PICALM phosphatidylinositol binding clathrin assembly protein [Homo sapiens] - Gene

Help top of page

Summary

Official Symbol: PICALMprovided by HGNC
Official Full Name: phosphatidylinositol binding clathrin assembly proteinprovided by HGNC
Primary source: HGNC:15514
See related: Ensembl:ENSG00000073921; HPRD:04320; MIM:603025; Vega:OTTHUMG00000166981
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]

Help top of page

Genomic context

Location :: 11q14

Sequence :: Chromosome: 11; NC_000011.9 (85668214..85780923, complement)

See PICALM in Epigenomics, MapViewer

Chromosome 11 - NC_000011.9 Genomic Context describing neighboring genes

Help top of page

Genomic regions, transcripts, and products

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Help top of page

Bibliography

GeneRIFs: Gene References Into Functions What's a GeneRIF?

variants in BIN1, CLU, CR1 or PICALM are associated with changes in the CSF levels of biomarkers
Title: Fine mapping of genetic variants in BIN1, CLU, CR1 and PICALM for association with cerebrospinal fluid biomarkers for Alzheimer's disease.
In leukemia cells, full-length CALM-AF10 localized to the nucleus with no consistent effect on growth factor endocyctosis, and suppressed histone H3 lysine 79 methylation regardless of the presence of clathrin
Title: The clathrin-binding domain of CALM-AF10 alters the phenotype of myeloid neoplasms in mice.
findings showed evidence of CR1, CLU, and PICALM and late-onset Alzheimer's disease (LOAD) susceptibility in an independent southern Chinese population
Title: Polymorphisms of CR1, CLU and PICALM confer susceptibility of Alzheimer's disease in a southern Chinese population.
AP-2 and epsin-1 are both required to promote efficient internalization of activated PAR1 and recognize discrete receptor sorting signals
Title: Adaptor protein complex-2 (AP-2) and epsin-1 mediate protease-activated receptor-1 internalization via phosphorylation- and ubiquitination-dependent sorting signals.
relationship of Parkinson's disease with SNPs of CLU, CR1 and PICALM
Title: An exploratory study on CLU, CR1 and PICALM and Parkinson disease.
This study suggested that the PICALM rs3851179 showed no statistically significant difference between LOAD cases and controls.
Title: Implication of a genetic variant at PICALM in Alzheimer’s disease patients and centenarians.
we confirmed that PICALM is a genetic determinants of Alzheimer disease.
Title: Evidence of the association of BIN1 and PICALM with the AD risk in contrasting European populations.
Data show that CALM influences the cell surface level of the AMPA receptor subunit GluR2.
Title: CALM, a clathrin assembly protein, influences cell surface GluR2 abundance.
In this review, PICALM is a major Alzheimer's disease susceptibility gene indirectly implicated in the herpes simplex virus life cycle; PICALM binds to a protein used by the virus for nuclear egress.
Title: APP, APOE, complement receptor 1, clusterin and PICALM and their involvement in the herpes simplex life cycle.
picalm polymorphisms were associated with late-onset Alzheimer disease in an independent cohort from the National Institute on Aging Late-Onset Alzheimer's Disease Family Study
Title: Identification of novel loci for Alzheimer disease and replication of CLU, PICALM, and BIN1 in Caribbean Hispanic individuals.

Submit: New GeneRIF Correction See all (35)

Help top of page

Phenotypes

Review eQTL and phenotype association data in this region using PheGenI

Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease.

Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease.

Leukemia, acute T-cell lymphoblastic

MIM: 603025

The membrane-spanning 4-domains, subfamily A (MS4A) gene cluster contains a common variant associated with Alzheimer's disease.

Help top of page

Products	Interactant	Other Gene	Source	Pubs	Description
Q13492	O95782	AP2A1	HPRD	PubMed
Q13492	P42574	CASP3	HPRD	PubMed
Q13492	Q14790	CASP8	HPRD	PubMed
Q13492	Q00610	CLTC	HPRD	PubMed
Q13492	P53675	CLTCL1	HPRD	PubMed
Q13492	P35638	DDIT3	HPRD	PubMed
Q13492	Q9NZN4	EHD2	HPRD	PubMed
Q13492	P19174	PLCG1	HPRD	PubMed
BioGRID:113902	BioGRID:107623	CLTC	BioGRID	PubMed	Affinity Capture-Western; Reconstituted Complex
BioGRID:113902	BioGRID:108016	DDIT3	BioGRID	PubMed	Affinity Capture-Western
BioGRID:113902	BioGRID:111351	PLCG1	BioGRID	PubMed	Reconstituted Complex
BioGRID:113902	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS

Function	Evidence Code	Pubs
1-phosphatidylinositol binding	ISS Inferred from Sequence or Structural Similarity more info
clathrin binding	IDA Inferred from Direct Assay more info	PubMed
clathrin heavy chain binding	IDA Inferred from Direct Assay more info	PubMed
phospholipid binding	IEA Inferred from Electronic Annotation more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
axonogenesis	IEA Inferred from Electronic Annotation more info
clathrin coat assembly	IMP Inferred from Mutant Phenotype more info	PubMed
dendrite morphogenesis	IEA Inferred from Electronic Annotation more info
endosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
hemopoiesis	IEA Inferred from Electronic Annotation more info
negative regulation of receptor-mediated endocytosis	IDA Inferred from Direct Assay more info	PubMed
positive regulation of transcription, DNA-dependent	IDA Inferred from Direct Assay more info	PubMed
protein complex assembly	TAS Traceable Author Statement more info	PubMed
receptor internalization	IMP Inferred from Mutant Phenotype more info	PubMed
receptor-mediated endocytosis	IDA Inferred from Direct Assay more info	PubMed
regulation of endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
regulation of protein localization	IDA Inferred from Direct Assay more info	PubMed
vesicle-mediated transport	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
colocalizes_with AP-2 adaptor complex	IDA Inferred from Direct Assay more info	PubMed
Golgi apparatus	IEA Inferred from Electronic Annotation more info
colocalizes_with clathrin coat of coated pit	IDA Inferred from Direct Assay more info	PubMed
clathrin-coated vesicle	IEA Inferred from Electronic Annotation more info
coated pit	IDA Inferred from Direct Assay more info	PubMed
cytoplasmic vesicle	IEA Inferred from Electronic Annotation more info
intracellular	IEA Inferred from Electronic Annotation more info
intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info	PubMed
membrane	IEA Inferred from Electronic Annotation more info
nucleus	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with perinuclear region of cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
postsynaptic membrane	ISS Inferred from Sequence or Structural Similarity more info
presynaptic membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

Preferred Names: phosphatidylinositol-binding clathrin assembly protein

Names: phosphatidylinositol-binding clathrin assembly protein; clathrin assembly lymphoid myeloid leukemia protein

Help top of page

NCBI Reference Sequences (RefSeq)

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_028942.1 RefSeqGene

Range

5001..117710

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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)

AB210017, AK128786, BC048259, BC073961, CA415536

Consensus CDS

CCDS31653.1

UniProtKB/Swiss-Prot

Q13492

UniProtKB/TrEMBL

Q4LE54

Related

ENSP00000436958, OTTHUMP00000234630, ENST00000532317, OTTHUMT00000392220

Conserved Domains (1) summary

cd03564
Location:22 – 138
Blast Score: 390

ANTH_AP180_CALM; ANTH domain family; composed of adaptor protein 180 (AP180), clathrin assembly lymphoid myeloid leukemia protein (CALM) and similar proteins. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet ...
NM_001206946.1 → NP_001193875.1 phosphatidylinositol-binding clathrin assembly protein isoform 3

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)

AB210017, AK128786, BC048259, CA415536

Consensus CDS

CCDS55784.1

UniProtKB/TrEMBL

F8VPG7

UniProtKB/Swiss-Prot

Q13492

UniProtKB/TrEMBL

Q4LE54

Related

ENSP00000433846, OTTHUMP00000234631, ENST00000526033, OTTHUMT00000392221

Conserved Domains (1) summary

cd03564
Location:22 – 138
Blast Score: 389

ANTH_AP180_CALM; ANTH domain family; composed of adaptor protein 180 (AP180), clathrin assembly lymphoid myeloid leukemia protein (CALM) and similar proteins. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet ...
NM_001206947.1 → NP_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/TrEMBL

B4DTM3

UniProtKB/TrEMBL

E9PN05

UniProtKB/Swiss-Prot

Q13492

Related

ENSP00000434884, OTTHUMP00000234635, ENST00000528398, OTTHUMT00000392226

Conserved Domains (1) summary

cd03564
Location:1 – 87
Blast Score: 279

ANTH_AP180_CALM; ANTH domain family; composed of adaptor protein 180 (AP180), clathrin assembly lymphoid myeloid leukemia protein (CALM) and similar proteins. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet ...
NM_007166.3 → NP_009097.2 phosphatidylinositol-binding clathrin assembly protein isoform 1

Status: REVIEWED

Description

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

Source sequence(s)

AB210017, AK128786, BC048259, CA415536

Consensus CDS

CCDS8272.1

UniProtKB/Swiss-Prot

Q13492

UniProtKB/TrEMBL

Q4LE54

Related

ENSP00000377015, OTTHUMP00000234633, ENST00000393346, OTTHUMT00000392224

Conserved Domains (1) summary

cd03564
Location:22 – 138
Blast Score: 389

ANTH_AP180_CALM; ANTH domain family; composed of adaptor protein 180 (AP180), clathrin assembly lymphoid myeloid leukemia protein (CALM) and similar proteins. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet ...

RefSeqs of Annotated Genomes: Build 37.3

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

Reference GRCh37.p5 Primary Assembly

Genomic

NC_000011.9 Reference GRCh37.p5 Primary Assembly

Range

85668214..85780923, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000143.1 Alternate HuRef

Range

81965384..82078030, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Help top of page

Related Sequences

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	AP000767.4 (25374..136997)	None
genomic	CH471076.1	EAW75118.1
		EAW75119.1
		EAW75120.1
		EAW75121.1
		EAW75122.1
		EAW75123.1
		EAW75124.1
		EAW75125.1
		EAW75126.1
		EAW75127.1
		EAW75128.1
mRNA	AB210017.1	BAE06099.1
mRNA	AB451308.1	BAG70122.1
mRNA	AF060939.1	AAC16711.1
mRNA	AF060940.1	AAC16712.1
mRNA	AK128786.1	None
mRNA	AK291414.1	BAF84103.1
mRNA	AK297062.1	BAG59583.1
mRNA	AK300275.1	BAG62035.1
mRNA	AY326466.1	AAR99516.1
mRNA	BC048259.1	AAH48259.2
mRNA	BC064357.1	AAH64357.1
mRNA	BC073961.1	AAH73961.1
mRNA	CA415536.1	None
mRNA	CN310579.1	None
mRNA	DC300074.1	None
mRNA	EF051633.1	ABK54356.1
mRNA	U45976.1	AAB07762.1

Protein Accession	Links
Protein Accession	GenPept Link	UniProtKB Link
Q13492.2	GenPept	UniProtKB/Swiss-Prot:Q13492
Q4LE54	GenPept	UniProtKB/TrEMBL:Q4LE54
Q6EHZ1	GenPept	UniProtKB/TrEMBL:Q6EHZ1