CLTA clathrin light chain A [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLTAprovided by HGNC
Official Full Name: clathrin light chain Aprovided by HGNC
Primary source: HGNC:HGNC:2090
See related: Ensembl:ENSG00000122705 MIM:118960; AllianceGenome:HGNC:2090
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: LCA
Summary: Clathrin is a large, soluble protein composed of heavy and light chains. It functions as the main structural component of the lattice-type cytoplasmic face of coated pits and vesicles which entrap specific macromolecules during receptor-mediated endocytosis. This gene encodes one of two clathrin light chain proteins which are believed to function as regulatory elements. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 8 and 12. [provided by RefSeq, May 2010]
Expression: Ubiquitous expression in colon (RPKM 66.3), kidney (RPKM 59.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9p13.3

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (36190874..36212059)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (36212880..36234065)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (36190918..36212056)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clathrin light chain A facilitates small extracellular vesicle uptake to promote hepatocellular carcinoma progression.
Title: Clathrin light chain A facilitates small extracellular vesicle uptake to promote hepatocellular carcinoma progression.
Role of Clathrin Light Chains in Regulating Invadopodia Formation.
Title: Role of Clathrin Light Chains in Regulating Invadopodia Formation.
GRK2-mediated receptor phosphorylation and Mdm2-mediated beta-arrestin2 ubiquitination drive clathrin-mediated endocytosis of G protein-coupled receptors.
Title: GRK2-mediated receptor phosphorylation and Mdm2-mediated β-arrestin2 ubiquitination drive clathrin-mediated endocytosis of G protein-coupled receptors.
There is coordinated action of myosin VI and CLCa at the apical surface where these proteins are essential for fission of clathrin-coated pits. Myosin VI and Huntingtin-interacting protein 1-related protein (Hip1R) are mutually exclusive interactors with CLCa, and suggest a model for the sequential function of myosin VI and Hip1R in actin-mediated clathrin-coated vesicle budding.
Title: Clathrin light chain A drives selective myosin VI recruitment to clathrin-coated pits under membrane tension.
Data indicate that clathrin-mediated endocytosis of proto-oncogene protein erbB-3 (ErbB3) is depending on epsin-1.
Title: Interaction with epsin 1 regulates the constitutive clathrin-dependent internalization of ErbB3.
Upon receptor activation, prostate alpha1A-adrenoceptors bind clathrin LCA.
Title: Noradrenaline induces binding of Clathrin light chain A to α1-adrenoceptors in the human prostate.
IGF1R internalization and co-localization with clathrin and CAV1 upon ligand binding, as well as the status of the IGF1R pathway, cellular proliferation, and the apoptosis of interfered and inhibited Ewing's sarcoma, were analyzed.
Title: IGF1R signaling in Ewing sarcoma is shaped by clathrin-/caveolin-dependent endocytosis.
upon ligand activation, CysLT(1)R is tyrosine-phosphorylated and released from heterodimers with CysLT(2)R and, subsequently, internalizes from the plasma membrane to the nuclear membrane in a clathrin-, arrestin-3-, and Rab-5-dependent manner
Title: Ligand-induced tyrosine phosphorylation of cysteinyl leukotriene receptor 1 triggers internalization and signaling in intestinal epithelial cells.
Data show that MAD2B interacts with CLTA during the G2/M phase of the cell cycle and that depletion of MAD2B leads to a marked increase in the percentage of misaligned chromosomes and a redistribution of CLTA during mitosis.
Title: The mitotic arrest deficient protein MAD2B interacts with the clathrin light chain A during mitosis.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of clathrin, light chain A (CLTA) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 matrix and gp120 co-localize with clathrin in primary T lymphocytes	PubMed
Gag-Pol	gag-pol	HIV-1 particles incorporate the clathrin heavy chain together with associated light chains through HIV-1 Gag-Pol in an IN-dependent manner	PubMed
Nef	nef	The leucine-based motif of Nef is required for targeting into clathrin-associated AP complexes and the Nef-mediated alterations of trafficking of CD4 receptor	PubMed
	nef	HIV-1 Nef induces the formation of clathrin-coated pits in the presence of CD4 in human lymphocytes by interacting with components of the clathrin-coated surface domain	PubMed
	nef	Knocking down either AP-1 gamma, AP-1 mu1, or clathrin strongly inhibits Nef-induced downregulation of HLA-A2	PubMed
Pol	gag-pol	Clathrin stabilizes HIV-1 Pol proteins in HIV-1 infected cells	PubMed
Vpr	vpr	HIV-1 Vpr C-terminus (residues 52-96) entry into cells is mediated through clathrin- and caveolae/raft-dependent endocytosis	PubMed
integrase	gag-pol	Deletion of the HIV-1 IN C-terminal domain and the IN N184L/F185K mutation abolish clathrin incorporation into virions	PubMed
	gag-pol	HIV-1 particles incorporate the clathrin heavy chain together with associated light chains through HIV-1 Gag-Pol in an IN-dependent manner	PubMed
matrix	gag	HIV-1 matrix and gp120 co-localize with clathrin in primary T lymphocytes	PubMed
reverse transcriptase	gag-pol	Mutations in HIV-1 RT, including L234A, that inhibit RT dimerization abolish clathrin incorporation into virions	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH79677 (e-PCR)
- UniSTS:84491

G43533 (e-PCR)
- UniSTS:94990

RH74929 (e-PCR)
- UniSTS:86681

RH67858 (e-PCR)
- UniSTS:59319

AV026556 (e-PCR)
- UniSTS:165318

STS-M20471 (e-PCR)
- UniSTS:42239

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase binding	IEA Inferred from Electronic Annotation more info
enables clathrin heavy chain binding	IBA Inferred from Biological aspect of Ancestor more info
enables clathrin heavy chain binding	IPI Inferred from Physical Interaction more info	PubMed
enables molecular_function	ND No biological Data available more info
enables peptide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
enables structural molecule activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in clathrin coat assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in clathrin-dependent endocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
involved_in synaptic vesicle endocytosis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of clathrin coat	IMP Inferred from Mutant Phenotype more info	PubMed
part_of clathrin coat	NAS Non-traceable Author Statement more info	PubMed
part_of clathrin coat of coated pit	IEA Inferred from Electronic Annotation more info
part_of clathrin coat of trans-Golgi network vesicle	IEA Inferred from Electronic Annotation more info
part_of clathrin complex	IDA Inferred from Direct Assay more info	PubMed
part_of clathrin vesicle coat	IBA Inferred from Biological aspect of Ancestor more info
located_in clathrin-coated endocytic vesicle	NAS Non-traceable Author Statement more info	PubMed
located_in cytoplasmic vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	TAS Traceable Author Statement more info
located_in endolysosome membrane	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
is_active_in postsynaptic endocytic zone cytoplasmic component	IBA Inferred from Biological aspect of Ancestor more info
located_in presynaptic endocytic zone membrane	IEA Inferred from Electronic Annotation more info
located_in spindle	IEA Inferred from Electronic Annotation more info
is_active_in synaptic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in trans-Golgi network membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: clathrin light chain A

Names: clathrin, light polypeptide (Lca)

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

NM_001076677.3 → NP_001070145.1 clathrin light chain A isoform c

See identical proteins and their annotated locations for NP_001070145.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an in-frame exon, compared to variant 2, resulting in a shorter protein (isoform c).

Source sequence(s)

CA306784, DQ270158, DT220470

Consensus CDS

CCDS43802.1

UniProtKB/Swiss-Prot

P09496

Related

ENSP00000379848.2, ENST00000396603.6

Conserved Domains (1) summary

pfam01086
Location:20 → 231

Clathrin_lg_ch; Clathrin light chain
NM_001184760.2 → NP_001171689.1 clathrin light chain A isoform d

See identical proteins and their annotated locations for NP_001171689.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate in-frame exon, compared to variant 2, resulting in a shorter protein (isoform d), compared to isoform b.

Source sequence(s)

AK295692, CA306784, DT220470

Consensus CDS

CCDS55306.1

UniProtKB/Swiss-Prot

P09496

Related

ENSP00000419746.1, ENST00000470744.5

Conserved Domains (1) summary

pfam01086
Location:20 → 225

Clathrin_lg_ch; Clathrin light chain
NM_001184761.2 → NP_001171690.1 clathrin light chain A isoform e

See identical proteins and their annotated locations for NP_001171690.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks two alternate in-frame exons and uses an alternate splice site in the 3' terminal exon that causes a translational frameshift compared to variant 2. These differences result in a shorter protein (isoform e), compared to isoform b.

Source sequence(s)

BM423666, CA306784, DT220470

Conserved Domains (1) summary

pfam01086
Location:22 → 161

Clathrin_lg_ch; Clathrin light chain
NM_001184762.2 → NP_001171691.1 clathrin light chain A isoform f

See identical proteins and their annotated locations for NP_001171691.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks four alternate in-frame exons, compared to variant 2, resulting in a shorter protein (isoform f), compared to isoform b.

Source sequence(s)

BI090227, CA306784, DT220470

Consensus CDS

CCDS55307.1

UniProtKB/Swiss-Prot

P09496

Related

ENSP00000437508.1, ENST00000540080.5

Conserved Domains (1) summary

pfam01086
Location:20 → 161

Clathrin_lg_ch; Clathrin light chain
NM_001311203.2 → NP_001298132.1 clathrin light chain A isoform g

Status: REVIEWED

Description

Transcript Variant: This variant (7) uses an alternate splice junction in the first exon and lacks an alternate in-frame segment compared to variant 2. The resulting isoform (g) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform b.

Source sequence(s)

CA306784, CN300759, DT220470

Conserved Domains (1) summary

pfam01086
Location:9 → 135

Clathrin_lg_ch; Clathrin light chain
NM_001311204.2 → NP_001298133.1 clathrin light chain A isoform h

Status: REVIEWED

Description

Transcript Variant: This variant (8) lacks an alternate in-frame segment compared to variant 2. The resulting isoform (h) has the same N- and C-termini but is shorter compared to isoform b.

Source sequence(s)

BI600540, CA306784, DT220470

Consensus CDS

CCDS83364.1

UniProtKB/TrEMBL

C9J8P9

Related

ENSP00000417698.1, ENST00000466396.6

Conserved Domains (1) summary

pfam01086
Location:20 → 191

Clathrin_lg_ch; Clathrin light chain
NM_001311205.2 → NP_001298134.1 clathrin light chain A isoform i

Status: REVIEWED

Description

Transcript Variant: This variant (9) lacks an alternate in-frame segment and an alternate in-frame exon compared to variant 2. The resulting isoform (i) has the same N- and C-termini but is shorter compared to isoform b.

Source sequence(s)

CA306784, DN991152, DT220470

Conserved Domains (1) summary

pfam01086
Location:20 → 173

Clathrin_lg_ch; Clathrin light chain
NM_001311206.2 → NP_001298135.1 clathrin light chain A isoform j

Status: REVIEWED

Description

Transcript Variant: This variant (10) lacks an alternate exon and an alternate in-frame segment compared to variant 2. The resulting isoform (j) is shorter at the N-terminus and lacks an internal segment compared to isoform b.

Source sequence(s)

BF797444, CA306784, DT220470

Conserved Domains (1) summary

pfam01086
Location:2 → 96

Clathrin_lg_ch; Clathrin light chain
NM_001833.4 → NP_001824.1 clathrin light chain A isoform a

See identical proteins and their annotated locations for NP_001824.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) lacks alternate in-frame exons compared to variant 2, resulting in a shorter protein (isoform a), compared to isoform b.

Source sequence(s)

BC009201, DT220470

Consensus CDS

CCDS6600.1

UniProtKB/Swiss-Prot

P09496

Related

ENSP00000242284.6, ENST00000345519.10

Conserved Domains (1) summary

pfam01086
Location:20 → 213

Clathrin_lg_ch; Clathrin light chain
NM_007096.4 → NP_009027.1 clathrin light chain A isoform b

See identical proteins and their annotated locations for NP_009027.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) represents the longest transcript variant and encodes the longest isoform (b).

Source sequence(s)

CA306784, DT220470, M20471

Consensus CDS

CCDS6601.1

UniProtKB/Swiss-Prot

A8K4W3, B4DIN1, F5H6N3, P09496, Q2XPN5, Q53XZ1

Related

ENSP00000242285.6, ENST00000242285.11

Conserved Domains (1) summary

pfam01086
Location:20 → 243

Clathrin_lg_ch; Clathrin light chain

RNA

NR_132349.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (11) lacks three alternate exons compared to variant 2. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK291078, CA306784, CA441539, DT220470