CLTCL1 (clathrin heavy chain like 1)

Download as csv Download as pdf

Log in to bookmark this gene

Bookmark This Gene

Title Project / Tag (optional) Note (optional)

Cancel Save

On this page

Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 8218
• Gene name: Clathrin heavy chain like 1
• Gene symbol: CLTCL1
• Synonyms (NCBI Gene): CHC22, CLH22, CLTCL, CLTD
• Chromosome: 22
• Chromosome location: 22q11.21
• Summary: 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs199652160	C>T	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant, genic upstream transcript variant

miRNA Show/Hide all (10)

miRTarBase ID	miRNA	Experiments	Reference
MIRT2202216	hsa-miR-149	CLIP-seq
MIRT2202217	hsa-miR-214	CLIP-seq
MIRT2202218	hsa-miR-338-3p	CLIP-seq
MIRT2202219	hsa-miR-3619-5p	CLIP-seq
MIRT2202220	hsa-miR-4459	CLIP-seq
MIRT2202221	hsa-miR-4530	CLIP-seq
MIRT2202222	hsa-miR-4722-5p	CLIP-seq
MIRT2202223	hsa-miR-4779	CLIP-seq
MIRT2202224	hsa-miR-761	CLIP-seq
MIRT2202225	hsa-miR-766	CLIP-seq

Gene ontology (GO) Show/Hide all (40)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000278	Process	Mitotic cell cycle	IDA	20065094
GO:0000278	Process	Mitotic cell cycle	IDA	19509056
GO:0005198	Function	Structural molecule activity	IEA
GO:0005515	Function	Protein binding	IPI	19478182, 19509056, 36217029
GO:0005769	Component	Early endosome	IDA	20065094
GO:0005770	Component	Late endosome	IDA	20065094
GO:0005802	Component	Trans-Golgi network	IDA	19509056
GO:0005802	Component	Trans-Golgi network	IEA
GO:0005819	Component	Spindle	IDA	19509056
GO:0005829	Component	Cytosol	TAS
GO:0005886	Component	Plasma membrane	IDA	20065094
GO:0005905	Component	Clathrin-coated pit	IDA	19509056
GO:0005905	Component	Clathrin-coated pit	IEA
GO:0006886	Process	Intracellular protein transport	IEA
GO:0006898	Process	Receptor-mediated endocytosis	IBA
GO:0006898	Process	Receptor-mediated endocytosis	IDA	19509056
GO:0006898	Process	Receptor-mediated endocytosis	IEA
GO:0006898	Process	Receptor-mediated endocytosis	TAS	8844170
GO:0009653	Process	Anatomical structure morphogenesis	TAS	8733128
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IEA
GO:0016192	Process	Vesicle-mediated transport	IEA
GO:0030130	Component	Clathrin coat of trans-Golgi network vesicle	IEA
GO:0030135	Component	Coated vesicle	IDA	19509056
GO:0030136	Component	Clathrin-coated vesicle	IDA	19478182
GO:0030136	Component	Clathrin-coated vesicle	IEA
GO:0030659	Component	Cytoplasmic vesicle membrane	IEA
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0032051	Function	Clathrin light chain binding	IBA
GO:0032051	Function	Clathrin light chain binding	IEA
GO:0042147	Process	Retrograde transport, endosome to Golgi	IEA
GO:0042147	Process	Retrograde transport, endosome to Golgi	IMP	20065094
GO:0045334	Component	Clathrin-coated endocytic vesicle	IBA
GO:0045334	Component	Clathrin-coated endocytic vesicle	NAS	25898166
GO:0046326	Process	Positive regulation of D-glucose import	IMP	19478182
GO:0055037	Component	Recycling endosome	IDA	20065094
GO:0070062	Component	Extracellular exosome	HDA	23533145
GO:0071439	Component	Clathrin complex	IBA
GO:0071439	Component	Clathrin complex	IEA
GO:0097443	Component	Sorting endosome	IDA	20065094

Other IDs

• MIM: 601273
• HGNC: 2093
• e!Ensembl: ENSG00000070371

Protein

• UniProt ID: P53675
• Protein name: Clathrin heavy chain 2 (Clathrin heavy chain on chromosome 22) (CLH-22)
• Protein function: Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. Two different adapter protein complexes link the clathrin lattice either to the plasma membrane or to the trans-Golgi network (By similarity).
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00637	Clathrin	979 → 1123	Region in Clathrin and VPS	Family
  PF00637	Clathrin	1274 → 1419	Region in Clathrin and VPS	Family
  PF00637	Clathrin	1423 → 1565	Region in Clathrin and VPS	Family
  PF00637	Clathrin	1128 → 1267	Region in Clathrin and VPS	Family
  PF00637	Clathrin	834 → 971	Region in Clathrin and VPS	Family
  PF00637	Clathrin	537 → 679	Region in Clathrin and VPS	Family
  PF00637	Clathrin	686 → 827	Region in Clathrin and VPS	Family
  PF01394	Clathrin_propel	296 → 330	Clathrin propeller repeat	Repeat
  PF01394	Clathrin_propel	148 → 187	Clathrin propeller repeat	Repeat
  PF01394	Clathrin_propel	198 → 234	Clathrin propeller repeat	Repeat
  PF01394	Clathrin_propel	19 → 56	Clathrin propeller repeat	Repeat
  PF09268	Clathrin-link	331 → 354	Clathrin, heavy-chain linker	Family
  PF13838	Clathrin_H_link	356 → 421		Domain

• Tissue specificity: TISSUE SPECIFICITY: Maximal levels in skeletal muscle. High levels in heart and testis. Low expression detected in all other tissues.
• Sequence:

  MAQILPVRFQEHFQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVTIIDMSDPMA
  PIRRPISAESAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMAEEVIFWKWVSVNTVA
  LVTETAVYHWSMEGDSQPMKMFDRHTSLVGCQVIHYRTDEYQKWLLLVGISAQQNRVVGA
  MQLYSVDRKVSQPIEGHAAAFAEFKMEGNAKPATLFCFAVRNPTGGKLHIIEVGQPAAGN
  QPFVKKAVDVFFPPEAQNDFPVAMQIGAKHGVIYLITKYGYLHLYDLESGVCICMNRISA
  DTIFVTAPHKPTSGIIGVNKKGQVLSVCVEEDNIVNYATNVLQNPDLGLRLAVRSNLAGA
  EKLFVRKFNTLFAQGSYAEAAKVAASAPKGILRTRETVQKFQSIPAQSGQASPLLQYFGI
  LLDQGQLNKLESLELCHLVLQQGRKQLLEKWLKEDKLECSEELGDLVKTTDPMLALSVYL
  RANVPSKVIQCFAETGQFQKIVLYAKKVGYTPDWIFLLRGVMKISPEQGLQFSRMLVQDE
  EPLANISQIVDIFMENSLIQQCTSFLLDALKNNRPAEGLLQTWLLEMNLVHAPQVADAIL
  GNKMFTHYDRAHIAQLCEKAGLLQQALEHYTDLYDIKRAVVHTHLLNPEWLVNFFGSLSV
  EDSVECLHAMLSANIRQNLQLCVQVASKYHEQLGTQALVELFESFKSYKGLFYFLGSIVN
  FSQDPDVHLKYIQAACKTGQIKEVERICRESSCYNPERVKNFLKEAKLTDQLPLIIVCDR
  FGFVHDLVLYLYRNNLQRYIEIYVQKVNPSRTPAVIGGLLDVDCSEEVIKHLIMAVRGQF
  STDELVAEVEKRNRLKLLLPWLESQIQEGCEEPATHNALAKIYIDSNNSPECFLRENAYY
  DSSVVGRYCEKRDPHLACVAYERGQCDLELIKVCNENSLFKSEARYLVCRKDPELWAHVL
  EETNPSRRQLIDQVVQTALSETRDPEEISVTVKAFMTADLPNELIELLEKIVLDNSVFSE
  HRNLQNLLILTAIKADRTRVMEYISRLDNYDALDIASIAVSSALYEEAFTVFHKFDMNAS
  AIQVLIEHIGNLDRAYEFAERCNEPAVWSQLAQAQLQKDLVKEAINSYIRGDDPSSYLEV
  VQSASRSNNWEDLVKFLQMARKKGRESYIETELIFALAKTSRVSELEDFINGPNNAHIQQ
  VGDRCYEEGMYEAAKLLYSNVSNFARLASTLVHLGEYQAAVDNSRKASSTRTWKEVCFAC
  MDGQEFRFAQLCGLHIVIHADELEELMCYYQDRGYFEELILLLEAALGLERAHMGMFTEL
  AILYSKFKPQKMLEHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAVLTMMS
  HPTEAWKEGQFKDIITKVANVELCYRALQFYLDYKPLLINDLLLVLSPRLDHTWTVSFFS
  KAGQLPLVKPYLRSVQSHNNKSVNEALNHLLTEEEDYQGLRASIDAYDNFDNISLAQQLE
  KHQLMEFRCIAAYLYKGNNWWAQSVELCKKDHLYKDAMQHAAESRDAELAQKLLQWFLEE
  GKRECFAACLFTCYDLLRPDMVLELAWRHNLVDLAMPYFIQVMREYLSKVDKLDALESLR
  KQEEHVTEPAPLVFDFDGHE

• Sequence length: 1640

Pathways

KEGG Pathway	Reactome Pathway
Lysosome	Gap junction degradation
Endocytosis	Formation of annular gap junctions
Synaptic vesicle cycle	EPH-ephrin mediated repulsion of cells
Endocrine and other factor-regulated calcium reabsorption	Cargo recognition for clathrin-mediated endocytosis
Huntington disease	Clathrin-mediated endocytosis
Bacterial invasion of epithelial cells

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations Show/Hide Unknown Diseases (22)
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	39998322	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	36810956	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CLTCL1-related disorder	Benign; Conflicting classifications of pathogenicity; Uncertain significance; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL INSENSITIVITY TO PAIN WITH SEVERE INTELLECTUAL DISABILITY	—	Disgenet	26068709, 26068709	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	29212778	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Conflicting classifications of pathogenicity	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOBLASTOMA MULTIFORME	—	GWAS catalog	36810956	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	36810956	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Uncertain significance; Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining Show/Hide Text Mining Associations (18)
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Autistic Disorder	Autism	Pubtator	22511880	Associate	★☆☆☆☆ Found in Text Mining only
Chromosome 22q11.2 Microduplication Syndrome	Chromosome 22q11.2 microduplication syndrome	Pubtator	36722223	Associate	★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognition disorder	Pubtator	26068709	Associate	★☆☆☆☆ Found in Text Mining only
Congenital Microtia	Congenital microtia	Pubtator	37107637	Associate	★☆☆☆☆ Found in Text Mining only
Congenital Pain Insensitivity	Congenital Pain Insensitivity	GENOMICS_ENGLAND_DG	26068709		★☆☆☆☆ Found in Text Mining only
Conotruncal cardiac defects	Conotruncal cardiac defect	Pubtator	22185286	Associate	★☆☆☆☆ Found in Text Mining only
DiGeorge Syndrome	Digeorge syndrome	Pubtator	22185286	Inhibit	★☆☆☆☆ Found in Text Mining only
DiGeorge Syndrome	Digeorge syndrome	Pubtator	29925309, 9326327	Associate	★☆☆☆☆ Found in Text Mining only
Insulin Resistance	Diabetes mellitus, type 2	Pubtator	29097553	Associate	★☆☆☆☆ Found in Text Mining only
Ki-1+ Anaplastic Large Cell Lymphoma	Anaplastic Lymphoma	BEFREE	12112524		★☆☆☆☆ Found in Text Mining only
Meningioma	Meningioma	Pubtator	32461543	Associate	★☆☆☆☆ Found in Text Mining only
Meningioma	Meningioma	BEFREE	8733129		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	8733129		★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	Pubtator	40593006	Inhibit	★☆☆☆☆ Found in Text Mining only
Pain Insensitivity Congenital	Congenital pain insensitivity	Pubtator	26068709	Associate	★☆☆☆☆ Found in Text Mining only
Rhabdomyosarcoma	Rhabdomyosarcoma	Pubtator	20956521	Associate	★☆☆☆☆ Found in Text Mining only
Rhabdomyosarcoma	Rhabdomyosarcoma	BEFREE	20956521		★☆☆☆☆ Found in Text Mining only
Sacral defect and anterior sacral meningocele	Sacral defect	Pubtator	28007035	Associate	★☆☆☆☆ Found in Text Mining only

Related Genes

Sort by: Blended Diseases Pathways Evidence source

CLTB 10 shared pathwaysLysosome, Endocytosis, Synaptic vesicle cycle, Endocrine and other factor-regulated calcium reabsorption, Bacterial invasion of epithelial cells, Clathrin-mediated endocytosis, Cargo recognition for clathrin-mediated endocytosis, EPH-ephrin mediated repulsion of cells, Gap junction degradation, Formation of annular gap junctions Related via 10 shared pathways including Lysosome, Endocytosis. DNM1 8 shared pathwaysEndocytosis, Synaptic vesicle cycle, Endocrine and other factor-regulated calcium reabsorption, Bacterial invasion of epithelial cells, Clathrin-mediated endocytosis, EPH-ephrin mediated repulsion of cells, Gap junction degradation, Formation of annular gap junctions Related via 8 shared pathways including Endocytosis, Synaptic vesicle cycle. CLTA 10 shared pathwaysLysosome, Endocytosis, Synaptic vesicle cycle, Endocrine and other factor-regulated calcium reabsorption, Bacterial invasion of epithelial cells, Clathrin-mediated endocytosis, Cargo recognition for clathrin-mediated endocytosis, EPH-ephrin mediated repulsion of cells, Gap junction degradation, Formation of annular gap junctions Related via 10 shared pathways including Lysosome, Endocytosis. CLTC 10 shared pathwaysLysosome, Endocytosis, Synaptic vesicle cycle, Endocrine and other factor-regulated calcium reabsorption, Bacterial invasion of epithelial cells, Clathrin-mediated endocytosis, Cargo recognition for clathrin-mediated endocytosis, EPH-ephrin mediated repulsion of cells, Gap junction degradation, Formation of annular gap junctions Related via 10 shared pathways including Lysosome, Endocytosis. DAB2 5 shared pathwaysEndocytosis, Clathrin-mediated endocytosis, Cargo recognition for clathrin-mediated endocytosis, Gap junction degradation, Formation of annular gap junctions Related via 5 shared pathways including Endocytosis, Clathrin-mediated endocytosis.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
CLTB	0	[]	10	["Lysosome","Endocytosis","Synaptic vesicle cycle","Endocrine and other factor-regulated calcium reabsorption","Bacterial invasion of epithelial cells","Clathrin-mediated endocytosis","Cargo recognition for clathrin-mediated endocytosis","EPH-ephrin mediated repulsion of cells","Gap junction degradation","Formation of annular gap junctions"]	0	[]
DNM1	0	[]	8	["Endocytosis","Synaptic vesicle cycle","Endocrine and other factor-regulated calcium reabsorption","Bacterial invasion of epithelial cells","Clathrin-mediated endocytosis","EPH-ephrin mediated repulsion of cells","Gap junction degradation","Formation of annular gap junctions"]	0	[]
CLTA	0	[]	10	["Lysosome","Endocytosis","Synaptic vesicle cycle","Endocrine and other factor-regulated calcium reabsorption","Bacterial invasion of epithelial cells","Clathrin-mediated endocytosis","Cargo recognition for clathrin-mediated endocytosis","EPH-ephrin mediated repulsion of cells","Gap junction degradation","Formation of annular gap junctions"]	0	[]
CLTC	0	[]	10	["Lysosome","Endocytosis","Synaptic vesicle cycle","Endocrine and other factor-regulated calcium reabsorption","Bacterial invasion of epithelial cells","Clathrin-mediated endocytosis","Cargo recognition for clathrin-mediated endocytosis","EPH-ephrin mediated repulsion of cells","Gap junction degradation","Formation of annular gap junctions"]	0	[]
DAB2	0	[]	5	["Endocytosis","Clathrin-mediated endocytosis","Cargo recognition for clathrin-mediated endocytosis","Gap junction degradation","Formation of annular gap junctions"]	0	[]

Diseases Linked via Similar Genes

Developmental and epileptic encephalopathy Linked via 2 of 5 related genesDNM1, CLTC Global developmental delay Linked via 2 of 5 related genesDNM1, CLTC Neurodevelopmental disorder Linked via 2 of 5 related genesDNM1, CLTC Lung neoplasms Linked via 1 of 5 related genesCLTB Obesity Linked via 1 of 5 related genesCLTB

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Developmental and epileptic encephalopathy	2	["DNM1","CLTC"]
Global developmental delay	2	["DNM1","CLTC"]
Neurodevelopmental disorder	2	["DNM1","CLTC"]
Lung neoplasms	1	["CLTB"]
Obesity	1	["CLTB"]