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    PPT2 palmitoyl-protein thioesterase 2 [ Homo sapiens (human) ]

    Gene ID: 9374, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PPT2provided by HGNC
    Official Full Name
    palmitoyl-protein thioesterase 2provided by HGNC
    Primary source
    HGNC:HGNC:9326
    See related
    Ensembl:ENSG00000221988 MIM:603298; AllianceGenome:HGNC:9326
    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
    G14; PPT-2; C6orf8
    Summary
    This gene encodes a member of the palmitoyl-protein thioesterase family. The encoded glycosylated lysosomal protein has palmitoyl-CoA hydrolase activity in vitro, but does not hydrolyze palmitate from cysteine residues in proteins. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the downstream EGFL8 (EGF-like-domain, multiple 8) gene. [provided by RefSeq, Feb 2011]
    Expression
    Ubiquitous expression in ovary (RPKM 15.5), placenta (RPKM 11.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    6p21.32
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32153528..32163675)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (32006716..32016865)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32121305..32131452)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr6.1802 Neighboring gene FKBP prolyl isomerase like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32116858-32117395 Neighboring gene uncharacterized LOC100507547 Neighboring gene proline rich transmembrane protein 1 Neighboring gene PPT2-EGFL8 readthrough (NMD candidate) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:32134815-32135567 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:32137076-32138275 Neighboring gene EGF like domain multiple 8 Neighboring gene 1-acylglycerol-3-phosphate O-acyltransferase 1 Neighboring gene microRNA 6721

    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. Genome-wide association studies identify locus on 6p21 influencing lung function in the Korean population. Kim WJ, et al. Respirology, 2014 Apr. PMID 24387323
    2. Structure of the human palmitoyl-protein thioesterase-2 gene (PPT2) in the major histocompatibility complex on chromosome 6p21.3. Soyombo AA, et al. Genomics, 1999 Mar 1. PMID 10051407
    3. The crystal structure of palmitoyl protein thioesterase-2 (PPT2) reveals the basis for divergent substrate specificities of the two lysosomal thioesterases, PPT1 and PPT2. Calero G, et al. J Biol Chem, 2003 Sep 26. PMID 12855696
    4. Characterization of a human MHC class III region gene product with S-thioesterase activity. Aguado B, et al. Biochem J, 1999 Aug 1. PMID 10417332, Free PMC Article
    5. Molecular cloning and expression of palmitoyl-protein thioesterase 2 (PPT2), a homolog of lysosomal palmitoyl-protein thioesterase with a distinct substrate specificity. Soyombo AA, et al. J Biol Chem, 1997 Oct 24. PMID 9341199

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. We identified that PPT2 on chromosome 6p21 is associated with loss of lung function in the Korean population.
      Title: Genome-wide association studies identify locus on 6p21 influencing lung function in the Korean population.
    2. Meta-analysis and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions.
    4. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Association of MHC SNP genotype with susceptibility to type 1 diabetes: a modified survival approach.
    5. The crystal structure of palmitoyl protein thioesterase-2 (PPT2) reveals the basis for divergent substrate specificities of the two lysosomal thioesterases, PPT1 and PPT2.
      Title: The crystal structure of palmitoyl protein thioesterase-2 (PPT2) reveals the basis for divergent substrate specificities of the two lysosomal thioesterases, PPT1 and PPT2.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu
    EBI GWAS Catalog
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    EBI GWAS Catalog
    Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function.
    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

    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

    Readthrough PPT2-EGFL8

    Readthrough gene: PPT2-EGFL8, Included gene: EGFL8

    Homology

    Clone Names

    • DKFZp564P1516

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables palmitoyl hydrolase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables palmitoyl hydrolase activity TAS
    Traceable Author Statement
    more info
    		  
    enables thiolester hydrolase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables thiolester hydrolase activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in fatty-acyl-CoA biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in macromolecule depalmitoylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
    		  
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lysosomal thioesterase PPT2
    Names
    S-thioesterase G14
    VE-statin2
    palmitoyl-protein hydrolase 2
    NP_001191032.1
    NP_005146.4
    NP_619731.2

    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_042283.1 RefSeqGene

      Range
      5690..15224
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001204103.2 → NP_001191032.1  lysosomal thioesterase PPT2 isoform a precursor

      See identical proteins and their annotated locations for NP_001191032.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode the same isoform (a).
      Source sequence(s)
      AI472281, DA153675, Y17958
      Consensus CDS
      CCDS4742.1
      UniProtKB/Swiss-Prot
      A2ABC9, A2ABD1, A2ARM7, A2BFH7, A2BFH9, A2BFI2, A8K9L4, B0S868, G8JLE1, O14799, Q0P6K0, Q5JP13, Q5JP14, Q5JQF0, Q5SSX4, Q5SSX5, Q5SSX6, Q5STJ4, Q5STJ5, Q5STJ6, Q6FI80, Q99945, Q9UMR5
      UniProtKB/TrEMBL
      A0A0G2JH76, A0A1U9X8D2
      Related
      ENSP00000364279.2, ENST00000375137.6
      Conserved Domains (1) summary
      PLN02633
      Location:38 → 273
      PLN02633; palmitoyl protein thioesterase family protein

    2. NM_005155.7 → NP_005146.4  lysosomal thioesterase PPT2 isoform a precursor

      See identical proteins and their annotated locations for NP_005146.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the shorter isoform (a). Both variants 1 and 3 encode the same isoform.
      Source sequence(s)
      AF020543, AI472281, DA153675
      Consensus CDS
      CCDS4742.1
      UniProtKB/Swiss-Prot
      A2ABC9, A2ABD1, A2ARM7, A2BFH7, A2BFH9, A2BFI2, A8K9L4, B0S868, G8JLE1, O14799, Q0P6K0, Q5JP13, Q5JP14, Q5JQF0, Q5SSX4, Q5SSX5, Q5SSX6, Q5STJ4, Q5STJ5, Q5STJ6, Q6FI80, Q99945, Q9UMR5
      UniProtKB/TrEMBL
      A0A0G2JH76, A0A1U9X8D2
      Related
      ENSP00000320528.6, ENST00000324816.11
      Conserved Domains (1) summary
      PLN02633
      Location:38 → 273
      PLN02633; palmitoyl protein thioesterase family protein

    3. NM_138717.3 → NP_619731.2  lysosomal thioesterase PPT2 isoform b precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The resulting isoform (b) is longer at the N-terminus, compared to isoform a.
      Source sequence(s)
      AI472281, AL110128, DA153675
      Consensus CDS
      CCDS4740.1
      UniProtKB/TrEMBL
      A0A140T8X7
      Related
      ENSP00000354608.2, ENST00000361568.6
      Conserved Domains (1) summary
      cl21494
      Location:44 → 286
      Abhydrolase; alpha/beta hydrolases

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      32153528..32163675
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      3486127..3496276
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      3591867..3602027
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      3394893..3399299
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      3458529..3468659
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      3495543..3505696
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      3376722..3386876
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      3469732..3479881
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      32006716..32016865
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_138934.1: Suppressed sequence

      Description
      NM_138934.1: This RefSeq was permanently suppressed because it represented a read-through transcript that spanned both the PPT2 and EGFL8 genes and is a candidate for nonsense-mediated decay (NMD).
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UMR5.4 GenPept UniProtKB/Swiss-Prot:Q9UMR5

    Gene LinkOut

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

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