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LSP1 lymphocyte specific protein 1 [ Homo sapiens (human) ]

Gene ID: 4046, updated on 31-Mar-2024

Summary

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Official Symbol
LSP1provided by HGNC
Official Full Name
lymphocyte specific protein 1provided by HGNC
Primary source
HGNC:HGNC:6707
See related
Ensembl:ENSG00000130592 MIM:153432; AllianceGenome:HGNC:6707
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
WP34; pp52
Summary
This gene encodes an intracellular F-actin binding protein. The protein is expressed in lymphocytes, neutrophils, macrophages, and endothelium and may regulate neutrophil motility, adhesion to fibrinogen matrix proteins, and transendothelial migration. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
Expression
Broad expression in spleen (RPKM 60.6), appendix (RPKM 43.3) and 19 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
11p15.5
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (1853084..1892263)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (1938882..1978157)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (1874314..1913493)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3062 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3063 Neighboring gene uncharacterized LOC107984299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4290 Neighboring gene troponin I2, fast skeletal type Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1870712-1871698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4293 Neighboring gene microRNA 4298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1891831-1892369 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1892370-1892907 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1896777-1897673 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1897674-1898570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4294 Neighboring gene microRNA 7847 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:1908437-1908603 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:1918050-1919249 Neighboring gene proline rich 33 Neighboring gene long intergenic non-protein coding RNA 1150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1927717-1928218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1928219-1928718 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4295 Neighboring gene troponin T3, fast skeletal type Neighboring gene ReSE screen-validated silencer GRCh37_chr11:1956346-1956534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:1956988-1957585

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. The correlation of leukocyte-specific protein 1 (LSP1) rs3817198(T>C) polymorphism with breast cancer: A meta-analysis. Chen J, et al. Medicine (Baltimore), 2022 Nov 11. PMID 36397430, Free PMC Article
  2. Predictive and prognostic value of LSP1 rs3817198 in sporadic breast cancer in northeastern population of Iran. Afzaljavan F, et al. Exp Mol Pathol, 2020 Oct. PMID 32738313
  3. Lymphocyte-specific protein 1 regulates mechanosensory oscillation of podosomes and actin isoform-based actomyosin symmetry breaking. Cervero P, et al. Nat Commun, 2018 Feb 6. PMID 29410425, Free PMC Article
  4. The LSP1 rs3817198 T > C polymorphism contributes to increased breast cancer risk: a meta-analysis of twelve studies. Tang J, et al. Oncotarget, 2016 Sep 27. PMID 27590509, Free PMC Article
  5. Correlation between LSP1 polymorphisms and the susceptibility to breast cancer. Chen H, et al. Int J Clin Exp Pathol, 2015. PMID 26191300, Free PMC Article

See all (79) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LSP1 promotes the progression of acute myelogenous leukemia by regulating KSR/ERK signaling pathway and cell migration.
    Title: LSP1 promotes the progression of acute myelogenous leukemia by regulating KSR/ERK signaling pathway and cell migration.
  2. Lymphocyte-Specific Protein 1 Regulates Expression and Stability of Endothelial Nitric Oxide Synthase.
    Title: Lymphocyte-Specific Protein 1 Regulates Expression and Stability of Endothelial Nitric Oxide Synthase.
  3. Tim-3 Is Differentially Expressed during Cell Activation and Interacts with the LSP-1 Protein in Human Macrophages.
    Title: Tim-3 Is Differentially Expressed during Cell Activation and Interacts with the LSP-1 Protein in Human Macrophages.
  4. The correlation of leukocyte-specific protein 1 (LSP1) rs3817198(T>C) polymorphism with breast cancer: A meta-analysis.
    Title: The correlation of leukocyte-specific protein 1 (LSP1) rs3817198(T>C) polymorphism with breast cancer: A meta-analysis.
  5. Identification of Diagnostic Signatures and Immune Cell Infiltration Characteristics in Rheumatoid Arthritis by Integrating Bioinformatic Analysis and Machine-Learning Strategies.
    Title: Identification of Diagnostic Signatures and Immune Cell Infiltration Characteristics in Rheumatoid Arthritis by Integrating Bioinformatic Analysis and Machine-Learning Strategies.
  6. MiR-920 and LSP1 co-regulate the growth and migration of glioblastoma cells by modulation of JAK2/STAT5 pathway.
    Title: MiR-920 and LSP1 co-regulate the growth and migration of glioblastoma cells by modulation of JAK2/STAT5 pathway.
  7. Lymphocyte-specific protein 1 (LSP1) regulates bone marrow stromal cell antigen 2 (BST-2)-mediated intracellular trafficking of HIV-1 in dendritic cells.
    Title: Lymphocyte-specific protein 1 (LSP1) regulates bone marrow stromal cell antigen 2 (BST-2)-mediated intracellular trafficking of HIV-1 in dendritic cells.
  8. Predictive and prognostic value of LSP1 rs3817198 in sporadic breast cancer in northeastern population of Iran.
    Title: Predictive and prognostic value of LSP1 rs3817198 in sporadic breast cancer in northeastern population of Iran.
  9. Differential gene expression by SFRP2(+), FMO1(+), and COL11A1(+) fibroblasts suggests roles in matrix deposition, inflammatory cell retention, and connective tissue cell differentiation, respectively.
    Title: SFRP2/DPP4 and FMO1/LSP1 Define Major Fibroblast Populations in Human Skin.
  10. LSP1 rs3817198 T > C polymorphism is associated with increased risk of breast cancer, especially in Caucasian and Asian populations [meta-analysis]
    Title: The LSP1 rs3817198 T > C polymorphism contributes to increased breast cancer risk: a meta-analysis of twelve studies.
Submit: New GeneRIF Correction See all GeneRIFs (32)

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
A possible mechanism behind autoimmune disorders discovered by genome-wide linkage and association analysis in celiac disease.
EBI GWAS Catalog
Genome-wide association study identifies five new breast cancer susceptibility loci.
EBI GWAS Catalog
Genome-wide association study identifies multiple loci associated with bladder cancer risk.
EBI GWAS Catalog
Genome-wide association study identifies multiple loci associated with both mammographic density and breast cancer risk.
EBI GWAS Catalog
Genome-wide association study identifies novel breast cancer susceptibility loci.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
EBI GWAS Catalog
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
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 gp120 env HIV-1 gp120 upregulates the expression of lymphocyte-specific protein 1 (LSP1) in human B cells PubMed
env Inhibition of M-tropic HIV-1 gp120-induced transendothelial migration by SLIT2N involves SLIT2N-mediated enhancement of co-localization of Robo1 with WASp and LSP1 in immature monocyte-derived dendritic cells PubMed
env SLIT2N, an active fragment of SLIT2, inhibits M-tropic HIV-1 gp120-induced association of LSP1, Wiskott-Aldrich Syndrome protein (WASp), Actin-Related Protein 2/3 (Arp2/3), and beta-actin in immature monocyte-derived dendritic cells PubMed
env HIV-1 gp120-induced migration of dendritic cells is regulated by a novel kinase cascade involving Pyk2, p38 MAP kinase, and LSP1 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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular defense response TAS
Traceable Author Statement
more info
 PubMed 
involved_in cellular response to interleukin-7 IEA
Inferred from Electronic Annotation
more info
  
involved_in chemotaxis IEA
Inferred from Electronic Annotation
more info
  
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in actin cytoskeleton TAS
Traceable Author Statement
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in membrane HDA PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
lymphocyte-specific protein 1
Names
47 kDa actin binding protein
52 kDa phosphoprotein
F-actin binding and cytoskeleton associated protein
leufactin (leukocyte F-actin binding protein)
leukocyte-specific protein 1
lymphocyte-specific antigen WP34

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_011509.1 RefSeqGene

    Range
    5115..44294
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001013253.2 → NP_001013271.1  lymphocyte-specific protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001013271.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon and lacks two exons in the 5' region, and uses a downstream start codon, compared to variant 5. The resulting protein (isoform 2) has a shorter N-terminus compared to isoform 3. Variants 2, 3, 4 and 6 encode the same protein (isoform 2).
    Source sequence(s)
    AC051649, BC001785
    Consensus CDS
    CCDS31335.1
    UniProtKB/TrEMBL
    A8K7L8
    Related
    ENSP00000383932.2, ENST00000405957.6
    Conserved Domains (1) summary
    pfam02029
    Location:129 → 252
    Caldesmon; Caldesmon

  2. NM_001013254.1 → NP_001013272.1  lymphocyte-specific protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001013272.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate exon and lacks two exons in the 5' region, and uses a downstream start codon, compared to variant 5. The resulting protein (isoform 2) has a shorter N-terminus compared to isoform 3. Variants 2, 3, 4 and 6 encode the same protein (isoform 2).
    Source sequence(s)
    AC051649, AK056576, BC001785
    Consensus CDS
    CCDS31335.1
    UniProtKB/TrEMBL
    A8K7L8
    Related
    ENSP00000384022.2, ENST00000406638.6
    Conserved Domains (1) summary
    pfam02029
    Location:129 → 252
    Caldesmon; Caldesmon

  3. NM_001013255.1 → NP_001013273.1  lymphocyte-specific protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001013273.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate exon and lacks two exons in the 5' region, and uses a downstream start codon, compared to variant 5. The resulting protein (isoform 2) has a shorter N-terminus compared to isoform 3. Variants 2, 3, 4 and 6 encode the same protein (isoform 2).
    Source sequence(s)
    AC051649, BC001785, BQ893821
    Consensus CDS
    CCDS31335.1
    UniProtKB/TrEMBL
    A8K7L8
    Conserved Domains (1) summary
    pfam02029
    Location:129 → 252
    Caldesmon; Caldesmon

  4. NM_001242932.2 → NP_001229861.1  lymphocyte-specific protein 1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) represents the longest transcript and encodes the longest isoform (3).
    Source sequence(s)
    AC051649, AK092071, BC001785, BE043985, BQ893037
    Consensus CDS
    CCDS58110.1
    UniProtKB/Swiss-Prot
    P33241
    Related
    ENSP00000371194.1, ENST00000381775.5
    Conserved Domains (1) summary
    pfam02029
    Location:319 → 413
    Caldesmon; Caldesmon

  5. NM_001289005.2 → NP_001275934.1  lymphocyte-specific protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001275934.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 5. The resulting isoform (2) has a shorter N-terminus, compared to isoform 3. Variants 2, 3, 4 and 6 encode the same protein (isoform 2).
    Source sequence(s)
    AC051649, AI817126, AK222733, AK292033
    Consensus CDS
    CCDS31335.1
    UniProtKB/TrEMBL
    A8K7L8
    Related
    ENSP00000484140.1, ENST00000612798.4
    Conserved Domains (1) summary
    pfam02029
    Location:129 → 252
    Caldesmon; Caldesmon

  6. NM_002339.3 → NP_002330.1  lymphocyte-specific protein 1 isoform 1

    See identical proteins and their annotated locations for NP_002330.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) contains an alternate exon and lacks two exons in the 5' coding region compared to variant 5. The resulting protein (isoform 1) has a distinct N-terminus and is shorter than isoform 3.
    Source sequence(s)
    AC051649, BC001785
    Consensus CDS
    CCDS31334.1
    UniProtKB/Swiss-Prot
    B3KPP1, B3KRR6, E9PBV6, E9PFP3, P33241, Q16096, Q53H48, Q6FHM3, Q9BUY8
    UniProtKB/TrEMBL
    A8K2L4
    Related
    ENSP00000308383.4, ENST00000311604.8
    Conserved Domains (1) summary
    pfam02029
    Location:191 → 314
    Caldesmon; Caldesmon

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    1853084..1892263
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160004.1 Reference GRCh38.p14 PATCHES

    Range
    43587..82766
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    1938882..1978157
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P33241.1 GenPept UniProtKB/Swiss-Prot:P33241

Gene LinkOut

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

Chemical Information
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