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PICALM phosphatidylinositol binding clathrin assembly protein [ Homo sapiens (human) ]

Gene ID: 8301, updated on 22-May-2022

Summary

Official Symbol
PICALMprovided by HGNC
Official Full Name
phosphatidylinositol binding clathrin assembly proteinprovided by HGNC
Primary source
HGNC:HGNC:15514
See related
Ensembl:ENSG00000073921 MIM:603025; AllianceGenome:HGNC:15514
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
LAP; CALM; CLTH
Summary
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]
Expression
Ubiquitous expression in fat (RPKM 64.4), appendix (RPKM 52.9) and 25 other tissues See more
Orthologs
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Genomic context

See PICALM in Genome Data Viewer
Location:
11q14.2
Exon count:
23
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (85957175..86069860, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (85893875..86006599, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (85668218..85780902, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 83 Neighboring gene adenosylhomocysteinase pseudogene 6 Neighboring gene solute carrier family 25 member 1 pseudogene 1 Neighboring gene uncharacterized LOC124902730 Neighboring gene uncharacterized LOC124902731 Neighboring gene small nucleolar RNA U13

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease.
EBI GWAS Catalog
Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease.
EBI GWAS Catalog
Genome-wide association study of Alzheimer's disease.
EBI GWAS Catalog
Genome-wide association study of Tourette's syndrome.
EBI GWAS Catalog
Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease.
EBI GWAS Catalog
The membrane-spanning 4-domains, subfamily A (MS4A) gene cluster contains a common variant associated with Alzheimer's disease.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 1-phosphatidylinositol binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables 1-phosphatidylinositol binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables SNARE binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables SNARE binding IDA
Inferred from Direct Assay
more info
PubMed 
enables amyloid-beta binding IC
Inferred by Curator
more info
 
enables cadherin binding HDA PubMed 
enables clathrin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables clathrin heavy chain binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables clathrin heavy chain binding IDA
Inferred from Direct Assay
more info
PubMed 
enables low-density lipoprotein particle receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables phosphatidylinositol-4,5-bisphosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables phosphatidylinositol-4,5-bisphosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables small GTPase binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables tau protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in amyloid-beta clearance by transcytosis IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in amyloid-beta clearance by transcytosis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in axonogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in clathrin coat assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in clathrin-coated pit assembly IDA
Inferred from Direct Assay
more info
PubMed 
involved_in clathrin-dependent endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in clathrin-dependent endocytosis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in dendrite morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in endocytosis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in endosomal transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in hemopoiesis IEA
Inferred from Electronic Annotation
more info
 
involved_in iron ion homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in learning or memory ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in membrane bending IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of protein localization to cell surface IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of protein localization to plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of receptor-mediated endocytosis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of GTPase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of amyloid-beta formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of neuron death IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
involved_in protein-containing complex assembly TAS
Traceable Author Statement
more info
PubMed 
involved_in receptor internalization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in receptor-mediated endocytosis IDA
Inferred from Direct Assay
more info
PubMed 
NOT involved_in regulation of amyloid-beta formation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of clathrin-dependent endocytosis IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of endocytosis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of protein localization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of vesicle size IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in synaptic vesicle budding from presynaptic endocytic zone membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in synaptic vesicle maturation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in vesicle budding from membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in vesicle budding from membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in vesicle cargo loading IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in vesicle-mediated transport TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
 
located_in cell surface IDA
Inferred from Direct Assay
more info
PubMed 
part_of clathrin coat of coated pit IDA
Inferred from Direct Assay
more info
PubMed 
located_in clathrin-coated endocytic vesicle NAS
Non-traceable Author Statement
more info
PubMed 
is_active_in clathrin-coated pit IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in clathrin-coated pit IDA
Inferred from Direct Assay
more info
PubMed 
located_in clathrin-coated pit IMP
Inferred from Mutant Phenotype
more info
PubMed 
is_active_in clathrin-coated vesicle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in clathrin-coated vesicle IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in early endosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in endosome to plasma membrane transport vesicle IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in extrinsic component of presynaptic endocytic zone membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
located_in intrinsic component of membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
located_in membrane HDA PubMed 
located_in neurofibrillary tangle IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in neuronal cell body IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in postsynaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in presynaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
is_active_in synaptic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in vesicle ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
phosphatidylinositol-binding clathrin assembly protein
Names
clathrin assembly lymphoid myeloid leukemia protein

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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

  1. NG_028942.1 RefSeqGene

    Range
    5022..117706
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001008660.3NP_001008660.1  phosphatidylinositol-binding clathrin assembly protein isoform 2

    See identical proteins and their annotated locations for NP_001008660.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon, but has an additional downstream in-frame exon, in the coding region, as compared to variant 1. The encoded isoform 2 thus lacks an internal segment and also has an additional segment, as compared to isoform 1.
    Source sequence(s)
    AP000767
    Consensus CDS
    CCDS31653.1
    UniProtKB/Swiss-Prot
    Q13492
    UniProtKB/TrEMBL
    A0A024R5L7
    Related
    ENSP00000436958.1, ENST00000532317.5
    Conserved Domains (2) summary
    COG4223
    Location:268366
    COG4223; Uncharacterized conserved protein [Function unknown]
    pfam07651
    Location:24282
    ANTH; ANTH domain
  2. NM_001206946.2NP_001193875.1  phosphatidylinositol-binding clathrin assembly protein isoform 3

    See identical proteins and their annotated locations for NP_001193875.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an alternate splice site in the coding sequence, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AP000767
    Consensus CDS
    CCDS55784.1
    UniProtKB/Swiss-Prot
    Q13492
    Related
    ENSP00000433846.1, ENST00000526033.5
    Conserved Domains (2) summary
    pfam07651
    Location:19282
    ANTH; ANTH domain
    pfam08287
    Location:265344
    DASH_Spc19; Spc19
  3. NM_001206947.2NP_001193876.1  phosphatidylinositol-binding clathrin assembly protein isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an alternate 5' exon, resulting in a downstream AUG start codon, and lacks an in-frame exon in the coding region, compared to variant 1. The resulting isoform (4) has a shorter N-terminus and lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AK128786, AK300275, BC073961, CA415536, DC300074
    Consensus CDS
    CCDS55783.1
    UniProtKB/Swiss-Prot
    Q13492
    Related
    ENSP00000434884.1, ENST00000528398.5
    Conserved Domains (2) summary
    pfam07651
    Location:1231
    ANTH; ANTH domain
    pfam08287
    Location:214293
    DASH_Spc19; Spc19
  4. NM_007166.4NP_009097.2  phosphatidylinositol-binding clathrin assembly protein isoform 1

    See identical proteins and their annotated locations for NP_009097.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AP000767
    Consensus CDS
    CCDS8272.1
    UniProtKB/Swiss-Prot
    Q13492
    UniProtKB/TrEMBL
    A0A024R5P1
    Related
    ENSP00000377015.3, ENST00000393346.8
    Conserved Domains (2) summary
    pfam07651
    Location:19282
    ANTH; ANTH domain
    pfam08287
    Location:265344
    DASH_Spc19; Spc19

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    85957175..86069860 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427666.1XP_047283622.1  phosphatidylinositol-binding clathrin assembly protein isoform X24

  2. XM_047427660.1XP_047283616.1  phosphatidylinositol-binding clathrin assembly protein isoform X8

  3. XM_047427669.1XP_047283625.1  phosphatidylinositol-binding clathrin assembly protein isoform X27

  4. XM_047427667.1XP_047283623.1  phosphatidylinositol-binding clathrin assembly protein isoform X25

  5. XM_047427665.1XP_047283621.1  phosphatidylinositol-binding clathrin assembly protein isoform X22

  6. XM_017018388.3XP_016873877.1  phosphatidylinositol-binding clathrin assembly protein isoform X21

  7. XM_047427668.1XP_047283624.1  phosphatidylinositol-binding clathrin assembly protein isoform X26

  8. XM_017018387.3XP_016873876.1  phosphatidylinositol-binding clathrin assembly protein isoform X20

  9. XM_017018384.3XP_016873873.1  phosphatidylinositol-binding clathrin assembly protein isoform X15

    Conserved Domains (2) summary
    pfam07651
    Location:19282
    ANTH; ANTH domain
    pfam08287
    Location:265344
    DASH_Spc19; Spc19
  10. XM_005274336.4XP_005274393.1  phosphatidylinositol-binding clathrin assembly protein isoform X13

    Conserved Domains (2) summary
    pfam07651
    Location:19282
    ANTH; ANTH domain
    pfam08287
    Location:265344
    DASH_Spc19; Spc19
  11. XM_005274340.4XP_005274397.1  phosphatidylinositol-binding clathrin assembly protein isoform X23

    Conserved Domains (2) summary
    pfam07651
    Location:19282
    ANTH; ANTH domain
    pfam08287
    Location:265344
    DASH_Spc19; Spc19
  12. XM_017018386.3XP_016873875.1  phosphatidylinositol-binding clathrin assembly protein isoform X19

  13. XM_017018383.3XP_016873872.1  phosphatidylinositol-binding clathrin assembly protein isoform X14

    Conserved Domains (2) summary
    pfam07651
    Location:19282
    ANTH; ANTH domain
    pfam08287
    Location:265344
    DASH_Spc19; Spc19
  14. XM_047427662.1XP_047283618.1  phosphatidylinositol-binding clathrin assembly protein isoform X12

  15. XM_047427659.1XP_047283615.1  phosphatidylinositol-binding clathrin assembly protein isoform X7

  16. XM_017018381.3XP_016873870.1  phosphatidylinositol-binding clathrin assembly protein isoform X5

  17. XM_047427663.1XP_047283619.1  phosphatidylinositol-binding clathrin assembly protein isoform X18

  18. XM_047427661.1XP_047283617.1  phosphatidylinositol-binding clathrin assembly protein isoform X11

  19. XM_024448700.2XP_024304468.1  phosphatidylinositol-binding clathrin assembly protein isoform X4

    Conserved Domains (2) summary
    COG4223
    Location:268366
    COG4223; Uncharacterized conserved protein [Function unknown]
    pfam07651
    Location:24282
    ANTH; ANTH domain
  20. XM_017018385.3XP_016873874.1  phosphatidylinositol-binding clathrin assembly protein isoform X17

  21. XM_005274334.4XP_005274391.1  phosphatidylinositol-binding clathrin assembly protein isoform X10

    Conserved Domains (2) summary
    pfam07651
    Location:19282
    ANTH; ANTH domain
    pfam08287
    Location:265344
    DASH_Spc19; Spc19
  22. XM_005274329.5XP_005274386.1  phosphatidylinositol-binding clathrin assembly protein isoform X6

    Conserved Domains (1) summary
    cd16985
    Location:22138
    ANTH_N_AP180; ANTH (AP180 N-Terminal Homology) domain, N-terminal region, of adaptor protein 180 (AP180) subfamily
  23. XM_005274328.4XP_005274385.1  phosphatidylinositol-binding clathrin assembly protein isoform X3

    Conserved Domains (2) summary
    pfam07651
    Location:19282
    ANTH; ANTH domain
    pfam08287
    Location:265344
    DASH_Spc19; Spc19
  24. XM_005274337.4XP_005274394.1  phosphatidylinositol-binding clathrin assembly protein isoform X16

    Conserved Domains (2) summary
    pfam07651
    Location:19282
    ANTH; ANTH domain
    pfam08287
    Location:265344
    DASH_Spc19; Spc19
  25. XM_005274331.4XP_005274388.1  phosphatidylinositol-binding clathrin assembly protein isoform X9

    See identical proteins and their annotated locations for XP_005274388.1

    UniProtKB/Swiss-Prot
    Q13492
    Related
    ENSP00000348718.5, ENST00000356360.9
    Conserved Domains (2) summary
    pfam07651
    Location:19282
    ANTH; ANTH domain
    pfam08287
    Location:265344
    DASH_Spc19; Spc19
  26. XM_005274326.4XP_005274383.1  phosphatidylinositol-binding clathrin assembly protein isoform X2

    See identical proteins and their annotated locations for XP_005274383.1

    Conserved Domains (2) summary
    pfam07651
    Location:19282
    ANTH; ANTH domain
    pfam08287
    Location:265344
    DASH_Spc19; Spc19
  27. XM_005274322.4XP_005274379.1  phosphatidylinositol-binding clathrin assembly protein isoform X1

    Conserved Domains (3) summary
    pfam07651
    Location:19282
    ANTH; ANTH domain
    pfam08287
    Location:265344
    DASH_Spc19; Spc19
    pfam11029
    Location:578657
    DAZAP2; DAZ associated protein 2 (DAZAP2)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    85893875..86006599 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)