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Aliases for PICALM Gene

Aliases for PICALM Gene

  • Phosphatidylinositol Binding Clathrin Assembly Protein 2 3 5
  • Clathrin Assembly Lymphoid Myeloid Leukemia Protein 3 4
  • CALM 3 4
  • Phosphatidylinositol-Binding Clathrin Assembly Protein 3
  • CLTH 3
  • LAP 3

External Ids for PICALM Gene

Previous GeneCards Identifiers for PICALM Gene

  • GC11M087996
  • GC11M087208
  • GC11M085892
  • GC11M085396
  • GC11M085346
  • GC11M085668
  • GC11M081965

Summaries for PICALM Gene

Entrez Gene Summary for PICALM Gene

  • This gene encodes a clathrin assembly protein, which recruits clathrin and adaptor protein complex 2 (AP2) to cell membranes at sites of coated-pit formation and clathrin-vesicle assembly. The protein may be required to determine the amount of membrane to be recycled, possibly by regulating the size of the clathrin cage. The protein is involved in AP2-dependent clathrin-mediated endocytosis at the neuromuscular junction. A chromosomal translocation t(10;11)(p13;q14) leading to the fusion of this gene and the MLLT10 gene is found in acute lymphoblastic leukemia, acute myeloid leukemia and malignant lymphomas. The polymorphisms of this gene are associated with the risk of Alzheimer disease. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]

GeneCards Summary for PICALM Gene

PICALM (Phosphatidylinositol Binding Clathrin Assembly Protein) is a Protein Coding gene. Diseases associated with PICALM include Leukemia, Acute Myeloid and Precursor T-Cell Acute Lymphoblastic Leukemia. Among its related pathways are Notch signaling pathway (KEGG) and Clathrin derived vesicle budding. GO annotations related to this gene include phospholipid binding and 1-phosphatidylinositol binding. An important paralog of this gene is SNAP91.

UniProtKB/Swiss-Prot for PICALM Gene

  • Assembly protein recruiting clathrin and adapter protein complex 2 (AP2) to cell membranes at sites of coated-pit formation and clathrin-vesicle assembly. May be required to determine the amount of membrane to be recycled, possibly by regulating the size of the clathrin cage. Involved in AP2-dependent clathrin-mediated endocytosis at the neuromuscular junction.

Gene Wiki entry for PICALM Gene

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

Genomics for PICALM Gene

Regulatory Elements for PICALM Gene

Enhancers for PICALM Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11G086138 2 FANTOM5 Ensembl ENCODE dbSUPER 34.8 -72.4 -72416 8.0 HNRNPUL1 HDGF PKNOX1 FOXA2 CREB3L1 MLX ARNT AGO1 ARID4B SIN3A PICALM CCDC83 SYTL2 HIKESHI GC11P086154
GH11G086201 1.9 FANTOM5 Ensembl ENCODE dbSUPER 27.4 -132.7 -132719 2.8 HDGF PKNOX1 ATF1 ARNT YY1 ZNF766 ELK1 KLF7 JUNB NCOA1 PICALM RNU6-560P EED HIKESHI CCDC81 FNTAP1 ENSG00000276669
GH11G086156 1.9 FANTOM5 Ensembl ENCODE dbSUPER 23.7 -90.5 -90522 8.4 HDGF PKNOX1 FOXA2 ARNT YY1 ZNF766 FOS SP5 ZNF592 KAT8 PICALM PRSS23 HIKESHI RNU6-560P ENSG00000254699
GH11G086171 1.9 FANTOM5 Ensembl ENCODE dbSUPER 19.7 -106.2 -106220 9.4 HDGF PKNOX1 FOXA2 CREB3L1 ARNT SIN3A ZNF2 ZNF766 FOS JUNB PICALM RNU6-560P PRSS23 EED CREBZF ENSG00000254699
GH11G086134 1.8 FANTOM5 Ensembl ENCODE dbSUPER 15.4 -65.1 -65138 1.4 HDGF PKNOX1 ATF1 ARNT FEZF1 TCF12 ZNF766 GATA2 NCOA1 ZNF592 PICALM CCDC83 EED GC11P086154
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PICALM on UCSC Golden Path with GeneCards custom track

Genomic Location for PICALM Gene

Chromosome:
11
Start:
85,957,171 bp from pter
End:
86,069,882 bp from pter
Size:
112,712 bases
Orientation:
Minus strand

Genomic View for PICALM Gene

Genes around PICALM on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PICALM Gene

Proteins for PICALM Gene

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

    Protein Symbol:
    Q13492-PICAL_HUMAN
    Recommended name:
    Phosphatidylinositol-binding clathrin assembly protein
    Protein Accession:
    Q13492
    Secondary Accessions:
    • B4DTM3
    • E9PN05
    • F8VPG7
    • O60700
    • Q4LE54
    • Q6GMQ6
    • Q86XZ9

    Protein attributes for PICALM Gene

    Size:
    652 amino acids
    Molecular mass:
    70755 Da
    Quaternary structure:
    • Binds clathrin; involves primarily the C-terminal sequences, but the full-length protein is required for full binding capacity. Binds phosphatidylinositol 4,5- bisphosphate. Interacts with FAM64A; this interaction may change the subcellular location into the nucleus.
    SequenceCaution:
    • Sequence=BAE06099.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for PICALM Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PICALM Gene

Post-translational modifications for PICALM Gene

  • Ubiquitination at posLast=134134, posLast=318318, and posLast=324324
  • Modification sites at PhosphoSitePlus

Antibody Products

No data available for DME Specific Peptides for PICALM Gene

Domains & Families for PICALM Gene

Suggested Antigen Peptide Sequences for PICALM Gene

Graphical View of Domain Structure for InterPro Entry

Q13492

UniProtKB/Swiss-Prot:

PICAL_HUMAN :
  • Belongs to the PICALM/SNAP91 family.
Family:
  • Belongs to the PICALM/SNAP91 family.
genes like me logo Genes that share domains with PICALM: view

No data available for Gene Families for PICALM Gene

Function for PICALM Gene

Molecular function for PICALM Gene

UniProtKB/Swiss-Prot Function:
Assembly protein recruiting clathrin and adapter protein complex 2 (AP2) to cell membranes at sites of coated-pit formation and clathrin-vesicle assembly. May be required to determine the amount of membrane to be recycled, possibly by regulating the size of the clathrin cage. Involved in AP2-dependent clathrin-mediated endocytosis at the neuromuscular junction.

Gene Ontology (GO) - Molecular Function for PICALM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16491119
GO:0005543 phospholipid binding IEA --
GO:0005545 1-phosphatidylinositol binding ISS,IEA --
GO:0030276 clathrin binding IEA,ISS --
GO:0032050 clathrin heavy chain binding IDA 10436022
genes like me logo Genes that share ontologies with PICALM: view
genes like me logo Genes that share phenotypes with PICALM: view

Animal Models for PICALM Gene

MGI Knock Outs for PICALM:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PICALM Gene

Localization for PICALM Gene

Subcellular locations from UniProtKB/Swiss-Prot for PICALM Gene

Membrane, clathrin-coated pit. Golgi apparatus. Cytoplasmic vesicle, clathrin-coated vesicle. Nucleus. Note=Colocalized with clathrin in the Golgi area (PubMed:10436022). Interaction with FAM64A may target PICALM to the nucleus in some cells (PubMed:16491119). {ECO:0000269 PubMed:10436022, ECO:0000269 PubMed:16491119}.

Subcellular locations from

COMPARTMENTS
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 PICALM gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 4
golgi apparatus 3
mitochondrion 1
endosome 1

Gene Ontology (GO) - Cellular Components for PICALM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IDA 16491119
GO:0005794 Golgi apparatus IEA --
GO:0005829 cytosol TAS --
GO:0005905 clathrin-coated pit ISS --
genes like me logo Genes that share ontologies with PICALM: view

Pathways & Interactions for PICALM Gene

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

SIGNOR curated interactions for PICALM Gene

Activates:
Is inactivated by:

Gene Ontology (GO) - Biological Process for PICALM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006461 protein complex assembly TAS 8643484
GO:0006897 endocytosis IEA --
GO:0006898 receptor-mediated endocytosis ISS --
GO:0007409 axonogenesis IEA --
GO:0008283 cell proliferation IMP 22952941
genes like me logo Genes that share ontologies with PICALM: view

Drugs & Compounds for PICALM Gene

(3) Drugs for PICALM Gene - From: PharmGKB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium channel blockers Pharma 1985

(1) Additional Compounds for PICALM Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with PICALM: view

Transcripts for PICALM Gene

Unigene Clusters for PICALM Gene

Phosphatidylinositol binding clathrin assembly protein:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

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

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^ 20 ^
SP1: - - -
SP2: - - - -
SP3: - - - -
SP4: - - -
SP5: -
SP6:
SP7: - - -
SP8: - - -
SP9:
SP10:
SP11: -

ExUns: 21 ^ 22a · 22b · 22c · 22d · 22e · 22f
SP1: -
SP2: -
SP3: -
SP4: -
SP5:
SP6:
SP7: -
SP8:
SP9: -
SP10:
SP11:

Relevant External Links for PICALM Gene

GeneLoc Exon Structure for
PICALM
ECgene alternative splicing isoforms for
PICALM

Expression for PICALM Gene

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

Protein differential expression in normal tissues from HIPED for PICALM Gene

This gene is overexpressed in Bone marrow stromal cell (12.8), Brain (6.3), and Spleen (6.2).

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



Protein tissue co-expression partners for PICALM Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PICALM Gene:

PICALM

SOURCE GeneReport for Unigene cluster for PICALM Gene:

Hs.163893

mRNA Expression by UniProt/SwissProt for PICALM Gene:

Q13492-PICAL_HUMAN
Tissue specificity: Expressed in all tissues examined.

Evidence on tissue expression from TISSUES for PICALM Gene

  • Nervous system(4.9)
  • Liver(4.6)
  • Bone marrow(4.3)
  • Kidney(2.9)
  • Blood(2.7)
  • Thyroid gland(2.5)
  • Gall bladder(2)
  • Intestine(2)
  • Spleen(2)

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

Germ Layers:
  • mesoderm
Systems:
  • immune
  • lymphatic
Organs:
General:
  • blood
  • bone marrow
  • white blood cell
genes like me logo Genes that share expression patterns with PICALM: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PICALM Gene

Orthologs for PICALM Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PICALM Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PICALM 34 35
  • 99.64 (n)
dog
(Canis familiaris)
Mammalia PICALM 34 35
  • 96.38 (n)
cow
(Bos Taurus)
Mammalia PICALM 34 35
  • 95.92 (n)
mouse
(Mus musculus)
Mammalia Picalm 34 16 35
  • 94.37 (n)
rat
(Rattus norvegicus)
Mammalia Picalm 34
  • 94.37 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PICALM 35
  • 89 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PICALM 35
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves PICALM 34 35
  • 87.24 (n)
lizard
(Anolis carolinensis)
Reptilia PICALM 35
  • 84 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia picalm.2 34
  • 79.08 (n)
Str.7553 34
zebrafish
(Danio rerio)
Actinopterygii picalmb 35
  • 84 (a)
OneToMany
picalma 34 35
  • 74.11 (n)
zgc55615 34
fruit fly
(Drosophila melanogaster)
Insecta lap 36 34 35
  • 54.26 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010087 34
  • 52.21 (n)
worm
(Caenorhabditis elegans)
Secernentea unc-11 36 35
  • 58 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YAP1802 35
  • 22 (a)
ManyToMany
YAP1801 35
  • 20 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 48 (a)
OneToMany
Species where no ortholog for PICALM 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)
  • 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)
  • 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 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 PICALM Gene

ENSEMBL:
Gene Tree for PICALM (if available)
TreeFam:
Gene Tree for PICALM (if available)

Paralogs for PICALM Gene

Paralogs for PICALM Gene

genes like me logo Genes that share paralogs with PICALM: view

Variants for PICALM Gene

Sequence variations from dbSNP and Humsavar for PICALM Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1000001718 -- 85,971,328(+) GAAAA(A/G)GTATT intron-variant
rs1000004003 -- 86,067,250(+) ATTAT(C/G)TTTCA intron-variant
rs1000024741 -- 86,018,284(+) ATATC(A/T)CCATT intron-variant
rs1000054863 -- 86,011,206(+) AAAAG(C/T)AGGTA intron-variant
rs1000077709 -- 85,978,978(+) TCAGT(C/G)AGGTG intron-variant

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

Variant ID Type Subtype PubMed ID
dgv1247n100 CNV gain 25217958
dgv164n27 CNV loss 19166990
dgv2041n54 CNV loss 21841781
esv3627080 CNV gain 21293372
esv3892049 CNV loss 25118596
nsv1035489 CNV gain 25217958
nsv1053808 CNV gain 25217958
nsv469975 CNV gain 18288195
nsv951049 CNV duplication 24416366

Variation tolerance for PICALM Gene

Residual Variation Intolerance Score: 18.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.17; 23.56% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PICALM Gene

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

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

Disorders for PICALM Gene

MalaCards: The human disease database

(10) MalaCards diseases for PICALM Gene - From: OMIM, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
leukemia, acute myeloid
  • leukemia, acute myeloid, somatic
precursor t-cell acute lymphoblastic leukemia
  • t-all
myeloid leukemia
  • leukemia myelogenous
subvalvular aortic stenosis
  • aortic stenosis, subvalvular
leukemia, acute lymphoblastic
  • leukemia, t-cell acute lymphocytic, somatic
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

PICAL_HUMAN
  • Note=A chromosomal aberration involving PICALM is found in diffuse histiocytic lymphomas. Translocation t(10;11)(p13;q14) with MLLT10. {ECO:0000269 PubMed:8643484}.

Relevant External Links for PICALM

Genetic Association Database (GAD)
PICALM
Human Genome Epidemiology (HuGE) Navigator
PICALM
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PICALM
genes like me logo Genes that share disorders with PICALM: view

No data available for Genatlas for PICALM Gene

Publications for PICALM Gene

  1. The t(10;11)(p13;q14) in the U937 cell line results in the fusion of the AF10 gene and CALM, encoding a new member of the AP-3 clathrin assembly protein family. (PMID: 8643484) Dreyling M.H. … Bohlander S.K. (Proc. Natl. Acad. Sci. U.S.A. 1996) 2 3 4 22 64
  2. Alternative splicing in wild-type AF10 and CALM cDNAs and in AF10- CALM and CALM-AF10 fusion cDNAs produced by the t(10;11)(p13-14;q14- q21) suggests a potential role for truncated AF10 polypeptides. (PMID: 9737689) Silliman C.C. … Hunger S.P. (Leukemia 1998) 3 4 22 64
  3. The membrane-spanning 4-domains, subfamily A (MS4A) gene cluster contains a common variant associated with Alzheimer's disease. (PMID: 21627779) AntA_nez C. … Ruiz A. (Genome Med 2011) 3 46 64
  4. The role of clusterin, complement receptor 1, and phosphatidylinositol binding clathrin assembly protein in Alzheimer disease risk and cerebrospinal fluid biomarker levels. (PMID: 21300948) Schjeide B.M. … Bertram L. (Arch. Gen. Psychiatry 2011) 3 46 64
  5. Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. (PMID: 21460841) Naj A.C. … Schellenberg G.D. (Nat. Genet. 2011) 3 46 64

Products for PICALM Gene

Sources for PICALM Gene

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