LMNB1 lamin B1 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

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_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Lamin B1: a novel biomarker in adult and pediatric adrenocortical carcinoma.
Title: Lamin B1: a novel biomarker in adult and pediatric adrenocortical carcinoma.
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.
Lamin B1 overexpression alters chromatin organization and gene expression.
Title: Lamin B1 overexpression alters chromatin organization and gene expression.
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.
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.
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.
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.
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.
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

Associated conditions

Description	Tests
Adult-onset autosomal dominant demyelinating leukodystrophy MedGen: C1868512 OMIM: 169500 GeneReviews: LMNB1-Related Autosomal Dominant Leukodystrophy	Compare labs
Microcephaly 26, primary, autosomal dominant MedGen: C5543048 OMIM: 619179 GeneReviews: Not available	Compare labs

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

LMNB1__6401 (e-PCR)
- UniSTS:468500

SGC33978 (e-PCR)
- UniSTS:67706

D5S804 (e-PCR), detects polymorphism
- UniSTS:44768

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 more info	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 more info	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

NG_008360.2 RefSeqGene

Range

4996..64880

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

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
NR_177109.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC137794