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LYPLAL1 lysophospholipase like 1 [ Homo sapiens (human) ]

Gene ID: 127018, updated on 10-Dec-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, Dec 2024]
Expression
Ubiquitous expression in kidney (RPKM 3.2), heart (RPKM 2.4) and 25 other tissues See more
Orthologs
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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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 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. 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
  5. ELAVL4 promotes the tumorigenesis of small cell lung cancer by stabilizing LncRNA LYPLAL1-DT and enhancing profilin 2 activation. Li S, et al. FASEB J, 2023 Oct. PMID 37676718

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 variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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 macromolecule depalmitoylation IEA
Inferred from Electronic Annotation
more info
  
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 cGAS/STING signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
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

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