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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
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Genomic context

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See PPT2 in Genome Data Viewer
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
    Download
    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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