CLTCL1 Gene

Name	clathrin, heavy chain-like 1
Description	This gene is a member of the clathrin heavy chain family and encodes a major protein of the polyhedral coat of coated pits and vesicles. Chromosomal aberrations involving this gene are associated with meningioma, DiGeorge syndrome, and velo-cardio-facial syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n The CLTCL1 gene encodes a clathrin heavy‐chain isoform (CHC22) that has emerged as a key regulator of intracellular membrane trafficking in diverse settings. Its normal function includes mediating the formation and retrograde sorting of specialized vesicles, most notably the insulin‐responsive GLUT4 compartments in muscle and adipose tissue, where CLTCL1/CHC22 facilitates proper glucose uptake and homeostasis (see."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": " In neurons, a transient reduction in CLTCL1 expression appears to trigger an autocrine/paracrine mechanism that controls neuropeptide processing, thereby influencing neural precursor differentiation and the development of pain‐ and touch‐sensing circuits. Indeed, a missense mutation in CLTCL1 has been shown to impair neural crest development, resulting in congenital insensitivity to pain (see."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": " Moreover, aberrations of CLTCL1 have been implicated in oncogenesis. For example, fusion of CLTCL1 (formerly designated as CLTCL when fused with ALK) results in constitutive activation of the ALK tyrosine kinase in a subset of anaplastic large‐cell lymphomas"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": ", and somatic mutations in CLTCL1 have also emerged as candidate driver events in oral squamous cell carcinoma."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": " In addition, rare variants in CLTCL1 have been identified in patients with congenital heart malformations such as total anomalous pulmonary venous connection"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": ", suggesting that altered dosage of this trafficking protein may also contribute to developmental defects. Collectively, these findings underscore the multifaceted role of CLTCL1 in regulating vesicle dynamics that are critical not only for metabolic and neural functions but also for maintaining cellular homeostasis, with its disruption contributing to a spectrum of human diseases.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Christopher Esk, Chih-Ying Chen, Ludger Johannes, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The clathrin heavy chain isoform CHC22 functions in a novel endosomal sorting step."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Biol (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1083/jcb.200908057"}], "href": "https://doi.org/10.1083/jcb.200908057"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20065094"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20065094"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Mhairi C Towler, Paul A Gleeson, Sachiko Hoshino, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Clathrin isoform CHC22, a component of neuromuscular and myotendinous junctions, binds sorting nexin 5 and has increased expression during myogenesis and muscle regeneration."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Biol Cell (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1091/mbc.e04-03-0249"}], "href": "https://doi.org/10.1091/mbc.e04-03-0249"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15133132"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15133132"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Michael S Nahorski, Lihadh Al-Gazali, Jozef Hertecant, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A novel disorder reveals clathrin heavy chain-22 is essential for human pain and touch development."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Brain (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/brain/awv149"}], "href": "https://doi.org/10.1093/brain/awv149"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26068709"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26068709"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Michael S Nahorski, Georg H H Borner, Samiha S Shaikh, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Clathrin heavy chain 22 contributes to the control of neuropeptide degradation and secretion during neuronal development."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Rep (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41598-018-19980-0"}], "href": "https://doi.org/10.1038/s41598-018-19980-0"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29402896"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29402896"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Jan Cools, Iwona Wlodarska, Riet Somers, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Identification of novel fusion partners of ALK, the anaplastic lymphoma kinase, in anaplastic large-cell lymphoma and inflammatory myofibroblastic tumor."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Chromosomes Cancer (2002)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/gcc.10033"}], "href": "https://doi.org/10.1002/gcc.10033"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12112524"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12112524"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Nezar Noor Al-Hebshi, Shiyong Li, Akram Thabet Nasher, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Exome sequencing of oral squamous cell carcinoma in users of Arabian snuff reveals novel candidates for driver genes."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Int J Cancer (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/ijc.30068"}], "href": "https://doi.org/10.1002/ijc.30068"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26934577"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26934577"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Xin Shi, Tao Huang, Jing Wang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Next-generation sequencing identifies novel genes with rare variants in total anomalous pulmonary venous connection."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "EBioMedicine (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.ebiom.2018.11.008"}], "href": "https://doi.org/10.1016/j.ebiom.2018.11.008"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30448225"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30448225"}]}]}]}
Synonyms	CLTCL, CLTD, CHC22, CLH22
Proteins	CLH2_HUMAN
NCBI Gene ID	8218
API
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

CLTCL1 has 7,934 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, disease, phenotype or trait, functional term, phrase or reference, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 112 datasets.

Click the + buttons to view associations for CLTCL1 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

CLTCL1 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of CLTCL1 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of CLTCL1 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of CLTCL1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of CLTCL1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of CLTCL1 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of CLTCL1 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of CLTCL1 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of CLTCL1 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of CLTCL1 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of CLTCL1 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Gene Mutation Profiles	cell lines with CLTCL1 gene mutations from the CCLE Cell Line Gene Mutation Profiles dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with CLTCL1 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of CLTCL1 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of CLTCL1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of CLTCL1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	ClinVar Gene-Phenotype Associations 2025	phenotypes associated with CLTCL1 gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset.
	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	gene perturbations changing expression of CLTCL1 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
	CM4AI U2OS Cell Map Protein Localization Assemblies	assemblies containing CLTCL1 protein from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of CLTCL1 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing CLTCL1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing CLTCL1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with CLTCL1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with CLTCL1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of CLTCL1 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with CLTCL1 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of CLTCL1 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by CLTCL1 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with CLTCL1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with CLTCL1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with CLTCL1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with CLTCL1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at CLTCL1 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of CLTCL1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of CLTCL1 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	GAD Gene-Disease Associations	diseases associated with CLTCL1 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with CLTCL1 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of CLTCL1 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with CLTCL1 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
	GeneSigDB Published Gene Signatures	PubMedIDs of publications reporting gene signatures containing CLTCL1 from the GeneSigDB Published Gene Signatures dataset.
	GEO Signatures of Differentially Expressed Genes for Diseases	disease perturbations changing expression of CLTCL1 gene from the GEO Signatures of Differentially Expressed Genes for Diseases dataset.