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    SERPINA2 serpin family A member 2 (gene/pseudogene) [ Homo sapiens (human) ]

    Gene ID: 390502, updated on 14-Nov-2024

    Summary

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    Official Symbol
    SERPINA2provided by HGNC
    Official Full Name
    serpin family A member 2 (gene/pseudogene)provided by HGNC
    Primary source
    HGNC:HGNC:8985
    See related
    Ensembl:ENSG00000258597 MIM:107410; AllianceGenome:HGNC:8985
    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
    ATR; PIL; ARGS; psiATR; SERPINA2P
    Summary
    This gene encodes a member of the serpin family of proteins, a group of proteins that inhibit serine proteases. The encoded intracellular glycoprotein is localized at the endoplasmic reticulum. This gene is a polymorphic pseudogene, with the non-functional allele being predominant in some populations. Some individuals, as represented by the reference genome allele, contain a 2kb coding region deletion and a start code mutation. [provided by RefSeq, Feb 2014]
    Annotation information
    Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
    Note: Population studies indicate that this gene is polymorphic. Deletions, frameshift mutations and a critical start codon mutation (ATG->ATA) have been found in some populations as well as an allele that can encode a functional protein. This gene may be an evolving pseudogene (PMID: 17135331). The reference genome contains the start codon mutation and has a coding region deletion. The NCBI RefSeq Project therefore treats this as a pseudogene. [13 Feb 2013]
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See SERPINA2 in Genome Data Viewer
    Location:
    14q32.13
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (94364318..94366702, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (88593837..88596220, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (94830655..94833039, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene serpin family A member 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:94757989-94758488 Neighboring gene serpin family A member 6 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:94812301-94813500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:94828015-94828515 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:94839554-94840753 Neighboring gene serpin family A member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:94856427-94856928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:94856929-94857428 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:94917415-94918091 Neighboring gene serpin family A member 11

    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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Specific features of SERPINA2 include the absence of insoluble aggregates and the insignificant response to cell stress, suggesting that it is a non-polymerogenic protein with divergent activity of SERPINA1.
      Title: SERPINA2 is a novel gene with a divergent function from SERPINA1.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: A linkage disequilibrium between genes at the serine protease inhibitor gene cluster on chromosome 14q32.1 is associated with Wegener's granulomatosis.
    3. Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
    4. Study found that a common haplotype in Africa had a 2-kb deletion in the SERPINA2 gene is associated with remarkable long-range homozygozity as if it was quickly driven to high frequency by natural selection acting on an advantageous variant.
      Title: Sequence diversity at the proximal 14q32.1 SERPIN subcluster: evidence for natural selection favoring the pseudogenization of SERPINA2.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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 Alpha1-Antitrypsin (alpha(1)AT) is cleaved by serine proteases, causing a conformational change in alpha(1)AT that sequesters HIV-1 protease, blocks both HIV-1 gp160 and p55 processing, and is a powerful inhibitor of HIV replication 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

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    alpha-1-antitrypsin-related protein
    Names
    AAT-related protein
    alpha-1 antitrypsin-related protein
    putative alpha-1-antitrypsin-related protein
    serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 2
    serpin A2
    serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 2, pseudogene

    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.

    mRNA and Protein(s)

    1. NM_006220.3 → NP_006211.2  alpha-1-antitrypsin-related protein precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the protein coding transcript. This allele is not found in the reference genome.
      Source sequence(s)
      AC235087
      UniProtKB/Swiss-Prot
      A0A0G2JPK4, P20848, S4UD68
      Conserved Domains (1) summary
      smart00093
      Location:62 → 418
      SERPIN; SERine Proteinase INhibitors

    RNA

    1. NR_110563.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, non-coding) represents the non-protein coding transcript. The non-coding allele, found in the reference genome, contains a 2 kb deletion and a start codon mutation when compared to the protein coding allele.
      Source sequence(s)
      AL117259
      Related
      ENST00000553483.4

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      94364318..94366702 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187601.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      1478202..1488979 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      88593837..88596220 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NG_032041.1: Suppressed sequence

      Description
      NG_032041.1: This RefSeq was permanently suppressed because it is now thought that this gene does encode a protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P20848.2 GenPept UniProtKB/Swiss-Prot:P20848

    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