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    LMNB1 lamin B1 [ Homo sapiens (human) ]

    Gene ID: 4001, updated on 5-May-2024

    Summary

    Official Symbol
    LMNB1provided by HGNC
    Official Full Name
    lamin B1provided by HGNC
    Primary source
    HGNC:HGNC:6637
    See related
    Ensembl:ENSG00000113368 MIM:150340; AllianceGenome:HGNC:6637
    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
    LMN; ADLD; LMN2; LMNB; MCPH26
    Summary
    This gene encodes one of the two B-type lamin proteins and is a component of the nuclear lamina. A duplication of this gene is associated with autosomal dominant adult-onset leukodystrophy (ADLD). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
    Expression
    Broad expression in lymph node (RPKM 25.5), appendix (RPKM 22.1) and 18 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LMNB1 in Genome Data Viewer
    Location:
    5q23.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (126776623..126837020)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (127296579..127357028)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (126112315..126172712)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23024 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:126084980-126085905 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:126089932-126090098 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23025 Neighboring gene RNA, U6 small nuclear 752, pseudogene Neighboring gene LMNB1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16284 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:126112589-126113389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23027 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23028 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:126174548-126175292 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:126175293-126176035 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:126176780-126177522 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:126181005-126181974 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:126183029-126183855 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:126211055-126211554 Neighboring gene membrane associated ring-CH-type finger 3 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:126231155-126231764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23032 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:126366588-126367132 Neighboring gene uncharacterized LOC105379163

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2023-10-25)

    ClinGen Genome Curation Page
    Triplosensitivity

    Sufficient evidence for dosage pathogenicity (Last evaluated 2023-10-25)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Genomic determinants of motor and cognitive outcomes in Parkinson's disease.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with LMNB1 PubMed
    Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of lamin B1 (LMNB1) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed
    vpr HIV-1 Vpr co-localizes with lamin B and induces localized disruptions in the normal nuclear lamin architecture, contributing to the formation of nuclear envelope herniations PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC111419

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phospholipase binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific double-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables structural constituent of cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables structural constituent of nuclear lamina TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cytoskeleton organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in nuclear envelope organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in nuclear envelope organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nuclear migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in nuclear pore localization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein localization to nuclear envelope IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in lamin filament IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane HDA PubMed 
    colocalizes_with nuclear envelope IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear envelope TAS
    Traceable Author Statement
    more info
     
    located_in nuclear inner membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in nuclear lamina IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nuclear lamina IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in nuclear matrix IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nuclear membrane HDA PubMed 
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_008360.2 RefSeqGene

      Range
      4996..64880
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001198557.2NP_001185486.1  lamin-B1 isoform 2

      See identical proteins and their annotated locations for NP_001185486.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an downstream start codon, compared to variant 1. The resulting protein (isoform 2) is shorter than isoform 1.
      Source sequence(s)
      AC137794, AK303084, AW512433
      UniProtKB/TrEMBL
      B4DZT3
      Conserved Domains (2) summary
      pfam00038
      Location:2177
      Filament; Intermediate filament protein
      pfam00932
      Location:229333
      LTD; Lamin Tail Domain
    2. NM_005573.4NP_005564.1  lamin-B1 isoform 1

      See identical proteins and their annotated locations for NP_005564.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC137794, AW512433, BC103723
      Consensus CDS
      CCDS4140.1
      UniProtKB/Swiss-Prot
      B2R6J6, P20700, Q3SYN7, Q96EI6
      Related
      ENSP00000261366.5, ENST00000261366.10
      Conserved Domains (2) summary
      pfam00038
      Location:31387
      Filament; Intermediate filament protein
      pfam00932
      Location:439543
      LTD; Lamin Tail Domain

    RNA

    1. NR_134488.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC137794, AW512433, BC052951, BC103723
      Related
      ENST00000460265.5
    2. NR_177109.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC137794

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      126776623..126837020
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417173.1XP_047273129.1  lamin-B1 isoform X1

    2. XM_047417174.1XP_047273130.1  lamin-B1 isoform X2

    3. XM_047417175.1XP_047273131.1  lamin-B1 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      127296579..127357028
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352579.1XP_054208554.1  lamin-B1 isoform X3

    2. XM_054352580.1XP_054208555.1  lamin-B1 isoform X3