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    PNPLA6 patatin like phospholipase domain containing 6 [ Homo sapiens (human) ]

    Gene ID: 10908, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PNPLA6provided by HGNC
    Official Full Name
    patatin like phospholipase domain containing 6provided by HGNC
    Primary source
    HGNC:HGNC:16268
    See related
    Ensembl:ENSG00000032444 MIM:603197; AllianceGenome:HGNC:16268
    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
    NTE; sws; BNHS; LNMS; OMCS; SPG39; NTEMND; iPLA2delta
    Summary
    This gene encodes a phospholipase that deacetylates intracellular phosphatidylcholine to produce glycerophosphocholine. It is thought to function in neurite outgrowth and process elongation during neuronal differentiation. The protein is anchored to the cytoplasmic face of the endoplasmic reticulum in both neurons and non-neuronal cells. Mutations in this gene result in autosomal recessive spastic paraplegia, and the protein is the target for neurodegeneration induced by organophosphorus compounds and chemical warfare agents. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]
    Expression
    Ubiquitous expression in lung (RPKM 16.4), testis (RPKM 15.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    19p13.2
    Exon count:
    37
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (7534164..7561767)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (7534898..7562499)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (7599050..7626653)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372261 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9986 Neighboring gene zinc finger protein 358 Neighboring gene mucolipin TRP cation channel 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13887 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:7614843-7615534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:7615535-7616226 Neighboring gene MPRA-validated peak3321 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9987 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:7661728-7662333 Neighboring gene calmodulin regulated spectrin associated protein family member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:7669777-7670278 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:7670279-7670778 Neighboring gene microRNA 6792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13888 Neighboring gene XPA binding protein 2

    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. The alteration of the expression level of neuropathy target esterase in human neuroblastoma SK-N-SH cells disrupts cellular phospholipids homeostasis. Hou WY, et al. Toxicol In Vitro, 2023 Feb. PMID 36336212
    2. Oliver McFarlane syndrome: two new cases and a review of the literature. Lisbjerg K, et al. Ophthalmic Genet, 2021 Aug. PMID 33818269
    3. Chorioretinal dystrophy, hypogonadotropic hypogonadism, and cerebellar ataxia: Boucher-Neuhauser syndrome due to a homozygous (c.3524C>G (p.Ser1175Cys)) variant in PNPLA6 gene. Doğan M, et al. Ophthalmic Genet, 2021 Jun. PMID 33650466
    4. A novel PNPLA6 mutation in a Turkish family with intractable Holmes tremor and spastic ataxia. Emekli AS, et al. Neurol Sci, 2021 Apr. PMID 33210227
    5. Reduced neuropathy target esterase in pre-eclampsia suppresses tube formation of HUVECs via dysregulation of phospholipid metabolism. Li M, et al. J Cell Physiol, 2021 Jun. PMID 33184906

    See all (100) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The alteration of the expression level of neuropathy target esterase in human neuroblastoma SK-N-SH cells disrupts cellular phospholipids homeostasis.
      Title: The alteration of the expression level of neuropathy target esterase in human neuroblastoma SK-N-SH cells disrupts cellular phospholipids homeostasis.
    2. Oliver McFarlane syndrome: two new cases and a review of the literature.
      Title: Oliver McFarlane syndrome: two new cases and a review of the literature.
    3. Chorioretinal dystrophy, hypogonadotropic hypogonadism, and cerebellar ataxia: Boucher-Neuhauser syndrome due to a homozygous (c.3524C>G (p.Ser1175Cys)) variant in PNPLA6 gene.
      Title: Chorioretinal dystrophy, hypogonadotropic hypogonadism, and cerebellar ataxia: Boucher-Neuhauser syndrome due to a homozygous (c.3524C>G (p.Ser1175Cys)) variant in PNPLA6 gene.
    4. CHORIORETINAL CHANGES IN A GENETICALLY CONFIRMED CASE OF BOUCHER-NEUHAUSER SYNDROME.
      Title: CHORIORETINAL CHANGES IN A GENETICALLY CONFIRMED CASE OF BOUCHER-NEUHÄUSER SYNDROME.
    5. Reduced neuropathy target esterase in pre-eclampsia suppresses tube formation of HUVECs via dysregulation of phospholipid metabolism.
      Title: Reduced neuropathy target esterase in pre-eclampsia suppresses tube formation of HUVECs via dysregulation of phospholipid metabolism.
    6. A novel PNPLA6 mutation in a Turkish family with intractable Holmes tremor and spastic ataxia.
      Title: A novel PNPLA6 mutation in a Turkish family with intractable Holmes tremor and spastic ataxia.
    7. Bi-allelic variants in PNPLA6 possibly associated with Parkinsonian features in addition to spastic paraplegia phenotype.
      Title: Bi-allelic variants in PNPLA6 possibly associated with Parkinsonian features in addition to spastic paraplegia phenotype.
    8. Novel variants in PNPLA6 causing syndromic retinal dystrophy.
      Title: Novel variants in PNPLA6 causing syndromic retinal dystrophy.
    9. This result further confirmed the role of PNPLA6 in BoucherNeuhauser syndrome (BNS) and suggested that whole exome sequencing may be applied for the diagnosis of complex syndromes, including BNS, prior to the observation of obvious symptoms.
      Title: A novel PNPLA6 compound heterozygous mutation identified in a Chinese patient with Boucher‑Neuhäuser syndrome.
    10. Silencing of PNPLA6, the neuropathy target esterase (NTE) codifying gene, alters early neurodevelopment.
      Title: Silencing of PNPLA6, the neuropathy target esterase (NTE) codifying gene, alters neurodifferentiation of human embryonal carcinoma stem cells (NT2).
    Submit: New GeneRIF Correction See all GeneRIFs (37)

    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

    Potential readthrough

    Included gene: MCOLN1

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables lysophospholipase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables lysophospholipase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables lysophospholipase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables phosphatidyl phospholipase B activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in glycerophospholipid catabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in phosphatidylcholine metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane HDA PubMed 

    General protein information

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    Preferred Names
    patatin-like phospholipase domain-containing protein 6
    Names
    neuropathy target esterase
    NP_001159583.1
    NP_001159584.1
    NP_001159585.1
    NP_001159586.1
    NP_006693.3

    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_013374.1 RefSeqGene

      Range
      6566..32613
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001166111.2 → NP_001159583.1  patatin-like phospholipase domain-containing protein 6 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AK294021, BC038229, BC051768, DB068563
      Consensus CDS
      CCDS54206.1
      UniProtKB/Swiss-Prot
      A6NGQ0, B4DFB9, B7Z7T2, F5H5K9, J3KQS3, O60859, Q86W58, Q8IY17, Q9UG58
      Related
      ENSP00000407509.2, ENST00000414982.7
      Conserved Domains (3) summary
      cd07225
      Location:964 → 1269
      Pat_PNPLA6_PNPLA7; Patatin-like phospholipase domain containing protein 6 and protein 7
      PHA03247
      Location:354 → 502
      PHA03247; large tegument protein UL36; Provisional
      cd00038
      Location:635 → 743
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

    2. NM_001166112.2 → NP_001159584.1  patatin-like phospholipase domain-containing protein 6 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) represents use of an alternate promoter and 5' UTR, uses two alternate in-frame splice sites, and lacks an alternate in-frame exon in the central coding region, compared to variant 1. The resulting isoform (c) lacks two internal segments and one internal residue, compared to isoform a.
      Source sequence(s)
      AK302462, BC051768
      Consensus CDS
      CCDS54207.1
      UniProtKB/Swiss-Prot
      Q8IY17
      Related
      ENSP00000443323.1, ENST00000545201.6
      Conserved Domains (4) summary
      cd07225
      Location:889 → 1194
      Pat_PNPLA6_PNPLA7; Patatin-like phospholipase domain containing protein 6 and protein 7
      COG0664
      Location:141 → 283
      Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
      COG1752
      Location:894 → 1178
      RssA; Predicted acylesterase/phospholipase RssA, containd patatin domain [General function prediction only]
      cd00038
      Location:561 → 669
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

    3. NM_001166113.1 → NP_001159585.1  patatin-like phospholipase domain-containing protein 6 isoform b

      See identical proteins and their annotated locations for NP_001159585.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) includes an alternate exon in the 5' UTR and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The full-extent of the 5' UTR has not been determined. The resulting isoform (b) lacks an internal segment near the N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform.
      Source sequence(s)
      AJ004832, BC050553, BC051768, BQ001677
      Consensus CDS
      CCDS32891.1
      UniProtKB/Swiss-Prot
      Q8IY17
      Related
      ENSP00000394348.2, ENST00000450331.7
      Conserved Domains (3) summary
      cd07225
      Location:916 → 1221
      Pat_PNPLA6_PNPLA7; Patatin-like phospholipase domain containing protein 6 and protein 7
      cd00038
      Location:587 → 695
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cl26464
      Location:306 → 454
      Atrophin-1; Atrophin-1 family

    4. NM_001166114.2 → NP_001159586.1  patatin-like phospholipase domain-containing protein 6 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) represents use of an alternate promoter and 5' UTR, uses a downstream start codon, and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The resulting isoform (d) has a shorter N-terminus and lacks one internal residue, compared to isoform a.
      Source sequence(s)
      BC038229, BC051768, DA096881
      Consensus CDS
      CCDS59343.1
      UniProtKB/TrEMBL
      A0A384DVU0
      Related
      ENSP00000473211.1, ENST00000600737.6
      Conserved Domains (3) summary
      cd07225
      Location:954 → 1259
      Pat_PNPLA6_PNPLA7; Patatin-like phospholipase domain containing protein 6 and protein 7
      PHA03247
      Location:345 → 493
      PHA03247; large tegument protein UL36; Provisional
      cd00038
      Location:626 → 734
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

    5. NM_006702.5 → NP_006693.3  patatin-like phospholipase domain-containing protein 6 isoform b

      See identical proteins and their annotated locations for NP_006693.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents use of an alternate promoter and 5' UTR and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The resulting isoform (b) lacks an internal segment near the N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform.
      Source sequence(s)
      BC050553, BC051768, DA104284
      Consensus CDS
      CCDS32891.1
      UniProtKB/Swiss-Prot
      Q8IY17
      Related
      ENSP00000221249.5, ENST00000221249.10
      Conserved Domains (3) summary
      cd07225
      Location:916 → 1221
      Pat_PNPLA6_PNPLA7; Patatin-like phospholipase domain containing protein 6 and protein 7
      cd00038
      Location:587 → 695
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cl26464
      Location:306 → 454
      Atrophin-1; Atrophin-1 family

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      7534164..7561767
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      7534898..7562499
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IY17.3 GenPept UniProtKB/Swiss-Prot:Q8IY17

    Gene LinkOut

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

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