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

Gene ID: 10908, updated on 3-May-2020

Summary

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
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

Genomic context

See PNPLA6 in Genome Data Viewer
Location:
19p13.2
Exon count:
37
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (7534164..7561767)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (7599033..7626653)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372261 Neighboring gene zinc finger protein 358 Neighboring gene mucolipin 1 Neighboring gene calmodulin regulated spectrin associated protein family member 3 Neighboring gene microRNA 6792 Neighboring gene XPA binding protein 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: MCOLN1

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
lysophospholipase activity EXP
Inferred from Experiment
more info
PubMed 
lysophospholipase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lysophospholipase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
glycerophospholipid catabolic process TAS
Traceable Author Statement
more info
 
phosphatidylcholine metabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
membrane HDA PubMed 

General protein information

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)

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
    5013..32613
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001166111.2NP_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
    Q8IY17
    Related
    ENSP00000407509.2, ENST00000414982.7
    Conserved Domains (3) summary
    cd07225
    Location:9641269
    Pat_PNPLA6_PNPLA7; Patatin-like phospholipase domain containing protein 6 and protein 7
    cd00038
    Location:635743
    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:354502
    Atrophin-1; Atrophin-1 family
  2. NM_001166112.1NP_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, BQ001677
    Consensus CDS
    CCDS54207.1
    UniProtKB/Swiss-Prot
    Q8IY17
    Related
    ENSP00000443323.1, ENST00000545201.6
    Conserved Domains (4) summary
    cd07225
    Location:8891194
    Pat_PNPLA6_PNPLA7; Patatin-like phospholipase domain containing protein 6 and protein 7
    COG0664
    Location:141283
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    COG1752
    Location:8941178
    RssA; Predicted acylesterase/phospholipase RssA, containd patatin domain [General function prediction only]
    cd00038
    Location:561669
    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_001166113.1NP_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:9161221
    Pat_PNPLA6_PNPLA7; Patatin-like phospholipase domain containing protein 6 and protein 7
    cd00038
    Location:587695
    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:306454
    Atrophin-1; Atrophin-1 family
  4. NM_001166114.2NP_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/Swiss-Prot
    Q8IY17
    Related
    ENSP00000473211.1, ENST00000600737.5
    Conserved Domains (4) summary
    cd07225
    Location:9541259
    Pat_PNPLA6_PNPLA7; Patatin-like phospholipase domain containing protein 6 and protein 7
    COG0664
    Location:180322
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    COG1752
    Location:9591243
    RssA; Predicted acylesterase/phospholipase RssA, containd patatin domain [General function prediction only]
    cd00038
    Location:626734
    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_006702.5NP_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:9161221
    Pat_PNPLA6_PNPLA7; Patatin-like phospholipase domain containing protein 6 and protein 7
    cd00038
    Location:587695
    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:306454
    Atrophin-1; Atrophin-1 family

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

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