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

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; 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

Location:: 19p13.2

Exon count:: 37

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (7534164..7561767)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (7534898..7562499)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (7599050..7626653)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Neuropathy target esterase activity defines phenotypes among PNPLA6 disorders.
Title: Neuropathy target esterase activity defines phenotypes among PNPLA6 disorders.
Two case reports of a novel missense mutation in the PNPLA6 gene in two siblings with chorioretinal dystrophy, hypogonadotropic hypogonadism, and cerebellar ataxia.
Title: Two case reports of a novel missense mutation in the PNPLA6 gene in two siblings with chorioretinal dystrophy, hypogonadotropic hypogonadism, and cerebellar ataxia.
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.
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.
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.
CHORIORETINAL CHANGES IN A GENETICALLY CONFIRMED CASE OF BOUCHER-NEUHAUSER SYNDROME.
Title: CHORIORETINAL CHANGES IN A GENETICALLY CONFIRMED CASE OF BOUCHER-NEUHÄUSER SYNDROME.
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.
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.
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.
Novel variants in PNPLA6 causing syndromic retinal dystrophy.
Title: Novel variants in PNPLA6 causing syndromic retinal dystrophy.

Submit: New GeneRIF Correction See all GeneRIFs (39)

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

Associated conditions

Description	Tests
Ataxia-hypogonadism-choroidal dystrophy syndrome MedGen: C1859093 OMIM: 215470 GeneReviews: PNPLA6 Disorders	not available
Hereditary spastic paraplegia 39 MedGen: C2677586 OMIM: 612020 GeneReviews: PNPLA6 Disorders	not available
Laurence-Moon syndrome MedGen: C0023138 OMIM: 245800 GeneReviews: PNPLA6 Disorders	not available
Trichomegaly-retina pigmentary degeneration-dwarfism syndrome MedGen: C1848745 OMIM: 275400 GeneReviews: PNPLA6 Disorders	not available

Variation

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See Variation Viewer (GRCh37.p13)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH91529 (e-PCR)
- UniSTS:89489

RH80512 (e-PCR)
- UniSTS:87491

RH11760 (e-PCR)
- UniSTS:64214

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

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 more info	PubMed

General protein information

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Preferred Names: patatin-like phospholipase domain-containing protein 6

Names: neuropathy target esterase

NP_001159583.1

EC 3.1.1.5

NP_001159584.1

EC 3.1.1.5

NP_001159585.1

EC 3.1.1.5

NP_001159586.1

EC 3.1.1.5

NP_006693.3

EC 3.1.1.5

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

NG_013374.1 RefSeqGene

Range

6566..32613

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
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 ...
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
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 ...
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