3IT31
    Related
    ENSP00000497690.1, ENST00000649934.3
    Conserved Domains (1) summary
    pfam04791
    Location:17 → 401
    LMBR1; LMBR1-like membrane protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    69674010..69797010 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    70854076..70977089 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NUN5.1 GenPept UniProtKB/Swiss-Prot:Q9NUN5

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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