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Aliases for PPT1 Gene

Aliases for PPT1 Gene

  • Palmitoyl-Protein Thioesterase 1 2 3 3 5
  • Palmitoyl-Protein Hydrolase 1 3 4
  • CLN1 3 4
  • PPT 3 4
  • Ceroid-Palmitoyl-Palmitoyl-Protein Thioesterase 1 3
  • Ceroid-Lipofuscinosis, Neuronal 1, Infantile 2
  • EC 4
  • PPT-1 4
  • INCL 3

External Ids for PPT1 Gene

Previous HGNC Symbols for PPT1 Gene

  • PPT

Previous GeneCards Identifiers for PPT1 Gene

  • GC01M040567
  • GC01M039541
  • GC01M040001
  • GC01M039951
  • GC01M040207
  • GC01M040310
  • GC01M038656

Summaries for PPT1 Gene

Entrez Gene Summary for PPT1 Gene

  • 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]

GeneCards Summary for PPT1 Gene

PPT1 (Palmitoyl-Protein Thioesterase 1) is a Protein Coding gene. Diseases associated with PPT1 include Ceroid Lipofuscinosis, Neuronal, 1 and Ceroid Storage Disease. Among its related pathways are Fatty Acyl-CoA Biosynthesis and Metabolism. Gene Ontology (GO) annotations related to this gene include palmitoyl-CoA hydrolase activity and palmitoyl hydrolase activity. An important paralog of this gene is PPT2.

UniProtKB/Swiss-Prot for PPT1 Gene

  • Removes thioester-linked fatty acyl groups such as palmitate from modified cysteine residues in proteins or peptides during lysosomal degradation. Prefers acyl chain lengths of 14 to 18 carbons (PubMed:8816748).

Gene Wiki entry for PPT1 Gene

Additional gene information for PPT1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PPT1 Gene

Genomics for PPT1 Gene

GeneHancer (GH) Regulatory Elements for PPT1 Gene

Promoters and enhancers for PPT1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J040096 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 683.9 +0.6 588 1.5 HDGF ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B ZNF766 PPT1 PPIE EXO5 TRIT1 NFYC PPIEL PABPC4 RLF LOC101929516 CAP1
GH01J040095 Enhancer 0.5 FANTOM5 dbSUPER 686.4 +1.9 1906 0.5 PPT1 RLF SMAP2 CAP1
GH01J040036 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 26.5 +58.1 58078 7.1 CLOCK ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 CAP1 LOC105378669 PPT1 PPIEL PPIE TRIT1 ZNF684 ZFP69 EXO5 BMP8B
GH01J040055 Enhancer 1.4 Ensembl ENCODE dbSUPER 32.4 +39.0 39035 6 HDGF PKNOX1 SMAD1 FOXA2 ARNT ARID4B ZNF766 E2F8 JUNB ZNF592 EXO5 PPIE PPT1 TRIT1 PPIEL NFYC RLF LOC105378668 ENSG00000202222 CAP1
GH01J040076 Enhancer 1.1 Ensembl ENCODE dbSUPER 32.8 +20.8 20796 1.8 ATF1 JUN CEBPG IRF9 FOSL1 CTBP1 ATF7 ZNF362 CEBPB ZEB2 PPT1 CAP1 ZMPSTE24 ENSG00000231296 TRIT1 ENSG00000202222
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PPT1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PPT1 gene promoter:
  • c-Jun
  • ATF-2
  • AP-1
  • Tal-1
  • E47

Genomic Locations for PPT1 Gene

Genomic Locations for PPT1 Gene
26,267 bases
Minus strand
24,997 bases
Minus strand

Genomic View for PPT1 Gene

Genes around PPT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PPT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PPT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PPT1 Gene

Proteins for PPT1 Gene

  • Protein details for PPT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Palmitoyl-protein thioesterase 1
    Protein Accession:
    Secondary Accessions:
    • B4DY24
    • Q6FGQ4

    Protein attributes for PPT1 Gene

    306 amino acids
    Molecular mass:
    34193 Da
    Quaternary structure:
    • Interacts with CLN5 (PubMed:19941651). Interacts with ATP5F1A and ATP5F1B (By similarity).

    Three dimensional structures from OCA and Proteopedia for PPT1 Gene

    Alternative splice isoforms for PPT1 Gene


neXtProt entry for PPT1 Gene

Post-translational modifications for PPT1 Gene

No data available for DME Specific Peptides for PPT1 Gene

Domains & Families for PPT1 Gene

Gene Families for PPT1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for PPT1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the palmitoyl-protein thioesterase family.
  • Belongs to the palmitoyl-protein thioesterase family.
genes like me logo Genes that share domains with PPT1: view

Function for PPT1 Gene

Molecular function for PPT1 Gene

UniProtKB/Swiss-Prot Function:
Removes thioester-linked fatty acyl groups such as palmitate from modified cysteine residues in proteins or peptides during lysosomal degradation. Prefers acyl chain lengths of 14 to 18 carbons (PubMed:8816748).
UniProtKB/Swiss-Prot CatalyticActivity:
Palmitoyl-[protein] + H(2)O = palmitate + [protein].

Enzyme Numbers (IUBMB) for PPT1 Gene

Phenotypes From GWAS Catalog for PPT1 Gene

Gene Ontology (GO) - Molecular Function for PPT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19941651
GO:0008474 palmitoyl-(protein) hydrolase activity TAS,IEA --
GO:0016290 palmitoyl-CoA hydrolase activity ISS --
GO:0016787 hydrolase activity IEA --
GO:0016790 thiolester hydrolase activity IBA --
genes like me logo Genes that share ontologies with PPT1: view
genes like me logo Genes that share phenotypes with PPT1: view

Human Phenotype Ontology for PPT1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PPT1 Gene

MGI Knock Outs for PPT1:

Animal Model Products

Clone Products

  • Addgene plasmids for PPT1

No data available for Transcription Factor Targets and HOMER Transcription for PPT1 Gene

Localization for PPT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PPT1 Gene

Lysosome. Secreted.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PPT1 gene
Compartment Confidence
extracellular 5
nucleus 5
lysosome 5
golgi apparatus 5
cytosol 4
mitochondrion 1
endoplasmic reticulum 1
endosome 1

Gene Ontology (GO) - Cellular Components for PPT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region ISS --
GO:0005615 extracellular space IEA --
GO:0005634 nucleus IDA 10992246
GO:0005764 lysosome ISS --
GO:0005794 Golgi apparatus IDA 7637805
genes like me logo Genes that share ontologies with PPT1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PPT1 Gene

Pathways & Interactions for PPT1 Gene

genes like me logo Genes that share pathways with PPT1: view

Gene Ontology (GO) - Biological Process for PPT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002084 protein depalmitoylation ISS --
GO:0006898 receptor-mediated endocytosis IMP 16542649
GO:0006907 pinocytosis IMP 16542649
GO:0007040 lysosome organization IEA --
GO:0007042 lysosomal lumen acidification IMP 11722572
genes like me logo Genes that share ontologies with PPT1: view

No data available for SIGNOR curated interactions for PPT1 Gene

Drugs & Compounds for PPT1 Gene

(9) Drugs for PPT1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Palmitic Acid Approved, Experimental Pharma Full agonist, Agonist, Target 23
Water Approved Pharma 0
1-Hexadecylsulfonyl Fluoride Experimental Pharma Target 0
Coenzyme A Investigational Nutra 0

(6) Additional Compounds for PPT1 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • coenzyme A, S-Hexadecanoate
  • Palmitoyl coenzyme A
  • S-Palmitoylcoenzyme A
  • coenzyme A, S-Hexadecanoic acid
  • Hexadecanoyl CoA
  • Hexadecanoyl coenzyme A
  • Palmitoyl CoA
  • Palmitoyl coenzyme A
  • Palmitoyl-CoA
genes like me logo Genes that share compounds with PPT1: view

Transcripts for PPT1 Gene

mRNA/cDNA for PPT1 Gene

Unigene Clusters for PPT1 Gene

Palmitoyl-protein thioesterase 1:
Representative Sequences:

Clone Products

  • Addgene plasmids for PPT1

Alternative Splicing Database (ASD) splice patterns (SP) for PPT1 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c · 10d ^ 11
SP1: -
SP2: - -
SP4: - - - - - -

Relevant External Links for PPT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PPT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PPT1 Gene

mRNA differential expression in normal tissues according to GTEx for PPT1 Gene

This gene is overexpressed in Whole Blood (x6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PPT1 Gene

Protein tissue co-expression partners for PPT1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PPT1 Gene:


SOURCE GeneReport for Unigene cluster for PPT1 Gene:


Evidence on tissue expression from TISSUES for PPT1 Gene

  • Nervous system(5)
  • Liver(4.3)
  • Blood(4)
  • Kidney(3.8)
  • Lung(3.6)
  • Spleen(3.4)
  • Eye(3.3)
  • Skin(3.1)
  • Intestine(3)
  • Pancreas(2.9)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PPT1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • head
  • mouth
  • pharynx
  • heart
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
  • blood vessel
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with PPT1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PPT1 Gene

Orthologs for PPT1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PPT1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PPT1 34 33
  • 99.46 (n)
(Canis familiaris)
Mammalia PPT1 34 33
  • 91.48 (n)
(Bos Taurus)
Mammalia CLN1 34
  • 91 (a)
PPT1 33
  • 90.27 (n)
(Mus musculus)
Mammalia Ppt1 16 34 33
  • 85.03 (n)
(Rattus norvegicus)
Mammalia Ppt1 33
  • 84.26 (n)
(Monodelphis domestica)
Mammalia PPT1 34
  • 81 (a)
(Ornithorhynchus anatinus)
Mammalia PPT1 34
  • 58 (a)
(Gallus gallus)
Aves PPT1 34 33
  • 72.3 (n)
(Anolis carolinensis)
Reptilia PPT1 34
  • 73 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ppt1 33
  • 68.24 (n)
(Danio rerio)
Actinopterygii ppt1 34 33
  • 66.56 (n)
fruit fly
(Drosophila melanogaster)
Insecta Ppt1 34 35 33
  • 58.03 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001058 33
  • 57.97 (n)
(Caenorhabditis elegans)
Secernentea ppt-1 34 35 33
  • 56.29 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G60340 33
  • 46.16 (n)
(Oryza sativa)
Liliopsida Os03g0101100 33
  • 44.87 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9019 34
  • 57 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU06530 33
  • 48.22 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes pdf1 33
  • 45.98 (n)
Species where no ortholog for PPT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PPT1 Gene

Gene Tree for PPT1 (if available)
Gene Tree for PPT1 (if available)
Evolutionary constrained regions (ECRs) for PPT1: view image

Paralogs for PPT1 Gene

Paralogs for PPT1 Gene

(4) SIMAP similar genes for PPT1 Gene using alignment to 7 proteins:

  • E9PK48_HUMAN
  • E9PP28_HUMAN
  • Q5T0S4_HUMAN
genes like me logo Genes that share paralogs with PPT1: view

Variants for PPT1 Gene

Sequence variations from dbSNP and Humsavar for PPT1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1012813914 uncertain-significance, Neuronal Ceroid-Lipofuscinosis, Recessive 40,073,721(-) A/C 3_prime_UTR_variant
rs1057515445 uncertain-significance, Neuronal Ceroid-Lipofuscinosis, Recessive 40,073,042(-) G/A 3_prime_UTR_variant
rs1057515446 uncertain-significance, Neuronal Ceroid-Lipofuscinosis, Recessive 40,073,151(-) G/A 3_prime_UTR_variant
rs1057515447 uncertain-significance, Neuronal Ceroid-Lipofuscinosis, Recessive 40,073,809(-) G/A 3_prime_UTR_variant
rs1057515448 uncertain-significance, Neuronal Ceroid-Lipofuscinosis, Recessive 40,078,581(-) A/G coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for PPT1 Gene

Variant ID Type Subtype PubMed ID
dgv35n67 CNV loss 20364138
esv2663819 CNV deletion 23128226
esv2747330 CNV deletion 23290073
esv2750836 CNV gain 17911159
esv2758933 CNV loss 17122850
esv3585798 CNV loss 21293372
esv6823 CNV loss 19470904
nsv10128 CNV loss 18304495
nsv1133843 CNV deletion 24896259
nsv1133844 CNV deletion 24896259
nsv476221 CNV novel sequence insertion 20440878
nsv829660 CNV gain+loss 17160897

Variation tolerance for PPT1 Gene

Residual Variation Intolerance Score: 27.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.15; 69.43% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PPT1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PPT1 Gene

Disorders for PPT1 Gene

MalaCards: The human disease database

(14) MalaCards diseases for PPT1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
ceroid lipofuscinosis, neuronal, 1
  • cln1
ceroid storage disease
  • lipofuscin storage disease
neuronal ceroid lipofuscinosis
  • batten disease
neuronal ceroid-lipofuscinoses
  • neuronal ceroid-lipofuscinosis, infantile
ceroid lipofuscinosis, neuronal, 3
  • cln3
- elite association - COSMIC cancer census association via MalaCards
Search PPT1 in MalaCards View complete list of genes associated with diseases


  • Ceroid lipofuscinosis, neuronal, 1 (CLN1) [MIM:256730]: A form of neuronal ceroid lipofuscinosis with variable age at onset. Infantile, late-infantile, juvenile, and adult onset have been reported. Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterized by intracellular accumulation of autofluorescent liposomal material, and clinically by seizures, dementia, visual loss, and/or cerebral atrophy. The lipopigment pattern seen most often in CLN1 is referred to as granular osmiophilic deposits (GROD). {ECO:0000269 PubMed:11506414, ECO:0000269 PubMed:19201763, ECO:0000269 PubMed:19941651, ECO:0000269 PubMed:21990111, ECO:0000269 PubMed:7637805, ECO:0000269 PubMed:9425237, ECO:0000269 PubMed:9664077}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PPT1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PPT1: view

No data available for Genatlas for PPT1 Gene

Publications for PPT1 Gene

  1. Mutations in CLN7/MFSD8 are a common cause of variant late-infantile neuronal ceroid lipofuscinosis. (PMID: 19201763) Kousi M … Lehesjoki AE (Brain : a journal of neurology 2009) 3 4 44 58
  2. Novel interactions of CLN5 support molecular networking between Neuronal Ceroid Lipofuscinosis proteins. (PMID: 19941651) Lyly A … Kyttälä A (BMC cell biology 2009) 3 4 22 58
  3. Adult neuronal ceroid lipofuscinosis with palmitoyl-protein thioesterase deficiency: first adult-onset patients of a childhood disease. (PMID: 11506414) van Diggelen OP … Voznyi YV (Annals of neurology 2001) 3 4 22 58
  4. Mutations in the palmitoyl-protein thioesterase gene (PPT; CLN1) causing juvenile neuronal ceroid lipofuscinosis with granular osmiophilic deposits. (PMID: 9425237) Mitchison HM … O'Rawe AM (Human molecular genetics 1998) 3 4 22 58
  5. Molecular genetics of palmitoyl-protein thioesterase deficiency in the U.S. (PMID: 9664077) Das AK … Hofmann SL (The Journal of clinical investigation 1998) 3 4 22 58

Products for PPT1 Gene

Sources for PPT1 Gene

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