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    LYPLAL1 lysophospholipase like 1 [ Homo sapiens (human) ]

    Gene ID: 127018, updated on 3-Nov-2024

    Summary

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    Official Symbol
    LYPLAL1provided by HGNC
    Official Full Name
    lysophospholipase like 1provided by HGNC
    Primary source
    HGNC:HGNC:20440
    See related
    Ensembl:ENSG00000143353 MIM:616548; AllianceGenome:HGNC:20440
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    Q96AV0
    Summary
    Enables palmitoyl-(protein) hydrolase activity. Involved in negative regulation of cGAS/STING signaling pathway. Located in cytosol. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 3.2), heart (RPKM 2.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LYPLAL1 in Genome Data Viewer
    Location:
    1q41
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (219173878..219445496)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (218409848..218681408)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (219347220..219386200)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904513 Neighboring gene MPRA-validated peak701 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1820 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2542 Neighboring gene LYPLAL1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2543 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2546 Neighboring gene ribosomal modification protein rimK like family member B pseudogene 2 Neighboring gene Sharpr-MPRA regulatory region 2527 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:219572714-219573343 Neighboring gene uncharacterized LOC107984018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1821 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:219615440-219616639 Neighboring gene LYPLAL1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2547 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:219674825-219676024 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:219728356-219729055 Neighboring gene uncharacterized LOC124904514 Neighboring gene uncharacterized LOC124904657

    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 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. Crystal structure of the predicted phospholipase LYPLAL1 reveals unexpected functional plasticity despite close relationship to acyl protein thioesterases. Bürger M, et al. J Lipid Res, 2012 Jan. PMID 22052940, Free PMC Article
    2. Replication study of 15 recently published Loci for body fat distribution in the Japanese population. Hotta K, et al. J Atheroscler Thromb, 2013. PMID 23221025
    3. A genetic variant in proximity to the gene LYPLAL1 is associated with lower hunger feelings and increased weight loss following Roux-en-Y gastric bypass surgery. Bandstein M, et al. Scand J Gastroenterol, 2016 Sep. PMID 27181159, Free PMC Article
    4. USP9X deubiquitinates and stabilizes CDC123 to promote breast carcinogenesis through regulating cell cycle. Song N, et al. Mol Carcinog, 2023 Oct. PMID 37314216
    5. Two obesity susceptibility loci in LYPLAL1 and ETV5 independently associated with childhood hypertension in Chinese population. Lv D, et al. Gene, 2017 Sep 5. PMID 28645872

    See all (56) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Targeting LYPLAL1-mediated cGAS depalmitoylation enhances the response to anti-tumor immunotherapy.
      Title: Targeting LYPLAL1-mediated cGAS depalmitoylation enhances the response to anti-tumor immunotherapy.
    2. ELAVL4 promotes the tumorigenesis of small cell lung cancer by stabilizing LncRNA LYPLAL1-DT and enhancing profilin 2 activation.
      Title: ELAVL4 promotes the tumorigenesis of small cell lung cancer by stabilizing LncRNA LYPLAL1-DT and enhancing profilin 2 activation.
    3. Metabolic effects of LYPLAL1 rs12137855-C were similar, but statistically less robust, to the effects of GCKR rs1260326-T. TM6SF2 rs58542926-T displayed opposite metabolic effects when compared with the fatty liver associations.
      Title: NAFLD risk alleles in PNPLA3, TM6SF2, GCKR and LYPLAL1 show divergent metabolic effects.
    4. Novel LYPLAL1 SNP rs2605100 is associated with childhood hypertension adjusted by obesity.
      Title: Two obesity susceptibility loci in LYPLAL1 and ETV5 independently associated with childhood hypertension in Chinese population.
    5. The LYPLAL1 genotype is associated with differences in eating behavior and loss of extensive body weight following Roux-en-Y gastric bypass (RYGB) surgery. Genotyping and the use of eating behavior-related questionnaires may help to estimate the RYGB-associated therapy success.
      Title: A genetic variant in proximity to the gene LYPLAL1 is associated with lower hunger feelings and increased weight loss following Roux-en-Y gastric bypass surgery.
    6. Among Mexicans, the PNPLA3 (rs738409), LYPLAL1 (rs12137855), PPP1R3B (rs4240624), and GCKR (rs780094) polymorphisms may be associated with a greater risk of chronic liver disease among overweight adults.
      Title: Association between PNPLA3 (rs738409), LYPLAL1 (rs12137855), PPP1R3B (rs4240624), GCKR (rs780094), and elevated transaminase levels in overweight/obese Mexican adults.
    7. Data provide evidence that variants of MC4R and LYPLAL1 modulate body fat distribution with sexual dimorphism in a Chinese population.
      Title: Effects of Obesity Related Genetic Variations on Visceral and Subcutaneous Fat Distribution in a Chinese Population.
    8. Our results suggest that LYPLAL1 rs4846567 and NISCH rs6784615 may influence fat distribution in the Japanese population.
      Title: Replication study of 15 recently published Loci for body fat distribution in the Japanese population.
    9. genetic association studies in Danish population: Quantitative metabolic phenotypes in obesity are associated with SNP in various genes: LYPLAL1 (rs4846567) is associated with waist-hip ratio and insulin sensitivity in women.
      Title: Association studies of novel obesity-related gene variants with quantitative metabolic phenotypes in a population-based sample of 6,039 Danish individuals.
    10. Gene-treatment interactions were observed for short-term weight loss. (LYPLAL1 rs2605100, Plifestyle*SNP = 0.032)
      Title: Genetic predictors of weight loss and weight regain after intensive lifestyle modification, metformin treatment, or standard care in the Diabetes Prevention Program.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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
    A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
    EBI GWAS Catalog
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog
    Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.
    EBI GWAS Catalog
    Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.
    EBI GWAS Catalog
    Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits.
    EBI GWAS Catalog

    Variation

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    See Variation Viewer (GRCh37.p13)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ99730, KIAA1238

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carboxylic ester hydrolase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables hydrolase activity, acting on ester bonds IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT enables lipase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables lysophospholipase activity NAS
    Non-traceable Author Statement
    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in macromolecule depalmitoylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cGAS/STING signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein depalmitoylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in mitochondrion HTP PubMed 

    General protein information

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    Preferred Names
    lysophospholipase-like protein 1
    NP_001287698.1
    NP_001287699.1
    NP_001287700.1
    NP_001287701.1
    NP_001337557.1
    NP_001337558.1
    NP_620149.2
    XP_016855760.1
    XP_047301090.1
    XP_047301094.1
    XP_054190285.1
    XP_054190286.1
    XP_054190287.1
    XP_054190288.1

    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_001300769.2 → NP_001287698.1  lysophospholipase-like protein 1 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon and uses an alternate splice site in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AK309689, AL360093, BC016711, BF115063
      UniProtKB/Swiss-Prot
      Q5VWZ2
      Related
      ENST00000474379.5
      Conserved Domains (1) summary
      cl21494
      Location:13 → 171
      Abhydrolase; alpha/beta hydrolases

    2. NM_001300770.2 → NP_001287699.1  lysophospholipase-like protein 1 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AA424278, AL360093, AY341430, BC016711, BF115063, HY106571
      Consensus CDS
      CCDS73032.1
      UniProtKB/Swiss-Prot
      Q5VWZ2
      Related
      ENSP00000355894.3, ENST00000366927.3
      Conserved Domains (2) summary
      COG0596
      Location:16 → 134
      MhpC; Pimeloyl-ACP methyl ester carboxylesterase [Coenzyme transport and metabolism, General function prediction only]
      cl21494
      Location:13 → 206
      Abhydrolase; alpha/beta hydrolases

    3. NM_001300771.2 → NP_001287700.1  lysophospholipase-like protein 1 isoform d

      See identical proteins and their annotated locations for NP_001287700.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' reading frame, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) has a shorter N-terminus than isoform a. Variants 4 and 5 encode the same isoform (d).
      Source sequence(s)
      AA424278, AL360093, BC016711, BF115063, CB851909
      UniProtKB/Swiss-Prot
      Q5VWZ2
      Related
      ENST00000483635.5
      Conserved Domains (1) summary
      cl21494
      Location:13 → 184
      Abhydrolase; alpha/beta hydrolases

    4. NM_001300772.2 → NP_001287701.1  lysophospholipase-like protein 1 isoform d

      See identical proteins and their annotated locations for NP_001287701.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' reading frame, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) has a shorter N-terminus than isoform a. Variants 4 and 5 encode the same isoform (d).
      Source sequence(s)
      AA417842, AA424278, AL360093, AW967835, BC016711, BF115063, BX282451
      UniProtKB/Swiss-Prot
      Q5VWZ2
      Conserved Domains (1) summary
      cl21494
      Location:13 → 184
      Abhydrolase; alpha/beta hydrolases

    5. NM_001350628.2 → NP_001337557.1  lysophospholipase-like protein 1 isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) contains an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (e) is longer than isoform a.
      Source sequence(s)
      AA424278, AL360093, BC016711, BF115063, BI830985, HY106571
      Related
      ENST00000463964.5
      Conserved Domains (1) summary
      cl21494
      Location:13 → 231
      Abhydrolase; alpha/beta hydrolases

    6. NM_001350629.2 → NP_001337558.1  lysophospholipase-like protein 1 isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) contains an alternate in-frame exon and uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (f) is shorter than isoform a
      Source sequence(s)
      AA424278, AL360093, BC016711, BF115063, BI830985, HY106571
      Related
      ENST00000477938.5
      Conserved Domains (1) summary
      cl21494
      Location:13 → 215
      Abhydrolase; alpha/beta hydrolases

    7. NM_138794.5 → NP_620149.2  lysophospholipase-like protein 1 isoform a

      See identical proteins and their annotated locations for NP_620149.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform a.
      Source sequence(s)
      AA424278, AL360093, BC016711, BF115063, HY106571
      Consensus CDS
      CCDS1522.1
      UniProtKB/Swiss-Prot
      A8K677, Q5VWZ2, Q5VWZ3, Q7Z4A3, Q96AV0
      Related
      ENSP00000355895.5, ENST00000366928.10
      Conserved Domains (2) summary
      COG0596
      Location:16 → 150
      MhpC; Pimeloyl-ACP methyl ester carboxylesterase [Coenzyme transport and metabolism, General function prediction only]
      cl21494
      Location:13 → 222
      Abhydrolase; alpha/beta hydrolases

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      219173878..219445496
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017000271.3 → XP_016855760.1  lysophospholipase-like protein 1 isoform X1

      Conserved Domains (1) summary
      cl21494
      Location:13 → 231
      Abhydrolase; alpha/beta hydrolases

    2. XM_047445134.1 → XP_047301090.1  lysophospholipase-like protein 1 isoform X2

      UniProtKB/Swiss-Prot
      A8K677, Q5VWZ2, Q5VWZ3, Q7Z4A3, Q96AV0

    3. XM_047445138.1 → XP_047301094.1  lysophospholipase-like protein 1 isoform X3

    RNA

    1. XR_007078557.1 RNA Sequence

    2. XR_007078562.1 RNA Sequence

    3. XR_001736967.3 RNA Sequence

    4. XR_007078564.1 RNA Sequence

    5. XR_007078559.1 RNA Sequence

    6. XR_007078561.1 RNA Sequence

    7. XR_001736964.3 RNA Sequence

    8. XR_007078558.1 RNA Sequence

    9. XR_007078563.1 RNA Sequence

    10. XR_001736968.3 RNA Sequence

    11. XR_007078556.1 RNA Sequence

    12. XR_007078567.1 RNA Sequence

    13. XR_007078555.1 RNA Sequence

    14. XR_007078560.1 RNA Sequence

    15. XR_007078565.1 RNA Sequence

    16. XR_007078568.1 RNA Sequence

    17. XR_001736965.3 RNA Sequence

    18. XR_007078566.1 RNA Sequence

    19. XR_007078569.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      218409848..218681408
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334310.1 → XP_054190285.1  lysophospholipase-like protein 1 isoform X1

    2. XM_054334311.1 → XP_054190286.1  lysophospholipase-like protein 1 isoform X2

    3. XM_054334312.1 → XP_054190287.1  lysophospholipase-like protein 1 isoform X3

    4. XM_054334313.1 → XP_054190288.1  lysophospholipase-like protein 1 isoform X4

    RNA

    1. XR_008485918.1 RNA Sequence

    2. XR_008485917.1 RNA Sequence

    3. XR_008485920.1 RNA Sequence

    4. XR_008485914.1 RNA Sequence

    5. XR_008485916.1 RNA Sequence

    6. XR_008485919.1 RNA Sequence

    7. XR_008485924.1 RNA Sequence

    8. XR_008485925.1 RNA Sequence

    9. XR_008485911.1 RNA Sequence

    10. XR_008485915.1 RNA Sequence

    11. XR_008485921.1 RNA Sequence

    12. XR_008485913.1 RNA Sequence

    13. XR_008485923.1 RNA Sequence

    14. XR_008485926.1 RNA Sequence

    15. XR_008485912.1 RNA Sequence

    16. XR_008485922.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VWZ2.3 GenPept UniProtKB/Swiss-Prot:Q5VWZ2

    Gene LinkOut

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

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