PPT1 palmitoyl-protein thioesterase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PPT1provided by HGNC
Official Full Name: palmitoyl-protein thioesterase 1provided by HGNC
Primary source: HGNC:HGNC:9325
See related: Ensembl:ENSG00000131238 MIM:600722; AllianceGenome:HGNC:9325
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: PPT; CLN1; INCL
Summary: The protein encoded by this gene is a small glycoprotein involved in the catabolism of lipid-modified proteins during lysosomal degradation. The encoded enzyme removes thioester-linked fatty acyl groups such as palmitate from cysteine residues. Defects in this gene are a cause of infantile neuronal ceroid lipofuscinosis 1 (CLN1, or INCL) and neuronal ceroid lipofuscinosis 4 (CLN4). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2008]
Expression: Ubiquitous expression in spleen (RPKM 86.1), lung (RPKM 62.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p34.2

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (40071461..40097252, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (39940889..39966711, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (40537133..40562924, complement)

Chromosome 1 - NC_000001.11 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
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?

Identification of PPT1 as a lysosomal core gene with prognostic value in hepatocellular carcinoma.
Title: Identification of PPT1 as a lysosomal core gene with prognostic value in hepatocellular carcinoma.
Computational and structural investigation of Palmitoyl-Protein Thioesterase 1 (PPT1) protein causing Neuronal Ceroid Lipofuscinoses (NCL).
Title: Computational and structural investigation of Palmitoyl-Protein Thioesterase 1 (PPT1) protein causing Neuronal Ceroid Lipofuscinoses (NCL).
Human INCL fibroblasts display abnormal mitochondrial and lysosomal networks and heightened susceptibility to ROS-induced cell death.
Title: Human INCL fibroblasts display abnormal mitochondrial and lysosomal networks and heightened susceptibility to ROS-induced cell death.
High PPT1 expression is associated with cancer.
Title: PPT1 Promotes Tumor Growth and Is the Molecular Target of Chloroquine Derivatives in Cancer.
The results demonstrate that these patient iPSC derived NCL NSCs are valid cell- based disease models with characteristic disease phenotypes that can be used for study of disease pathophysiology and drug development.
Title: Neural stem cells for disease modeling and evaluation of therapeutics for infantile (CLN1/PPT1) and late infantile (CLN2/TPP1) neuronal ceroid lipofuscinoses.
the study contributes four novel variants to the spectrum of PPT1 gene mutations and eight novel variants to the TPP1 gene mutation data in neuronal ceroid lipofuscinoses type I and type II
Title: Batten disease: biochemical and molecular characterization revealing novel PPT1 and TPP1 gene mutations in Indian patients.
Targeting PPT1 blocks mTOR signaling in a manner distinct from catalytic inhibitors, while concurrently inhibiting autophagy, thereby providing a new strategy for cancer therapy.
Title: A Unified Approach to Targeting the Lysosome's Degradative and Growth Signaling Roles.
the combination of elevated glycolysis and deficient MRPL13 activity was closely linked to CLN1-mediated tumor activity in human hepatoma cells
Title: Lactate-mediated mitoribosomal defects impair mitochondrial oxidative phosphorylation and promote hepatoma cell invasiveness.
Proteomics analysis on isolated cilia revealed 660 proteins, which differed in their abundance levels between wild type and Ppt1 knock out.
Title: Proteomics insights into infantile neuronal ceroid lipofuscinosis (CLN1) point to the involvement of cilia pathology in the disease.
we reveal the existence of a positive feedback loop, where palmitoylation of PPT1 results in decreased activity and subsequent elevation in the amount of palmitoylated proteins.
Title: Reversible Cysteine Acylation Regulates the Activity of Human Palmitoyl-Protein Thioesterase 1 (PPT1).

Submit: New GeneRIF Correction See all GeneRIFs (28)

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
Neuronal ceroid lipofuscinosis 1 MedGen: C1850451 OMIM: 256730 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D1S1857E (e-PCR)
- UniSTS:63807

AL010071 (e-PCR)
- UniSTS:33642

SHGC-74659 (e-PCR)
- UniSTS:47759

WI-12268 (e-PCR)
- UniSTS:32966

A006O26 (e-PCR)
- UniSTS:56573

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables long-chain fatty acyl-CoA hydrolase activity	IDA Inferred from Direct Assay more info	PubMed
enables long-chain fatty acyl-CoA hydrolase activity	ISS Inferred from Sequence or Structural Similarity more info
enables lysophosphatidic acid binding	IDA Inferred from Direct Assay more info	PubMed
enables palmitoyl-(protein) hydrolase activity	IBA Inferred from Biological aspect of Ancestor more info
enables palmitoyl-(protein) hydrolase activity	IDA Inferred from Direct Assay more info	PubMed
enables palmitoyl-(protein) hydrolase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables palmitoyl-(protein) hydrolase activity	ISS Inferred from Sequence or Structural Similarity more info
enables palmitoyl-(protein) hydrolase activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sulfatide binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in adult locomotory behavior	IEA Inferred from Electronic Annotation more info
involved_in associative learning	IEA Inferred from Electronic Annotation more info
involved_in brain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in fatty-acyl-CoA biosynthetic process	TAS Traceable Author Statement more info
involved_in grooming behavior	IEA Inferred from Electronic Annotation more info
involved_in lipid catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in lysosomal lumen acidification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in membrane raft organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cell growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron development	TAS Traceable Author Statement more info	PubMed
involved_in neurotransmitter secretion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within pinocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of pinocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of receptor-mediated endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein catabolic process	NAS Non-traceable Author Statement more info	PubMed
involved_in protein depalmitoylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein depalmitoylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein depalmitoylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in receptor-mediated endocytosis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within receptor-mediated endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of synapse structure or activity	NAS Non-traceable Author Statement more info	PubMed
involved_in response to stimulus	IEA Inferred from Electronic Annotation more info
involved_in sphingolipid catabolic process	TAS Traceable Author Statement more info	PubMed
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	ISS Inferred from Sequence or Structural Similarity more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in lysosomal lumen	TAS Traceable Author Statement more info
is_active_in lysosome	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in lysosome	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	HDA more info	PubMed
located_in membrane raft	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	IEA Inferred from Electronic Annotation more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: palmitoyl-protein thioesterase 1

Names: ceroid-palmitoyl-palmitoyl-protein thioesterase 1; palmitoyl-protein hydrolase 1

NP_000301.1

EC 3.1.2.22

NP_001136076.1

EC 3.1.2.22

NP_001350624.1

EC 3.1.2.22

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_009192.1 RefSeqGene

Range

5001..29761

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_690

mRNA and Protein(s)

NM_000310.4 → NP_000301.1 palmitoyl-protein thioesterase 1 isoform 1 precursor

See identical proteins and their annotated locations for NP_000301.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AL512599, BC008426, DA504318

Consensus CDS

CCDS447.1

UniProtKB/Swiss-Prot

B4DY24, P50897, Q6FGQ4

UniProtKB/TrEMBL

A0A2C9F2P4

Related

ENSP00000493153.1, ENST00000642050.2

Conserved Domains (1) summary

cl21494
Location:28 → 305

Abhydrolase; alpha/beta hydrolases
NM_001142604.2 → NP_001136076.1 palmitoyl-protein thioesterase 1 isoform 2 precursor

See identical proteins and their annotated locations for NP_001136076.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame segment compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AK302232, AL512599, BC008426

Consensus CDS

CCDS44119.1

UniProtKB/Swiss-Prot

P50897

Related

ENSP00000392293.2, ENST00000449045.7

Conserved Domains (1) summary

cl21494
Location:22 → 202

Abhydrolase; alpha/beta hydrolases
NM_001363695.2 → NP_001350624.1 palmitoyl-protein thioesterase 1 isoform 3 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an in-frame exon in the 3' coding region compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AL512599

Consensus CDS

CCDS85955.1

UniProtKB/TrEMBL

A0A2C9F2P4, Q5T0S4

Related

ENSP00000403207.2, ENST00000439754.6

Conserved Domains (1) summary

cl21494
Location:28 → 281

Abhydrolase; alpha/beta hydrolases