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LYPLA1 lysophospholipase 1 [ Homo sapiens (human) ]

Gene ID: 10434, updated on 11-Apr-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
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Genomic context

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Location:
8q11.23
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (54046367..54101947, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (54423759..54479027, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (54958927..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 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 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. Inhibition of cell proliferation and migration in non‑small cell lung cancer cells through the suppression of LYPLA1. Mohammed A, et al. Oncol Rep, 2019 Feb. PMID 30431103
  2. Active and dynamic mitochondrial S-depalmitoylation revealed by targeted fluorescent probes. Kathayat RS, et al. Nat Commun, 2018 Jan 23. PMID 29362370, Free PMC Article
  3. Identification and characterization of acyl-protein thioesterase 1/lysophospholipase I as a ghrelin deacylation/lysophospholipid hydrolyzing enzyme in fetal bovine serum and conditioned medium. Satou M, et al. Endocrinology, 2010 Oct. PMID 20685872
  4. A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis. Siegel G, et al. Nat Cell Biol, 2009 Jun. PMID 19465924, Free PMC Article
  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 (50) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Depalmitoylation and cell physiology: APT1 as a mediator of metabolic signals.
    Title: Depalmitoylation and cell physiology: APT1 as a mediator of metabolic signals.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Dynamic palmitoylation links cytosol-membrane shuttling of acyl-protein thioesterase-1 and acyl-protein thioesterase-2 with that of proto-oncogene H-ras product and growth-associated protein-43
    Title: Dynamic palmitoylation links cytosol-membrane shuttling of acyl-protein thioesterase-1 and acyl-protein thioesterase-2 with that of proto-oncogene H-ras product and growth-associated protein-43.
Submit: New GeneRIF Correction See all GeneRIFs (13)

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

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 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 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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cell surface IDA
Inferred from Direct Assay
more info
 PubMed 
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 nuclear membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
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_006321.1
XP_005251184.1
XP_016868445.1
XP_016868447.1
XP_016868449.1
XP_047277179.1
XP_047277180.1
XP_047277181.1
XP_047277182.1
XP_047277183.1
XP_047277184.1
XP_054215511.1
XP_054215512.1
XP_054215513.1
XP_054215514.1
XP_054215515.1
XP_054215516.1
XP_054215517.1
XP_054215518.1
XP_054215519.1
XP_054215520.1
XP_054215521.1

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

  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

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    54046367..54101947 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047421225.1 → XP_047277181.1  acyl-protein thioesterase 1 isoform X4

  2. XM_017012956.3 → XP_016868445.1  acyl-protein thioesterase 1 isoform X3

    UniProtKB/TrEMBL
    E5RGR0

  3. XM_017012958.2 → XP_016868447.1  acyl-protein thioesterase 1 isoform X6

    Conserved Domains (1) summary
    cl21494
    Location:20 → 164
    Abhydrolase; alpha/beta hydrolases

  4. XM_047421228.1 → XP_047277184.1  acyl-protein thioesterase 1 isoform X1

  5. XM_017012960.2 → XP_016868449.1  acyl-protein thioesterase 1 isoform X7

    UniProtKB/TrEMBL
    A0A087X1K9
    Conserved Domains (1) summary
    pfam02230
    Location:1 → 162
    Abhydrolase_2; Phospholipase/Carboxylesterase

  6. XM_005251127.6 → XP_005251184.1  acyl-protein thioesterase 1 isoform X5

    See identical proteins and their annotated locations for XP_005251184.1

    Conserved Domains (1) summary
    pfam02230
    Location:8 → 177
    Abhydrolase_2; Phospholipase/Carboxylesterase

  7. XM_047421226.1 → XP_047277182.1  acyl-protein thioesterase 1 isoform X5

  8. XM_047421227.1 → XP_047277183.1  acyl-protein thioesterase 1 isoform X7

    UniProtKB/TrEMBL
    A0A087X1K9

  9. XM_047421224.1 → XP_047277180.1  acyl-protein thioesterase 1 isoform X2

  10. XM_047421223.1 → XP_047277179.1  acyl-protein thioesterase 1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    54423759..54479027 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054359540.1 → XP_054215515.1  acyl-protein thioesterase 1 isoform X4

  2. XM_054359539.1 → XP_054215514.1  acyl-protein thioesterase 1 isoform X3

  3. XM_054359543.1 → XP_054215518.1  acyl-protein thioesterase 1 isoform X6

  4. XM_054359546.1 → XP_054215521.1  acyl-protein thioesterase 1 isoform X1

  5. XM_054359545.1 → XP_054215520.1  acyl-protein thioesterase 1 isoform X7

    UniProtKB/TrEMBL
    A0A087X1K9

  6. XM_054359541.1 → XP_054215516.1  acyl-protein thioesterase 1 isoform X5

  7. XM_054359542.1 → XP_054215517.1  acyl-protein thioesterase 1 isoform X5

  8. XM_054359544.1 → XP_054215519.1  acyl-protein thioesterase 1 isoform X7

    UniProtKB/TrEMBL
    A0A087X1K9

  9. XM_054359537.1 → XP_054215512.1  acyl-protein thioesterase 1 isoform X2

  10. XM_054359536.1 → XP_054215511.1  acyl-protein thioesterase 1 isoform X1

  11. XM_054359538.1 → XP_054215513.1  acyl-protein thioesterase 1 isoform X8

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75608.1 GenPept UniProtKB/Swiss-Prot:O75608

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