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    PPT1 palmitoyl-protein thioesterase 1 [ Homo sapiens (human) ]

    Gene ID: 5538, updated on 3-May-2024

    Summary

    Official Symbol
    PPT1provided by HGNC
    Official Full Name
    palmitoyl-protein thioesterase 1provided by HGNC
    Primary source
    HGNC:HGNC:9325
    See related
    Ensembl:ENSG00000131238 MIM:600722; AllianceGenome:HGNC:9325
    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
    PPT; CLN1; INCL
    Summary
    The protein encoded by this gene is a small glycoprotein involved in the catabolism of lipid-modified proteins during lysosomal degradation. The encoded enzyme removes thioester-linked fatty acyl groups such as palmitate from cysteine residues. Defects in this gene are a cause of infantile neuronal ceroid lipofuscinosis 1 (CLN1, or INCL) and neuronal ceroid lipofuscinosis 4 (CLN4). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2008]
    Expression
    Ubiquitous expression in spleen (RPKM 86.1), lung (RPKM 62.1) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PPT1 in Genome Data Viewer
    Location:
    1p34.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (40071461..40097252, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (39940889..39966711, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (40537133..40562924, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MFSD2 lysolipid transporter A, lysophospholipid Neighboring gene ribosomal protein S2 pseudogene 12 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40446045-40446898 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 718 Neighboring gene uncharacterized LOC105378669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 824 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40505419-40506052 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40506053-40506687 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:40518723-40519222 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:40524580-40525341 Neighboring gene cyclase associated actin cytoskeleton regulatory protein 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:40535511-40536710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 720 Neighboring gene Sharpr-MPRA regulatory region 13734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:40598557-40599056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 830 Neighboring gene uncharacterized LOC105378671 Neighboring gene OAZ1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 831 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 721 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:40625521-40625722 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40626731-40627347

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables long-chain fatty acyl-CoA hydrolase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables long-chain fatty acyl-CoA hydrolase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables lysophosphatidic acid binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables palmitoyl-(protein) hydrolase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables palmitoyl-(protein) hydrolase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables palmitoyl-(protein) hydrolase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables palmitoyl-(protein) hydrolase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables palmitoyl-(protein) hydrolase activity TAS
    Traceable Author Statement
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sulfatide binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in adult locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in associative learning IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in brain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in fatty-acyl-CoA biosynthetic process TAS
    Traceable Author Statement
    more info
     
    involved_in grooming behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lipid catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in lysosomal lumen acidification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in membrane raft organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cell growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of neuron apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of toll-like receptor 9 signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuron development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in neurotransmitter secretion IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within pinocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of pinocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of receptor-mediated endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein catabolic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in protein depalmitoylation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein depalmitoylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein depalmitoylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in receptor-mediated endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within receptor-mediated endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of synapse structure or activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in sphingolipid catabolic process TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in axon IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in extracellular region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular region ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
     
    is_active_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in membrane HDA PubMed 
    located_in membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in synaptic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    palmitoyl-protein thioesterase 1
    Names
    ceroid-palmitoyl-palmitoyl-protein thioesterase 1
    palmitoyl-protein hydrolase 1
    NP_000301.1
    NP_001136076.1
    NP_001350624.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_009192.1 RefSeqGene

      Range
      5001..29761
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_690

    mRNA and Protein(s)

    1. NM_000310.4NP_000301.1  palmitoyl-protein thioesterase 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_000301.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL512599, BC008426, DA504318
      Consensus CDS
      CCDS447.1
      UniProtKB/Swiss-Prot
      B4DY24, P50897, Q6FGQ4
      UniProtKB/TrEMBL
      A0A2C9F2P4
      Related
      ENSP00000493153.1, ENST00000642050.2
      Conserved Domains (1) summary
      cl21494
      Location:28305
      Abhydrolase; alpha/beta hydrolases
    2. NM_001142604.2NP_001136076.1  palmitoyl-protein thioesterase 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001136076.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame segment compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AK302232, AL512599, BC008426
      Consensus CDS
      CCDS44119.1
      UniProtKB/Swiss-Prot
      P50897
      Related
      ENSP00000392293.2, ENST00000449045.7
      Conserved Domains (1) summary
      cl21494
      Location:22202
      Abhydrolase; alpha/beta hydrolases
    3. NM_001363695.2NP_001350624.1  palmitoyl-protein thioesterase 1 isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the 3' coding region compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AL512599
      Consensus CDS
      CCDS85955.1
      UniProtKB/TrEMBL
      A0A2C9F2P4, Q5T0S4
      Related
      ENSP00000403207.2, ENST00000439754.6
      Conserved Domains (1) summary
      cl21494
      Location:28281
      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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      40071461..40097252 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      39940889..39966711 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)