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    LYPLA1 lysophospholipase 1 [ Homo sapiens (human) ]

    Gene ID: 10434, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LYPLA1provided by HGNC
    Official Full Name
    lysophospholipase 1provided by HGNC
    Primary source
    HGNC:HGNC:6737
    See related
    Ensembl:ENSG00000120992 MIM:605599; AllianceGenome:HGNC:6737
    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
    APT1; LPL1; APT-1; LPL-I; hAPT1
    Summary
    This gene encodes a member of the alpha/beta hydrolase superfamily. The encoded protein functions as a homodimer, exhibiting both depalmitoylating as well as lysophospholipase activity, and may be involved in Ras localization and signaling. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene have been defined on chromosomes 4, 6, and 7. [provided by RefSeq, Jul 2013]
    Expression
    Ubiquitous expression in urinary bladder (RPKM 38.7), testis (RPKM 35.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LYPLA1 in Genome Data Viewer
    Location:
    8q11.23
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (54042987..54101947, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (54420379..54479027, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (54955547..55014507, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene regulator of G protein signaling 20 Neighboring gene RNA, U6 small nuclear 1331, pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:54856969-54858168 Neighboring gene LYPLA1-TCEA1 readthrough Neighboring gene ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae) pseudogene Neighboring gene transcription elongation factor A1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19197 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19198 Neighboring gene Uncharacterized LOC133039971 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:54934747-54935540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:54935541-54936332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:54942814-54943544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:54943545-54944276 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:54958280-54958473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27370 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:54997169-54998116 Neighboring gene CRIPTO pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27371 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19199 Neighboring gene MPRA-validated peak7022 silencer Neighboring gene RNA, U6atac small nuclear 32, pseudogene Neighboring gene mitochondrial ribosomal protein L15

    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. Depalmitoylation and cell physiology: APT1 as a mediator of metabolic signals. Speck SL, et al. Am J Physiol Cell Physiol, 2024 Apr 1. PMID 38344800,
    2. A conserved but structurally divergent loop in acyl protein thioesterase 1 regulates its catalytic activity, ligand binding, and folded stability. Harris WT 3rd, et al. Proteins, 2024 Jun. PMID 38179877
    3. A specific human lysophospholipase: cDNA cloning, tissue distribution and kinetic characterization. Wang A, et al. Biochim Biophys Acta, 1999 Feb 25. PMID 10064899
    4. Subcellular localization and PKC-dependent regulation of the human lysophospholipase A/acyl-protein thioesterase in WISH cells. Wang A, et al. Biochim Biophys Acta, 2000 Apr 12. PMID 10760470
    5. Crystal structure of the human acyl protein thioesterase I from a single X-ray data set to 1.5 A. Devedjiev Y, et al. Structure, 2000 Nov 15. PMID 11080636

    See all (57) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A conserved but structurally divergent loop in acyl protein thioesterase 1 regulates its catalytic activity, ligand binding, and folded stability.
      Title: A conserved but structurally divergent loop in acyl protein thioesterase 1 regulates its catalytic activity, ligand binding, and folded stability.
    2. Depalmitoylation and cell physiology: APT1 as a mediator of metabolic signals.
      Title: Depalmitoylation and cell physiology: APT1 as a mediator of metabolic signals.
    3. LncRNA LOXL1-AS1 Facilitates the Oncogenic Character in Cervical Cancer by the miR-526b-5p /LYPLA1 Axis.
      Title: LncRNA LOXL1-AS1 Facilitates the Oncogenic Character in Cervical Cancer by the miR-526b-5p /LYPLA1 Axis.
    4. LYPLA1 and LYPLA2 are each able to account for the loss of the other to maintain lipid homeostasis in cells
      Title: Lysophospholipases cooperate to mediate lipid homeostasis and lysophospholipid signaling.
    5. The depalmitoylating enzyme acyl-protein thioesterase 1 (APT1) directs the asymmetric localization of Numb and beta-catenin in MDA-MB-231 triple receptor-negative breast cancer cells.
      Title: The depalmitoylase APT1 directs the asymmetric partitioning of Notch and Wnt signaling during cell division.
    6. Study results suggest that the LYPLA1 gene plays a tumorpromotor role in nonsmall cell lung cancer cells in vitro.
      Title: Inhibition of cell proliferation and migration in non‑small cell lung cancer cells through the suppression of LYPLA1.
    7. Data show taht active S-depalmitoylation in mitochondria, in part mediated by acyl-protein thioesterase 1 (APT1)
      Title: Active and dynamic mitochondrial S-depalmitoylation revealed by targeted fluorescent probes.
    8. Here, we describe the conserved functions of APT1 and APT2 across organisms and discuss the possibility that these enzymes are members of a larger family of depalmitoylation enzymes.
      Title: Enzymatic protein depalmitoylation by acyl protein thioesterases.
    9. High expression of APT1 is associated with chronic lymphocytic leukemia.
      Title: miRs-138 and -424 control palmitoylation-dependent CD95-mediated cell death by targeting acyl protein thioesterases 1 and 2 in CLL.
    10. identifcation APT1 as one of the thioesterases in the acylation cycle and demonstration that this protein is a cellular target of the inhibitor.
      Title: Small-molecule inhibition of APT1 affects Ras localization and signaling.
    Submit: New GeneRIF Correction See all GeneRIFs (14)

    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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of lysophospholipase I (LYPLA1) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carboxylic ester hydrolase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables lipase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables lysophospholipase activity 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 phospholipase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in fatty acid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in fatty acid transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of Golgi to plasma membrane protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of Golgi to plasma membrane protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of aggrephagy IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein depalmitoylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein depalmitoylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    acyl-protein thioesterase 1
    Names
    lysoPLA I
    lysophospholipase I
    lysophospholipid-specific lysophospholipase
    palmitoyl-protein hydrolase
    NP_001266285.1
    NP_001266286.1
    NP_001266287.1
    NP_001266288.1
    NP_001266289.1
    NP_001412766.1
    NP_006321.1

    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_001279356.2 → NP_001266285.1  acyl-protein thioesterase 1 isoform 2

      See identical proteins and their annotated locations for NP_001266285.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AA827237, AF035293, AF052112, AK298206
      Consensus CDS
      CCDS75739.1
      UniProtKB/TrEMBL
      B4DP64, E5RGR0
      Related
      ENSP00000482430.1, ENST00000618914.4
      Conserved Domains (1) summary
      pfam02230
      Location:11 → 192
      Abhydrolase_2; Phospholipase/Carboxylesterase

    2. NM_001279357.2 → NP_001266286.1  acyl-protein thioesterase 1 isoform 3

      See identical proteins and their annotated locations for NP_001266286.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.
      Source sequence(s)
      AA827237, AF035293, AF052112, AF077199
      Consensus CDS
      CCDS64899.1
      UniProtKB/TrEMBL
      E5RGR0
      Related
      ENSP00000344477.6, ENST00000343231.10
      Conserved Domains (1) summary
      pfam02230
      Location:11 → 210
      Abhydrolase_2; Phospholipase/Carboxylesterase

    3. NM_001279358.2 → NP_001266287.1  acyl-protein thioesterase 1 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (4) is shorter, compared to isoform 1.
      Source sequence(s)
      AA827237, AF035293, AF052112, DA881616
      UniProtKB/TrEMBL
      B4DJV9
      Conserved Domains (1) summary
      pfam02230
      Location:11 → 212
      Abhydrolase_2; Phospholipase/Carboxylesterase

    4. NM_001279359.2 → NP_001266288.1  acyl-protein thioesterase 1 isoform 5

      See identical proteins and their annotated locations for NP_001266288.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in its 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (5) has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AA307642, AA827237, AF035293, AF052112
      UniProtKB/Swiss-Prot
      O75608
      Conserved Domains (1) summary
      pfam02230
      Location:8 → 177
      Abhydrolase_2; Phospholipase/Carboxylesterase

    5. NM_001279360.2 → NP_001266289.1  acyl-protein thioesterase 1 isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate 5'-terminal exon, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (6) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AA827237, AF035293, DA817192, DA883059
      Consensus CDS
      CCDS75738.1
      UniProtKB/TrEMBL
      A0A087X1K9
      Related
      ENSP00000484280.1, ENST00000618741.1
      Conserved Domains (1) summary
      pfam02230
      Location:1 → 162
      Abhydrolase_2; Phospholipase/Carboxylesterase

    6. NM_001425837.1 → NP_001412766.1  acyl-protein thioesterase 1 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC100821
      UniProtKB/TrEMBL
      E5RGR0
      Related
      ENSP00000428729.1, ENST00000518546.5

    7. NM_006330.4 → NP_006321.1  acyl-protein thioesterase 1 isoform 1

      See identical proteins and their annotated locations for NP_006321.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA827237, AF035293, AF052112
      Consensus CDS
      CCDS6157.1
      UniProtKB/Swiss-Prot
      O43202, O75608, Q9UQF9
      UniProtKB/TrEMBL
      B4DJV9, Q6IAQ1
      Related
      ENSP00000320043.3, ENST00000316963.8
      Conserved Domains (1) summary
      pfam02230
      Location:11 → 226
      Abhydrolase_2; Phospholipase/Carboxylesterase

    RNA

    1. NR_189621.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC100821

    2. NR_189622.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC100821

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      54042987..54101947 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      54420379..54479027 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75608.1 GenPept UniProtKB/Swiss-Prot:O75608

    Gene LinkOut

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

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