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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
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Genomic context

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See PNPLA6 in Genome Data Viewer
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

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