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    ACP6 acid phosphatase 6, lysophosphatidic [ Homo sapiens (human) ]

    Gene ID: 51205, updated on 3-Nov-2024

    Summary

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    Official Symbol
    ACP6provided by HGNC
    Official Full Name
    acid phosphatase 6, lysophosphatidicprovided by HGNC
    Primary source
    HGNC:HGNC:29609
    See related
    Ensembl:ENSG00000162836 MIM:611471; AllianceGenome:HGNC:29609
    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
    LPAP; ACPL1; PACPL1
    Summary
    This gene encodes a member of the histidine acid phosphatase protein family. The encoded protein hydrolyzes lysophosphatidic acid, which is involved in G protein-coupled receptor signaling, lipid raft modulation, and in balancing lipid composition within the cell. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2016]
    Expression
    Ubiquitous expression in thyroid (RPKM 3.4), prostate (RPKM 3.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ACP6 in Genome Data Viewer
    Location:
    1q21.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (147629658..147670524, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (147137207..147181884)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (147114029..147142646, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 624 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:146958668-146958835 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:146974675-146975522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:146975523-146976368 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:146976369-146977214 Neighboring gene olfactory receptor family 13 subfamily Z member 3 pseudogene Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:146981878-146982536 Neighboring gene MPRA-validated peak403 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:147012942-147013696 Neighboring gene NANOG hESC enhancer GRCh37_chr1:147016860-147017378 Neighboring gene BCL9 transcription coactivator Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:147067805-147068328 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1281 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1282 Neighboring gene uncharacterized LOC128071544 Neighboring gene Sharpr-MPRA regulatory region 10305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:147091237-147092116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:147092117-147092996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:147113153-147113654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:147141494-147142437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1635 Neighboring gene uncharacterized LOC105371230 Neighboring gene uncharacterized LOC102723321 Neighboring gene RNA, 7SL, cytoplasmic 261, pseudogene

    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. Purification and characterization of a lysophosphatidic acid-specific phosphatase. Hiroyama M, et al. Biochem J, 1998 Dec 1. PMID 9820827, Free PMC Article
    2. The expression characteristics and clinical significance of ACP6, a potential target of nitidine chloride, in hepatocellular carcinoma. Gao L, et al. BMC Cancer, 2022 Dec 1. PMID 36456931, Free PMC Article
    3. Mutant p53 regulates LPA signaling through lysophosphatidic acid phosphatase type 6. Chryplewicz A, et al. Sci Rep, 2019 Mar 26. PMID 30914657, Free PMC Article
    4. Crystal structures and biochemical studies of human lysophosphatidic acid phosphatase type 6. Li J, et al. Protein Cell, 2013 Jul. PMID 23807634, Free PMC Article
    5. Isolation of a cDNA encoding human lysophosphatidic acid phosphatase that is involved in the regulation of mitochondrial lipid biosynthesis. Hiroyama M, et al. J Biol Chem, 1999 Oct 8. PMID 10506173

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The expression characteristics and clinical significance of ACP6, a potential target of nitidine chloride, in hepatocellular carcinoma.
      Title: The expression characteristics and clinical significance of ACP6, a potential target of nitidine chloride, in hepatocellular carcinoma.
    2. Mutant p53 regulates LPA signaling through lysophosphatidic acid phosphatase type 6.
      Title: Mutant p53 regulates LPA signaling through lysophosphatidic acid phosphatase type 6.
    3. structures and biochemical studies of human lysophosphatidic acid phosphatase type 6
      Title: Crystal structures and biochemical studies of human lysophosphatidic acid phosphatase type 6.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    5. Human seminal plasma contains this enzyme which converts lysophospholipids to lysophosphatidic acid.
      Title: Prostatic acid phosphatase degrades lysophosphatidic acid in seminal plasma.
    6. acid phosphatase-like protein 1 from human intestinal tissue could be associated with interstitial cells of Cajal function ACPL1
      Title: Novel human and mouse genes encoding an acid phosphatase family member and its downregulation in W/W(V) mouse jejunum.
    Submit: New GeneRIF Correction

    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

    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 acid phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables lysophosphatidic acid phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables lysophosphatidic acid phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables lysophosphatidic acid phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in hematopoietic progenitor cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lysobisphosphatidic acid metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in lysobisphosphatidic acid metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in phosphatidic acid biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in phospholipid metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lysophosphatidic acid phosphatase type 6
    Names
    acid phosphatase-like protein 1
    NP_001310554.1
    NP_057445.4
    XP_011507903.1
    XP_054192891.1

    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.

    Genomic

    1. NG_050757.1 RefSeqGene

      Range
      5020..33314
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001323625.2 → NP_001310554.1  lysophosphatidic acid phosphatase type 6 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding region, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC241644

    2. NM_016361.5 → NP_057445.4  lysophosphatidic acid phosphatase type 6 isoform 1

      See identical proteins and their annotated locations for NP_057445.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AB031478, AB209248, AC241644, AL520992, BC009965
      Consensus CDS
      CCDS928.1
      UniProtKB/Swiss-Prot
      Q59G61, Q5T490, Q6IAQ3, Q7LG81, Q9NPH0, Q9UIG6, X5D289
      Related
      ENSP00000463574.1, ENST00000583509.7
      Conserved Domains (1) summary
      cd07061
      Location:49 → 379
      HP_HAP_like; Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction

    RNA

    1. NR_136633.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate internal exon and includes an alternate segment in the 3' end, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC241644

    2. NR_136634.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the 5'-terminal exon, includes two alternate internal exons, and includes an alternate segment in the 3' end, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC241644

    3. NR_136635.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC241644

    4. NR_136636.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate splice site in the 5'-terminal exon, includes an alternate internal exon, and includes an alternate segment in the 3' end, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC241644

    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
      147629658..147670524 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011509601.4 → XP_011507903.1  lysophosphatidic acid phosphatase type 6 isoform X1

      Conserved Domains (1) summary
      cd07061
      Location:49 → 379
      HP_HAP_like; Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      147137207..147181884
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336916.1 → XP_054192891.1  lysophosphatidic acid phosphatase type 6 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NPH0.3 GenPept UniProtKB/Swiss-Prot:Q9NPH0

    Gene LinkOut

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