CLTB clathrin light chain B [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLTBprovided by HGNC
Official Full Name: clathrin light chain Bprovided by HGNC
Primary source: HGNC:HGNC:2091
See related: Ensembl:ENSG00000175416 MIM:118970; AllianceGenome:HGNC:2091
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: LCB
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. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in esophagus (RPKM 44.6), skin (RPKM 37.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q35.2

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (176392455..176416569, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (176936813..176960926, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (175819456..175843570, complement)

Chromosome 5 - NC_000005.10 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
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?

Role of Clathrin Light Chains in Regulating Invadopodia Formation.
Title: Role of Clathrin Light Chains in Regulating Invadopodia Formation.
CLCb/Dyn1-dependent adaptive clathrin-mediated endocytosis selectively altered EGF receptor trafficking.
Title: Crosstalk between CLCb/Dyn1-Mediated Adaptive Clathrin-Mediated Endocytosis and Epidermal Growth Factor Receptor Signaling Increases Metastasis.
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.
Supporting a physiological role for CLC in migration, the CLCb isoform of CLC is upregulated in migratory human trophoblast cells during uterine invasion.
Title: Clathrin light chains are required for the gyrating-clathrin recycling pathway and thereby promote cell migration.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
This protein has been found differentially expressed in the temporal lobe from patients with schizophrenia.
Title: Alterations in oligodendrocyte proteins, calcium homeostasis and new potential markers in schizophrenia anterior temporal lobe are revealed by shotgun proteome analysis.
Data suggest that clathrin heavy chains bound to light chains (LC) a and b contribute to pit formation, but the affinity of LCa-free HC in pits is reduced, and the Ca(2+)- and ATP-mediated control of clathrin function is lost.
Title: Differential control of clathrin subunit dynamics measured with EW-FRAP microscopy.

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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

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

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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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	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	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	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

G54012 (e-PCR)
- UniSTS:109394

RH98811 (e-PCR)
- UniSTS:84078

RH69093 (e-PCR)
- UniSTS:58244

WI-7674 (e-PCR)
- UniSTS:58080

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables clathrin heavy chain binding	IBA Inferred from Biological aspect of Ancestor more info
enables peptide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural molecule activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
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
located_in ciliary membrane	IEA Inferred from Electronic Annotation more info
part_of clathrin coat	ISS Inferred from Sequence or Structural Similarity more info
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 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 cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay 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
is_active_in synaptic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in trans-Golgi network	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: clathrin light chain B

Names: clathrin, light chain (Lcb); clathrin, light polypeptide (Lcb)

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_001364126.3 → NP_001351055.1 clathrin light chain B isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 2. The resulting isoform (c) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform b.

Source sequence(s)

AC138956

Conserved Domains (1) summary

pfam01086
Location:27 → 140

Clathrin_lg_ch; Clathrin light chain
NM_001364127.2 → NP_001351056.1 clathrin light chain B isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 3' UTR and coding sequence compared to variant 2. The resulting isoform (d) has a shorter and distinct C-terminus compared to isoform b.

Source sequence(s)

AC138956

Consensus CDS

CCDS87350.1

UniProtKB/TrEMBL

B4DTF9

Related

ENSP00000422978.1, ENST00000510734.5

Conserved Domains (1) summary

pfam01086
Location:1 → 63

Clathrin_lg_ch; Clathrin light chain
NM_001834.5 → NP_001825.1 clathrin light chain B isoform a

See identical proteins and their annotated locations for NP_001825.1

Status: REVIEWED

Description

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

Source sequence(s)

AC138956

Consensus CDS

CCDS4402.1

Related

ENSP00000310812.4, ENST00000345807.7

Conserved Domains (1) summary

pfam01086
Location:1 → 207

Clathrin_lg_ch; Clathrin light chain
NM_007097.5 → NP_009028.1 clathrin light chain B isoform b

See identical proteins and their annotated locations for NP_009028.1

Status: REVIEWED

Description

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

Source sequence(s)

AC138956

Consensus CDS

CCDS4403.1

UniProtKB/Swiss-Prot

P09497, Q53Y37, Q6FHW1

Related

ENSP00000309415.4, ENST00000310418.9

Conserved Domains (1) summary

pfam01086
Location:1 → 225

Clathrin_lg_ch; Clathrin light chain

RNA

NR_045724.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) has an additional exon in the center region, which results in an early translation termination and a nonsense-mediated mRNA decay candidate, compared to variant 2. The transcript does not encode a functinal protein.

Source sequence(s)

AC138956
NR_157088.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC138956