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    LPAL2 lipoprotein(a) like 2 (pseudogene) [ Homo sapiens (human) ]

    Gene ID: 80350, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LPAL2provided by HGNC
    Official Full Name
    lipoprotein(a) like 2 (pseudogene)provided by HGNC
    Primary source
    HGNC:HGNC:21210
    See related
    Ensembl:ENSG00000290613 MIM:611682; AllianceGenome:HGNC:21210
    Gene type
    pseudo
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    APOA2; APOAL; APOARGC; apo(a)rg-C
    Summary
    Apolipoprotein(a) is the distinguishing protein moiety of lipoprotein(a), of which elevated plasma levels are correlated with an increased risk of atherosclerosis. This gene is similar to the lipoprotein, Lp(a) gene, but all transcripts produced by this gene contain a truncated open reading frame and are candidates for nonsense-mediated decay. Consequently, this gene is considered to be a pseudogene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2009]
    Expression
    Biased expression in liver (RPKM 3.4), testis (RPKM 0.5) and 8 other tissues See more
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    Genomic context

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    See LPAL2 in Genome Data Viewer
    Location:
    6q25.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (160466555..160511124, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (161717854..161762809, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (160887587..160932156, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378088 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:160694323-160695522 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:160719355-160719855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:160720893-160721479 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:160724446-160724946 Neighboring gene uncharacterized LOC124901453 Neighboring gene solute carrier family 22 member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:160807441-160807942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25402 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:160907332-160908531 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17759 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17760 Neighboring gene uncharacterized LOC124901454 Neighboring gene lipoprotein(a) Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:161025992-161027191 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:161106525-161107079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17762 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:161158745-161159944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25403 Neighboring gene plasminogen

    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 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. LPAL2 Suppresses Tumor Growth and Metastasis of Hepatocellular Carcinoma by Modulating MMP9 Expression. Lin YH, et al. Cells, 2022 Aug 22. PMID 36010685, Free PMC Article
    2. Characterization by yeast artificial chromosome cloning of the linked apolipoprotein(a) and plasminogen genes and identification of the apolipoprotein(a) 5' flanking region. Malgaretti N, et al. Proc Natl Acad Sci U S A, 1992 Dec 1. PMID 1454851, Free PMC Article
    3. Definition of the transcription initiation site of human plasminogen gene in liver and non hepatic cell lines. Malgaretti N, et al. Biochem Biophys Res Commun, 1990 Dec 31. PMID 2268308
    4. Loss of a splice donor site at a 'skipped exon' in a gene homologous to apolipoprotein(a) leads to an mRNA encoding a protein consisting of a single kringle domain. Byrne CD, et al. Arterioscler Thromb Vasc Biol, 1995 Jan. PMID 7749817
    5. Lack of significant associations between single nucleotide polymorphisms in LPAL2-LPA genetic region and all cancer incidence and mortality in Japanese population: The Japan public health center-based prospective study. Mieno MN, et al. Cancer Epidemiol, 2023 Aug. PMID 37321067

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Lack of significant associations between single nucleotide polymorphisms in LPAL2-LPA genetic region and all cancer incidence and mortality in Japanese population: The Japan public health center-based prospective study.
      Title: Lack of significant associations between single nucleotide polymorphisms in LPAL2-LPA genetic region and all cancer incidence and mortality in Japanese population: The Japan public health center-based prospective study.
    2. LPAL2 Suppresses Tumor Growth and Metastasis of Hepatocellular Carcinoma by Modulating MMP9 Expression.
      Title: LPAL2 Suppresses Tumor Growth and Metastasis of Hepatocellular Carcinoma by Modulating MMP9 Expression.
    3. The genotype of rs3088442 within the SLC22A3-LPAL2-LPA gene cluster may contribute to regulation of plasma Lp(a) levels and possibly to the severity of coronary artery disease in a Chinese Han population.
      Title: Functional Variant in the SLC22A3-LPAL2-LPA Gene Cluster Contributes to the Severity of Coronary Artery Disease.
    4. The risk for coronary artery disease in a Chinese Han population is not associated with single nucleotide polymorphisms in the SLC22A3-LPAL2-LPA gene cluster.
      Title: Lack of association between four SNPs in the SLC22A3-LPAL2-LPA gene cluster and coronary artery disease in a Chinese Han population: a case control study.
    5. Identification of the SLC22A3-LPAL2-LPA gene cluster as a strong susceptibility locus for coronary artery disease.
      Title: Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease.
    6. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genetic and clinical correlates of early-outgrowth colony-forming units.
    EBI GWAS Catalog
    Genetic variants, plasma lipoprotein(a) levels, and risk of cardiovascular morbidity and mortality among two prospective cohorts of type 2 diabetes.
    EBI GWAS Catalog
    Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease.
    EBI GWAS Catalog
    Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
    EBI GWAS Catalog

    Variation

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    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Other Names

    • apolipoprotein (a) related gene C
    • apolipoprotein A-II
    • lipoprotein, Lp(a)-like 2, pseudogene

    Clone Names

    • MGC129532

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    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.

    RNA

    1. NR_028092.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AL591069
      Related
      ENST00000335388.5

    2. NR_028093.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate 3' splice pattern, compared to variant 1.
      Source sequence(s)
      AL591069
      Related
      ENST00000435757.6

    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
      160466555..160511124 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      161717854..161762809 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_024492.2: Suppressed sequence

      Description
      NM_024492.2: This RefSeq was permanently suppressed because it is now thought that this gene is a pseudogene.

    2. NM_145727.2: Suppressed sequence

      Description
      NM_145727.2: This RefSeq was permanently suppressed because it is now thought that this gene is a pseudogene.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q16609.1 GenPept UniProtKB/Swiss-Prot:Q16609

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials