CLTB

gene
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Also known as Lcb

Summary

CLTB (clathrin light chain B, HGNC:2091) is a protein-coding gene on chromosome 5q35.2, encoding Clathrin light chain B (P09497). Clathrin is the major protein of the polyhedral coat of coated pits and vesicles.

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.

Source: NCBI Gene 1212 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 14 total
  • Druggable target: yes
  • MANE Select transcript: NM_007097

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2091
Approved symbolCLTB
Nameclathrin light chain B
Location5q35.2
Locus typegene with protein product
StatusApproved
AliasesLcb
Ensembl geneENSG00000175416
Ensembl biotypeprotein_coding
OMIM118970
Entrez1212

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000310418, ENST00000345807, ENST00000502877, ENST00000507821, ENST00000508425, ENST00000509319, ENST00000510734, ENST00000942043

RefSeq mRNA: 4 — MANE Select: NM_007097 NM_001364126, NM_001364127, NM_001834, NM_007097

CCDS: CCDS4402, CCDS4403, CCDS87350

Canonical transcript exons

ENST00000310418 — 6 exons

ExonStartEnd
ENSE00001196736176396479176396532
ENSE00001262536176410257176410303
ENSE00001323510176416177176416539
ENSE00003468928176397930176398047
ENSE00003630550176397607176397718
ENSE00003897628176392501176392945

Expression profiles

Bgee: expression breadth ubiquitous, 298 present calls, max score 99.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 62.3355 / max 1053.0501, expressed in 1828 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
6500848.38241825
6501010.98921793
650071.3430836
650060.8905495
2038050.5666319
650030.100843
650020.057325
650010.00574

Top tissues by expression

301 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583499.46gold quality
skin of legUBERON:000151199.38gold quality
skin of abdomenUBERON:000141699.28gold quality
esophagus mucosaUBERON:000246999.22gold quality
gingival epitheliumUBERON:000194999.16gold quality
gingivaUBERON:000182899.08gold quality
apex of heartUBERON:000209899.08gold quality
zone of skinUBERON:000001498.83gold quality
mucosa of transverse colonUBERON:000499198.81gold quality
esophagusUBERON:000104398.80gold quality
tongue squamous epitheliumUBERON:000691998.78gold quality
gastrocnemiusUBERON:000138898.68gold quality
right atrium auricular regionUBERON:000663198.66gold quality
muscle of legUBERON:000138398.53gold quality
heart left ventricleUBERON:000208498.44gold quality
right frontal lobeUBERON:000281098.43gold quality
lower esophagusUBERON:001347398.38gold quality
lower esophagus muscularis layerUBERON:003583398.38gold quality
hindlimb stylopod muscleUBERON:000425298.36gold quality
esophagogastric junction muscularis propriaUBERON:003584198.29gold quality
cardiac ventricleUBERON:000208298.26gold quality
cardiac atriumUBERON:000208198.21gold quality
upper arm skinUBERON:000426398.20gold quality
tibial nerveUBERON:000132398.18gold quality
right hemisphere of cerebellumUBERON:001489098.17gold quality
cerebellar hemisphereUBERON:000224598.11gold quality
ileal mucosaUBERON:000033198.10gold quality
adenohypophysisUBERON:000219698.10gold quality
transverse colonUBERON:000115798.09gold quality
cerebellar cortexUBERON:000212998.09gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 9.

ExperimentMarker?Max mean expression
E-HCAD-1yes278.61
E-MTAB-7008yes274.82
E-MTAB-3929yes155.92
E-MTAB-7316yes44.71
E-ANND-3yes21.09
E-GEOD-137537yes15.75
E-MTAB-8410yes14.29
E-HCAD-13yes7.20
E-MTAB-6678yes6.13
E-GEOD-125970no16.92

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 6)

  • 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. (PMID:16138905)
  • This protein has been found differentially expressed in the temporal lobe from patients with schizophrenia. (PMID:19034380)
  • Supporting a physiological role for CLC in migration, the CLCb isoform of CLC is upregulated in migratory human trophoblast cells during uterine invasion. (PMID:24852344)
  • Data indicate that clathrin-mediated endocytosis of proto-oncogene protein erbB-3 (ErbB3) is depending on epsin-1. (PMID:26975582)
  • CLCb/Dyn1-dependent adaptive clathrin-mediated endocytosis selectively altered EGF receptor trafficking. (PMID:28171750)
  • Role of Clathrin Light Chains in Regulating Invadopodia Formation. (PMID:33672612)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriocltbENSDARG00000052368
mus_musculusCltbENSMUSG00000047547
rattus_norvegicusCltbENSRNOG00000017506
drosophila_melanogasterClcFBGN0024814
caenorhabditis_elegansWBGENE00020246

Paralogs (1): CLTA (ENSG00000122705)

Protein

Protein identifiers

Clathrin light chain BP09497 (reviewed: P09497)

All UniProt accessions (4): B4DTF9, D6RJD1, P09497, H0Y9Q6

UniProt curated annotations — full annotation on UniProt →

Function. Clathrin is the major protein of the polyhedral coat of coated pits and vesicles.

Subunit / interactions. Clathrin coats are formed from molecules containing 3 heavy chains and 3 light chains. Interacts (via N-terminus) with HIP1. Interacts with HIP1R.

Subcellular location. Cytoplasmic vesicle membrane. Membrane. Coated pit.

Similarity. Belongs to the clathrin light chain family.

Isoforms (2)

UniProt IDNamesCanonical?
P09497-1Brainyes
P09497-2Non-brain

RefSeq proteins (4): NP_001351055, NP_001351056, NP_001825, NP_009028* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000996Clathrin_L-chainFamily

Pfam: PF01086

UniProt features (13 total): modified residue 5, region of interest 2, compositionally biased region 2, chain 1, disulfide bond 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P09497-F174.350.28

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (5): 11, 13, 187, 204, 217

Disulfide bonds (1): 199–209

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

IDPathway
R-HSA-190873Gap junction degradation
R-HSA-196025Formation of annular gap junctions
R-HSA-3928665EPH-ephrin mediated repulsion of cells
R-HSA-432720Lysosome Vesicle Biogenesis
R-HSA-5099900WNT5A-dependent internalization of FZD4
R-HSA-5140745WNT5A-dependent internalization of FZD2, FZD5 and ROR2
R-HSA-8856825Cargo recognition for clathrin-mediated endocytosis
R-HSA-8856828Clathrin-mediated endocytosis

MSigDB gene sets: 243 (showing top): MODY_HIPPOCAMPUS_POSTNATAL, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GGTGTGT_MIR329, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, JAEGER_METASTASIS_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, KEGG_LYSOSOME, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_SYNAPTIC_VESICLE_RECYCLING, BROWNE_HCMV_INFECTION_24HR_UP, GOCC_TRANS_GOLGI_NETWORK, GOCC_COATED_VESICLE, KEGG_HUNTINGTONS_DISEASE

GO Biological Process (4): intracellular protein transport (GO:0006886), synaptic vesicle endocytosis (GO:0048488), clathrin-dependent endocytosis (GO:0072583), vesicle-mediated transport (GO:0016192)

GO Molecular Function (4): structural molecule activity (GO:0005198), clathrin heavy chain binding (GO:0032050), peptide binding (GO:0042277), protein binding (GO:0005515)

GO Cellular Component (15): trans-Golgi network (GO:0005802), cytosol (GO:0005829), plasma membrane (GO:0005886), clathrin coat (GO:0030118), clathrin vesicle coat (GO:0030125), clathrin coat of trans-Golgi network vesicle (GO:0030130), clathrin coat of coated pit (GO:0030132), synaptic vesicle membrane (GO:0030672), clathrin-coated endocytic vesicle (GO:0045334), ciliary membrane (GO:0060170), presynaptic endocytic zone membrane (GO:0098835), clathrin-coated pit (GO:0005905), membrane (GO:0016020), cytoplasmic vesicle membrane (GO:0030659), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-7 pathways:

CategoryPathways
PCP/CE pathway2
Gap junction trafficking1
Gap junction degradation1
EPH-Ephrin signaling1
trans-Golgi Network Vesicle Budding1
Clathrin-mediated endocytosis1
Membrane Trafficking1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
cytoplasm2
cellular anatomical structure2
membrane2
clathrin coat2
intracellular protein localization1
protein transport1
intracellular transport1
synaptic vesicle recycling1
presynaptic endocytosis1
receptor-mediated endocytosis1
transport1
cellular process1
molecular_function1
clathrin binding1
Golgi apparatus subcompartment1
cell periphery1
membrane coat1
vesicle coat1
clathrin-coated vesicle membrane1
Golgi apparatus1
trans-Golgi network transport vesicle membrane1
clathrin vesicle coat1
clathrin-coated pit1
plasma membrane protein complex1
synaptic vesicle1
exocytic vesicle membrane1
clathrin-coated vesicle1
endocytic vesicle1
cilium1
cell projection membrane1
bounding membrane of organelle1
presynaptic membrane1
synaptic membrane1
presynaptic endocytic zone1
endomembrane system1
vesicle membrane1
cytoplasmic vesicle1
intracellular vesicle1

Protein interactions and networks

STRING

1248 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CLTBCLTCQ00610974
CLTBCLTCL1P53675968
CLTBEPN2O95208806
CLTBHIP1RO75146800
CLTBAP2A1O95782793
CLTBEPN3Q9H201790
CLTBCLINT1Q14677674
CLTBDNAJC6O75061613
CLTBCLTAP09496609
CLTBAMPHP49418602
CLTBBIN1O00499601
CLTBNECAP1Q8NC96585
CLTBAP1B1P78436555
CLTBEPS15P42566537
CLTBAP2S1P53680495

IntAct

48 interactions, top by confidence:

ABTypeScore
CLTBPIK3C2Apsi-mi:“MI:0914”(association)0.530
CFTRCNOT1psi-mi:“MI:0914”(association)0.480
ADRA1ACLTBpsi-mi:“MI:0915”(physical association)0.460
ADRA1ACLTBpsi-mi:“MI:0403”(colocalization)0.460
CLTBHTR4psi-mi:“MI:0915”(physical association)0.370
CLTBWNK1psi-mi:“MI:0914”(association)0.350
OCRLEIF3CLpsi-mi:“MI:0914”(association)0.350
OCRLERC2psi-mi:“MI:0914”(association)0.350
OCRLMYO1Cpsi-mi:“MI:0914”(association)0.350
ARRB2psi-mi:“MI:0914”(association)0.350
HSPA8PPP6Cpsi-mi:“MI:0914”(association)0.350
DLDNFKBIEpsi-mi:“MI:0914”(association)0.350
PRNPWDR91psi-mi:“MI:0914”(association)0.350
ALYREFpsi-mi:“MI:0914”(association)0.350
ZDHHC5IGKV2D-24psi-mi:“MI:0914”(association)0.350
CFTRPOTEFpsi-mi:“MI:0914”(association)0.350
PTPN23CLTApsi-mi:“MI:0914”(association)0.350
ROCK2CLTBpsi-mi:“MI:0914”(association)0.350
ULK1HNRNPCL1psi-mi:“MI:0914”(association)0.350
RPS6KA5CNOT1psi-mi:“MI:0914”(association)0.350
STK16CLTBpsi-mi:“MI:0914”(association)0.350
SIK1CLTBpsi-mi:“MI:0914”(association)0.350
MAP3K9DNAJB6psi-mi:“MI:0914”(association)0.350
STK38SEC16Apsi-mi:“MI:0914”(association)0.350
MAP3K21HSP90AA1psi-mi:“MI:0914”(association)0.350
OBSCNHMGN1psi-mi:“MI:0914”(association)0.350
TP53RKCLTBpsi-mi:“MI:0914”(association)0.350
WNK3PIK3C2Apsi-mi:“MI:0914”(association)0.350
RAF1psi-mi:“MI:0914”(association)0.350

BioGRID (271): CLTB (Affinity Capture-MS), CLTB (Co-fractionation), CLTB (Co-fractionation), CLTB (Co-fractionation), CLTB (Co-fractionation), CLTCL1 (Co-fractionation), HSPE1 (Co-fractionation), PDAP1 (Co-fractionation), AP2A1 (Affinity Capture-MS), AP2A2 (Affinity Capture-MS), AP2B1 (Affinity Capture-MS), AP2M1 (Affinity Capture-MS), AP2S1 (Affinity Capture-MS), CLTA (Affinity Capture-MS), CLTB (Affinity Capture-MS)

ESM2 similar proteins: A2VDK6, B5X3I1, O08585, O43290, O88271, P04973, P04975, P08081, P08082, P09496, P09497, P09741, P13805, P41236, P50751, P50753, Q02614, Q0VFP5, Q2QY04, Q3U155, Q40554, Q5BK07, Q5EA95, Q5I0B5, Q5PQS7, Q5RGJ6, Q5XIW8, Q5ZIH9, Q5ZK95, Q6INR1, Q6IRU5, Q6NUB2, Q6NXS1, Q6PII3, Q75QI0, Q75UQ2, Q7SXU0, Q8BH43, Q8LDQ4, Q8R1N0

Diamond homologs: O08585, P04973, P04975, P08081, P08082, P09496, P09497, Q6IRU5, Q9VWA1, Q8MN58

SIGNOR signaling

8 interactions.

AEffectBMechanism
GRK2unknownCLTBphosphorylation
CLTB“form complex”“AP-2/clathrin vescicle”binding
CLTB“form complex”“AP-3/clathrin vescicle”binding
CLTB“form complex”“AP-1/clathrin vescicle”binding
CSNK2A1unknownCLTBphosphorylation
CSNK2A2unknownCLTBphosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 55 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Golgi Associated Vesicle Biogenesis524.4×3e-04
Clathrin-mediated endocytosis714.6×1e-04

GO biological processes:

GO termPartnersFoldFDR
protein autophosphorylation617.8×3e-04
protein phosphorylation1216.6×3e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

14 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance11
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

800 predictions. Top by Δscore:

VariantEffectΔscore
5:176396477:A:ACdonor_gain1.0000
5:176396478:C:CCdonor_gain1.0000
5:176396478:CA:Cdonor_gain1.0000
5:176396532:CC:Cacceptor_loss1.0000
5:176397594:ACAGC:Adonor_gain1.0000
5:176397595:CAGCC:Cdonor_gain1.0000
5:176397603:TCACC:Tdonor_loss1.0000
5:176397605:A:ACdonor_gain1.0000
5:176397606:C:CCdonor_gain1.0000
5:176397606:CCGG:Cdonor_gain1.0000
5:176397714:AGCAT:Aacceptor_gain1.0000
5:176397715:GCAT:Gacceptor_gain1.0000
5:176397716:CAT:Cacceptor_gain1.0000
5:176397716:CATC:Cacceptor_gain1.0000
5:176397717:AT:Aacceptor_gain1.0000
5:176397719:C:CCacceptor_gain1.0000
5:176397719:CTAGG:Cacceptor_loss1.0000
5:176397728:C:CTacceptor_gain1.0000
5:176397728:C:Tacceptor_gain1.0000
5:176397924:CCTCA:Cdonor_loss1.0000
5:176397925:CTCAC:Cdonor_loss1.0000
5:176397926:TCACC:Tdonor_loss1.0000
5:176397927:CACC:Cdonor_loss1.0000
5:176397928:A:ACdonor_gain1.0000
5:176397928:AC:Adonor_gain1.0000
5:176397929:C:CCdonor_gain1.0000
5:176397929:CC:Cdonor_gain1.0000
5:176397929:CCCAG:Cdonor_gain1.0000
5:176397933:G:Cdonor_gain1.0000
5:176397948:T:TAdonor_gain1.0000

AlphaMissense

1515 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:176392888:C:AW192C1.000
5:176392888:C:GW192C1.000
5:176392890:A:GW192R1.000
5:176392890:A:TW192R1.000
5:176397656:A:GW139R1.000
5:176397656:A:TW139R1.000
5:176397664:A:GL136P1.000
5:176397677:C:GA132P1.000
5:176397962:C:GR107P1.000
5:176397964:C:AW106C1.000
5:176397964:C:GW106C1.000
5:176397966:A:GW106R1.000
5:176397966:A:TW106R1.000
5:176416283:G:CF27L1.000
5:176416283:G:TF27L1.000
5:176416284:A:CF27C1.000
5:176416285:A:GF27L1.000
5:176392799:A:GL222P0.999
5:176392808:A:GL219P0.999
5:176392817:C:GR216P0.999
5:176392818:G:TR216S0.999
5:176392824:G:TR214S0.999
5:176392833:C:GD211H0.999
5:176392889:C:GW192S0.999
5:176397607:C:GR155P0.999
5:176397654:C:AW139C0.999
5:176397654:C:GW139C0.999
5:176397655:C:GW139S0.999
5:176397676:G:TA132D0.999
5:176397941:A:GL114P0.999

dbSNP variants (sampled 300 via entrez): RS1000027940 (5:176400004 C>G,T), RS1000162708 (5:176405779 C>T), RS1000214507 (5:176405976 C>G,T), RS1000563581 (5:176417819 T>C), RS1000576641 (5:176418144 G>A), RS1000807544 (5:176395295 A>C), RS1000856645 (5:176395512 C>T), RS1001048582 (5:176401635 G>A), RS1001296226 (5:176412897 G>A,C), RS1001479238 (5:176393416 A>G), RS1001529850 (5:176393760 C>T), RS1001590569 (5:176406429 G>A), RS1001690793 (5:176401042 C>T), RS1001719202 (5:176398779 G>A), RS1001887320 (5:176404426 C>T)

Disease associations

OMIM: gene MIM:118970 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST001762_725Obesity-related traits8.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004530triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5291549 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.97Kd1072nMCHEMBL5653589
5.97ED501072nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148091: Binding affinity to human CLTB incubated for 45 mins by Kinobead based pull down assaykd1.0718uM

CTD chemical–gene interactions

57 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression5
bisphenol Adecreases expression, increases expression3
Benzo(a)pyreneaffects methylation, increases expression3
sodium arseniteincreases expression, affects cotreatment, increases abundance2
nickel sulfateincreases expression, decreases expression2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment2
Air Pollutantsdecreases expression, increases abundance, increases expression2
Cocainedecreases expression2
Doxorubicinaffects expression, increases expression2
Tobacco Smoke Pollutionaffects expression, increases expression2
Tretinoinincreases expression2
Cyclosporinedecreases expression, increases expression2
Particulate Matterdecreases expression, increases abundance, increases expression2
aristolochic acid Iincreases expression1
bisphenol Fincreases expression1
triphenyl phosphateaffects expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, affects localization, increases expression, decreases expression1
beta-lapachoneincreases expression1
arseniteincreases reaction, affects binding1
cobaltous chlorideincreases expression1
butyraldehydeincreases expression1
manganese chlorideincreases expression, affects cotreatment, increases abundance1
tamibaroteneincreases expression1
azoxystrobindecreases expression1
abrineincreases expression1
pyrachlostrobindecreases expression1
bromovanindecreases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Sincreases expression1
jinfukangdecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651133BindingBinding affinity to human CLTB incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E0AEUbigene HeLa CLTB KOCancer cell lineFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.