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LMNB1 lamin B1 [ Homo sapiens (human) ]

Gene ID: 4001, updated on 11-Apr-2024

Summary

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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
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Genomic context

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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

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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. Lamin B1 overexpression alters chromatin organization and gene expression. Kaneshiro JM, et al. Nucleus, 2023 Dec. PMID 37071033, Free PMC Article
  2. LMNB1 deletion in ovarian cancer inhibits the proliferation and metastasis of tumor cells through PI3K/Akt pathway. Dong J, et al. Exp Cell Res, 2023 May 15. PMID 37003558
  3. Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function. Reilly A, et al. Cell Stem Cell, 2022 Apr 7. PMID 35278369, Free PMC Article
  4. Lamin B1 sequesters 53BP1 to control its recruitment to DNA damage. Etourneaud L, et al. Sci Adv, 2021 Aug. PMID 34452908, Free PMC Article
  5. Timing of pacemaker and ICD implantation in LMNA mutation carriers. Ollila LH, et al. Open Heart, 2021 Apr. PMID 33893211, Free PMC Article

See all (311) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ENPP1 inhibits the transcription activity of the hepatitis B virus pregenomic promoter by upregulating the acetylation of LMNB1.
    Title: ENPP1 inhibits the transcription activity of the hepatitis B virus pregenomic promoter by upregulating the acetylation of LMNB1.
  2. Lamin B1: a novel biomarker in adult and pediatric adrenocortical carcinoma.
    Title: Lamin B1: a novel biomarker in adult and pediatric adrenocortical carcinoma.
  3. Decreased lamin A and B1 expression results in nuclear enlargement in serous ovarian carcinoma, whereas lamin A-expressing tumor cells metastasize to lymph nodes.
    Title: Decreased lamin A and B1 expression results in nuclear enlargement in serous ovarian carcinoma, whereas lamin A-expressing tumor cells metastasize to lymph nodes.
  4. Lamin B1 overexpression alters chromatin organization and gene expression.
    Title: Lamin B1 overexpression alters chromatin organization and gene expression.
  5. LMNB1 deletion in ovarian cancer inhibits the proliferation and metastasis of tumor cells through PI3K/Akt pathway.
    Title: LMNB1 deletion in ovarian cancer inhibits the proliferation and metastasis of tumor cells through PI3K/Akt pathway.
  6. Differentiation-dependent changes in lamin B1 dynamics and lamin B receptor localization.
    Title: Differentiation-dependent changes in lamin B1 dynamics and lamin B receptor localization.
  7. Knockdown of Lamin B1 and the Corresponding Lamin B Receptor Leads to Changes in Heterochromatin State and Senescence Induction in Malignant Melanoma.
    Title: Knockdown of Lamin B1 and the Corresponding Lamin B Receptor Leads to Changes in Heterochromatin State and Senescence Induction in Malignant Melanoma.
  8. Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function.
    Title: Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function.
  9. Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells.
    Title: Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells.
  10. Genome sequencing reveals novel noncoding variants in PLA2G6 and LMNB1 causing progressive neurologic disease.
    Title: Genome sequencing reveals novel noncoding variants in PLA2G6 and LMNB1 causing progressive neurologic disease.
Submit: New GeneRIF Correction See all GeneRIFs (89)

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

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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

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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

  • 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 

General protein information

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Preferred Names
lamin-B1

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_008360.2 RefSeqGene

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

mRNA and Protein(s)

  1. NM_001198557.2 → NP_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:2 → 177
    Filament; Intermediate filament protein
    pfam00932
    Location:229 → 333
    LTD; Lamin Tail Domain

  2. NM_005573.4 → NP_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:31 → 387
    Filament; Intermediate filament protein
    pfam00932
    Location:439 → 543
    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_047417173.1 → XP_047273129.1  lamin-B1 isoform X1

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

  3. XM_047417175.1 → XP_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_054352579.1 → XP_054208554.1  lamin-B1 isoform X3

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

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P20700.2 GenPept UniProtKB/Swiss-Prot:P20700

Gene LinkOut

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

Chemical Information
Medical
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