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    PGAP6 post-GPI attachment to proteins 6 [ Homo sapiens (human) ]

    Gene ID: 58986, updated on 7-Apr-2024

    Summary

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    Official Symbol
    PGAP6provided by HGNC
    Official Full Name
    post-GPI attachment to proteins 6provided by HGNC
    Primary source
    HGNC:HGNC:17205
    See related
    Ensembl:ENSG00000129925 MIM:619342; AllianceGenome:HGNC:17205
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    M83; TMEM6; TMEM8; TMEM8A; GPI-PLA2
    Summary
    Predicted to enable phospholipase A2 activity. Located in extracellular exosome and lysosomal membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 24.1), placenta (RPKM 22.5) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See PGAP6 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (370788..386979, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (366436..382868, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (420788..431978, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene axin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:359414-359928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:359929-360443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:366745-367498 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:367499-368250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:368251-369004 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:374949-375556 Neighboring gene Sharpr-MPRA regulatory region 4309 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:389458-390182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:391465-392016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10203 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6907 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6909 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6910 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6911 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:410874-411722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:411723-412570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:413199-413706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:413707-414213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:414214-414720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:422268-422839 Neighboring gene mitochondrial ribosomal protein L28 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:431071-431970 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6916 Neighboring gene uncharacterized LOC100134368 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:440484-440661 Neighboring gene ribosomal protein L23a pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10204 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:449109-449694 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:450865-451450 Neighboring gene NME/NM23 nucleoside diphosphate kinase 4 Neighboring gene 2,4-dienoyl-CoA reductase 2

    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. PGAP6, a GPI-specific phospholipase A2, has narrow substrate specificity against GPI-anchored proteins. Lee GH, et al. J Biol Chem, 2020 Oct 16. PMID 32816994, Free PMC Article
    2. Molecular cloning and chromosomal mapping of a novel five-span transmembrane protein gene, M83. Motohashi T, et al. Biochem Biophys Res Commun, 2000 Sep 16. PMID 11006113
    3. A GPI processing phospholipase A2, PGAP6, modulates Nodal signaling in embryos by shedding CRIPTO. Lee GH, et al. J Cell Biol, 2016 Dec 5. PMID 27881714, Free PMC Article
    4. Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways. Palmieri M, et al. Hum Mol Genet, 2011 Oct 1. PMID 21752829
    5. Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16. Daniels RJ, et al. Hum Mol Genet, 2001 Feb 15. PMID 11157797

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PGAP6, a GPI-specific phospholipase A2, has narrow substrate specificity against GPI-anchored proteins.
      Title: PGAP6, a GPI-specific phospholipase A2, has narrow substrate specificity against GPI-anchored proteins.
    2. PGAP6 plays a critical role in Nodal signaling modulation through CRIPTO shedding.
      Title: A GPI processing phospholipase A2, PGAP6, modulates Nodal signaling in embryos by shedding CRIPTO.
    3. TMEM8A protein localizes in lysosomes in HeLa cells
      Title: Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways.
    Submit: New GeneRIF Correction

    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

    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

    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 molecular_function ND
    No biological Data available
    more info
    		  
    enables phospholipase A2 activity IEA
    Inferred from Electronic Annotation
    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
    		  
    involved_in lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in lysosomal membrane HDA PubMed 
    located_in plasma membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    post-GPI attachment to proteins factor 6
    Names
    GPI processing phospholipase A2
    five-span transmembrane protein M83
    post-glycosylphosphatidylinositol attachment to proteins 6
    transmembrane protein 6
    transmembrane protein 8 (five membrane-spanning domains)
    transmembrane protein 8A
    NP_067082.2
    XP_047290369.1
    XP_054169546.1

    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_021259.3 → NP_067082.2  post-GPI attachment to proteins factor 6 precursor

      See identical proteins and their annotated locations for NP_067082.2

      Status: VALIDATED

      Source sequence(s)
      AB045292, AI678371, AL537021, AL546643, BC004276, BC021557, DB224383, Z97634
      Consensus CDS
      CCDS10407.1
      UniProtKB/Swiss-Prot
      D3DU49, Q4TT35, Q8WU24, Q96S25, Q9BR03, Q9BT97, Q9H7B9, Q9HCN3
      Related
      ENSP00000401338.2, ENST00000431232.7
      Conserved Domains (1) summary
      pfam12036
      Location:547 → 727
      DUF3522; Protein of unknown function (DUF3522)

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      370788..386979 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434413.1 → XP_047290369.1  post-GPI attachment to proteins factor 6 isoform X1

      UniProtKB/TrEMBL
      K4DI83
      Related
      ENSP00000250930.3, ENST00000250930.7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      366436..382868 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054313571.1 → XP_054169546.1  post-GPI attachment to proteins factor 6 isoform X1

      UniProtKB/TrEMBL
      K4DI83
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HCN3.3 GenPept UniProtKB/Swiss-Prot:Q9HCN3

    Gene LinkOut

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

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