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Aliases for PCLO Gene

Aliases for PCLO Gene

  • Piccolo Presynaptic Cytomatrix Protein 2 3 5
  • Aczonin 2 3 4
  • ACZ 3 4
  • Piccolo (Presynaptic Cytomatrix Protein) 2
  • Protein Piccolo 3
  • KIAA0559 4
  • PCH3 3

External Ids for PCLO Gene

Previous GeneCards Identifiers for PCLO Gene

  • GC07M080985
  • GC07M082048
  • GC07M082061
  • GC07M081999
  • GC07M082094
  • GC07M082266
  • GC07M082383
  • GC07M076984

Summaries for PCLO Gene

Entrez Gene Summary for PCLO Gene

  • The protein encoded by this gene is part of the presynaptic cytoskeletal matrix, which is involved in establishing active synaptic zones and in synaptic vesicle trafficking. Variations in this gene have been associated with bipolar disorder and major depressive disorder. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

GeneCards Summary for PCLO Gene

PCLO (Piccolo Presynaptic Cytomatrix Protein) is a Protein Coding gene. Diseases associated with PCLO include Pontocerebellar Hypoplasia, Type 3 and Pontocerebellar Hypoplasia. Among its related pathways are Aldosterone synthesis and secretion. Gene Ontology (GO) annotations related to this gene include calcium ion binding and transporter activity. An important paralog of this gene is BSN.

UniProtKB/Swiss-Prot for PCLO Gene

  • May act as a scaffolding protein involved in the organization of synaptic active zones and in synaptic vesicle trafficking.

Gene Wiki entry for PCLO Gene

Additional gene information for PCLO Gene

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

Genomics for PCLO Gene

GeneHancer (GH) Regulatory Elements for PCLO Gene

Promoters and enhancers for PCLO 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
GH07J083161 Promoter/Enhancer 1.4 Ensembl ENCODE 657.1 +0.3 305 1.8 ARID4B SIN3A DMAP1 ZNF2 ZNF48 YY1 ETS1 ZNF143 SP3 SP5 PCLO RNA5SP235
GH07J083162 Enhancer 0.5 ENCODE 650.7 +1.5 1530 0.2 SAP130 SIN3A MIER2 REST SP7 PCLO RNA5SP235
GH07J082894 Promoter 0.5 EPDnew 650.1 +268.4 268433 0.1 PCLO GC07P083018 LOC105375376
GH07J082804 Enhancer 0.8 Ensembl ENCODE 0.1 +357.4 357359 1.3 RXRA JUN MAX BACH1 EP300 MAFF JUND POLR2A RCOR1 FOSL2 LOC105375376 GC07P083018 PCLO
GH07J082759 Enhancer 0.5 ENCODE 0.1 +402.6 402635 0.9 SP1 NANOG POLR2A POU5F1 LOC105375376 GC07P083018 PCLO
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCLO on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCLO gene promoter:
  • CHOP-10
  • C/EBPalpha
  • E2F-5
  • E2F-4
  • E2F-3a
  • E2F-2
  • E2F-1
  • E2F
  • AREB6
  • PPAR-gamma2

Genomic Locations for PCLO Gene

Genomic Locations for PCLO Gene
408,926 bases
Minus strand
408,926 bases
Minus strand

Genomic View for PCLO Gene

Genes around PCLO on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PCLO Gene

Proteins for PCLO Gene

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

    Protein Symbol:
    Recommended name:
    Protein piccolo
    Protein Accession:
    Secondary Accessions:
    • A4D1A7
    • A6NNX9
    • O43373
    • O60305
    • Q08E72
    • Q9BVC8
    • Q9UIV2
    • Q9Y6U9

    Protein attributes for PCLO Gene

    5142 amino acids
    Molecular mass:
    560699 Da
    Quaternary structure:
    • Interacts with RABAC1/PRA1, RIMS2 and profilin.
    • Sequence=AAB97937.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=AAD21789.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=EAL24187.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PCLO Gene

    Alternative splice isoforms for PCLO Gene


neXtProt entry for PCLO Gene

Post-translational modifications for PCLO Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PCLO Gene

Domains & Families for PCLO Gene

Gene Families for PCLO Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for PCLO Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • C2 domain 1 is involved in binding calcium and phospholipids. Calcium binds with low affinity but with high specificity and induces a large conformational change.
  • C2 domain 1 is involved in binding calcium and phospholipids. Calcium binds with low affinity but with high specificity and induces a large conformational change.
genes like me logo Genes that share domains with PCLO: view

Function for PCLO Gene

Molecular function for PCLO Gene

UniProtKB/Swiss-Prot Function:
May act as a scaffolding protein involved in the organization of synaptic active zones and in synaptic vesicle trafficking.

Phenotypes From GWAS Catalog for PCLO Gene

Gene Ontology (GO) - Molecular Function for PCLO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding ISS --
GO:0005515 protein binding IEA --
GO:0005522 profilin binding ISS --
GO:0005544 calcium-dependent phospholipid binding ISS --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PCLO: view
genes like me logo Genes that share phenotypes with PCLO: view

Human Phenotype Ontology for PCLO Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PCLO Gene

MGI Knock Outs for PCLO:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PCLO Gene

Localization for PCLO Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCLO Gene

Cell junction, synapse. Note=Concentrated at the presynaptic side of synaptic junctions. {ECO:0000250}.

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 PCLO gene
Compartment Confidence
extracellular 5
cytoskeleton 5
cytosol 3
plasma membrane 2
nucleus 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCLO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005856 cytoskeleton NAS 10508862
GO:0014069 postsynaptic density IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with PCLO: view

Pathways & Interactions for PCLO Gene

SuperPathway Contained pathways
1 Aldosterone synthesis and secretion
genes like me logo Genes that share pathways with PCLO: view

Pathways by source for PCLO Gene

1 KEGG pathway for PCLO Gene

Gene Ontology (GO) - Biological Process for PCLO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007010 cytoskeleton organization ISS --
GO:0007416 synapse assembly IEA --
GO:0016079 synaptic vesicle exocytosis NAS 10508862
GO:0017157 regulation of exocytosis IEA --
GO:0019933 cAMP-mediated signaling IEA --
genes like me logo Genes that share ontologies with PCLO: view

No data available for SIGNOR curated interactions for PCLO Gene

Drugs & Compounds for PCLO Gene

(1) Drugs for PCLO Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with PCLO: view

Transcripts for PCLO Gene

mRNA/cDNA for PCLO Gene

(4) REFSEQ mRNAs :
(10) Additional mRNA sequences :
(4) Selected AceView cDNA sequences:
(9) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PCLO Gene

Piccolo presynaptic cytomatrix protein:
Representative Sequences:

Clone Products

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

No ASD Table

Relevant External Links for PCLO Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCLO Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Brain - Cerebellum (x6.6), Brain - Cerebellar Hemisphere (x6.3), and Brain - Nucleus accumbens (basal ganglia) (x4.1).

Protein differential expression in normal tissues from HIPED for PCLO Gene

This gene is overexpressed in Frontal cortex (25.1), Fetal gut (12.3), and Spinal cord (11.1).

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

NURSA nuclear receptor signaling pathways regulating expression of PCLO Gene:


SOURCE GeneReport for Unigene cluster for PCLO Gene:


mRNA Expression by UniProt/SwissProt for PCLO Gene:

Tissue specificity: Moderately expressed in the developing cerebral cortex.

Evidence on tissue expression from TISSUES for PCLO Gene

  • Nervous system(4.8)
  • Blood(2.1)

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

Germ Layers:
  • ectoderm
  • mesoderm
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cheek
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • lip
  • mouth
  • neck
  • nose
  • outer ear
  • skull
  • chest wall
  • abdominal wall
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with PCLO: view

No data available for Protein tissue co-expression partners for PCLO Gene

Orthologs for PCLO Gene

This gene was present in the common ancestor of animals.

Orthologs for PCLO Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCLO 34 33
  • 99.57 (n)
(Bos Taurus)
Mammalia PCLO 34 33
  • 88.47 (n)
(Mus musculus)
Mammalia Pclo 16 34 33
  • 84.46 (n)
(Rattus norvegicus)
Mammalia Pclo 33
  • 84.19 (n)
(Canis familiaris)
Mammalia PCLO 34 33
  • 82.74 (n)
(Monodelphis domestica)
Mammalia PCLO 34
  • 78 (a)
(Ornithorhynchus anatinus)
Mammalia PCLO 34
  • 75 (a)
(Gallus gallus)
Aves PCLO 34 33
  • 71.34 (n)
(Anolis carolinensis)
Reptilia PCLO 34
  • 64 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pclo 33
  • 66.36 (n)
(Danio rerio)
Actinopterygii si:dkey-108d22.4 33
  • 60.73 (n)
pcloa 34
  • 49 (a)
pclob 34
  • 43 (a)
(Caenorhabditis elegans)
Secernentea F45E4.3 34
  • 26 (a)
Species where no ortholog for PCLO was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • 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 (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PCLO Gene

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

Paralogs for PCLO Gene

Paralogs for PCLO Gene

(11) SIMAP similar genes for PCLO Gene using alignment to 6 proteins:

  • E9PE96_HUMAN
  • H7C114_HUMAN
  • H7C261_HUMAN
  • L8E9M5_HUMAN
  • Q32P40_HUMAN
genes like me logo Genes that share paralogs with PCLO: view

Variants for PCLO Gene

Sequence variations from dbSNP and Humsavar for PCLO Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs746260871 pathogenic, Pontocerebellar hypoplasia type 3 82,949,964(-) G/A/C coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant, stop_gained
rs149360770 likely-benign, not specified 82,822,584(-) T/C coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs370030206 uncertain-significance, not provided 82,949,751(-) C/A coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs372909168 uncertain-significance, not provided 82,955,559(-) T/C coding_sequence_variant, intron_variant, non_coding_transcript_variant, synonymous_variant
rs1060499888 uncertain-significance, not specified 82,953,681(-) G/A coding_sequence_variant, intron_variant, non_coding_transcript_variant, synonymous_variant

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

Variant ID Type Subtype PubMed ID
dgv6516n100 CNV gain 25217958
esv1000997 CNV deletion 20482838
esv1579695 CNV insertion 17803354
esv2641869 CNV deletion 19546169
esv2675648 CNV deletion 23128226
esv2677988 CNV deletion 23128226
esv2752186 CNV gain 17911159
esv3305049 CNV mobile element insertion 20981092
esv3305139 CNV mobile element insertion 20981092
esv3341429 CNV insertion 20981092
esv3344369 CNV insertion 20981092
esv3411020 CNV insertion 20981092
esv3613915 CNV loss 21293372
esv3613918 CNV loss 21293372
esv3613920 CNV loss 21293372
esv3613921 CNV loss 21293372
esv3613922 CNV loss 21293372
esv3613923 CNV loss 21293372
nsv1023612 CNV loss 25217958
nsv1137264 CNV deletion 24896259
nsv1139902 CNV duplication 24896259
nsv1161574 CNV deletion 26073780
nsv442054 CNV loss 18776908
nsv464614 CNV loss 19166990
nsv519920 CNV loss 19592680
nsv524315 CNV gain 19592680
nsv528771 CNV loss 19592680
nsv5817 CNV deletion 18451855
nsv607700 CNV gain 21841781
nsv607701 CNV loss 21841781
nsv607702 CNV loss 21841781
nsv818530 CNV loss 17921354
nsv819983 CNV gain 19587683
nsv824188 CNV loss 20364138
nsv831046 CNV gain 17160897

Variation tolerance for PCLO Gene

Residual Variation Intolerance Score: 1.62% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 20.90; 99.19% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCLO 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 PCLO Gene

Disorders for PCLO Gene

MalaCards: The human disease database

(14) MalaCards diseases for PCLO Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
pontocerebellar hypoplasia, type 3
  • pch3
pontocerebellar hypoplasia
  • pch
splenic flexure cancer
  • ca splenic flexure - colon
vertebral artery insufficiency
  • vertebral artery syndrome
descending colon cancer
  • ca descending colon
- elite association - COSMIC cancer census association via MalaCards
Search PCLO in MalaCards View complete list of genes associated with diseases


  • Pontocerebellar hypoplasia 3 (PCH3) [MIM:608027]: A form of pontocerebellar hypoplasia, a disorder characterized by structural defects of the pons and cerebellum. Brain MRI shows an abnormally small cerebellum and brainstem, decreased cerebral white matter, and a thin corpus callosum. PCH3 features include seizures, short stature, optic atrophy, progressive microcephaly, severe developmental delay. {ECO:0000269 PubMed:25832664}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PCLO

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 PCLO: view

No data available for Genatlas for PCLO Gene

Publications for PCLO Gene

  1. Genome-wide association for major depressive disorder: a possible role for the presynaptic protein piccolo. (PMID: 19065144) Sullivan PF … Penninx BW (Molecular psychiatry 2009) 3 22 44 58
  2. Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9628581) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 58
  3. Loss of PCLO function underlies pontocerebellar hypoplasia type III. (PMID: 25832664) Ahmed MY … Mochida GH (Neurology 2015) 3 4 58
  4. Genome-wide association analysis of gender differences in major depressive disorder in the Netherlands NESDA and NTR population-based samples. (PMID: 21621269) Aragam N … Pan Y (Journal of affective disorders 2011) 3 44 58
  5. Human variation in alcohol response is influenced by variation in neuronal signaling genes. (PMID: 20201926) Joslyn G … White RL (Alcoholism, clinical and experimental research 2010) 3 44 58

Products for PCLO Gene

Sources for PCLO Gene

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