CLTCL1 (clathrin heavy chain like 1)

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

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)

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
  PF01394	Clathrin_propel	19 → 56	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	296 → 330	Clathrin propeller repeat	Repeat
  PF09268	Clathrin-link	331 → 354	Clathrin, heavy-chain linker	Family
  PF13838	Clathrin_H_link	356 → 421		Domain
  PF00637	Clathrin	537 → 679	Region in Clathrin and VPS	Family
  PF00637	Clathrin	686 → 827	Region in Clathrin and VPS	Family
  PF00637	Clathrin	834 → 971	Region in Clathrin and VPS	Family
  PF00637	Clathrin	979 → 1123	Region in Clathrin and VPS	Family
  PF00637	Clathrin	1128 → 1267	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

• 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:

Lysosome
Endocytosis
Synaptic vesicle cycle
Endocrine and other factor-regulated calcium reabsorption
Huntington disease
Bacterial invasion of epithelial cells

Reactome:

Gap junction degradation
Formation of annular gap junctions
EPH-ephrin mediated repulsion of cells
Cargo recognition for clathrin-mediated endocytosis
Clathrin-mediated endocytosis

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
Phenotype Name	Clinical Significance	Source	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	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★☆☆☆ 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
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ 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	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★☆☆☆ 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
Disease Name	Relationship Type	References	Evidence Score
Autistic Disorder	Associate	22511880	★☆☆☆☆ Found in Text Mining only
Chromosome 22q11.2 Microduplication Syndrome	Associate	36722223	★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Associate	26068709	★☆☆☆☆ Found in Text Mining only
Congenital Microtia	Associate	37107637	★☆☆☆☆ Found in Text Mining only
Conotruncal cardiac defects	Associate	22185286	★☆☆☆☆ Found in Text Mining only
DiGeorge Syndrome	Inhibit	22185286	★☆☆☆☆ Found in Text Mining only
DiGeorge Syndrome	Associate	29925309, 9326327	★☆☆☆☆ Found in Text Mining only
Genetic Diseases Inborn	Associate	26068709	★☆☆☆☆ Found in Text Mining only
Insulin Resistance	Associate	29097553	★☆☆☆☆ Found in Text Mining only
Meningioma	Associate	32461543	★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	32461543	★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Inhibit	40593006	★☆☆☆☆ Found in Text Mining only
Pain	Associate	26068709	★☆☆☆☆ Found in Text Mining only
Pain Insensitivity Congenital	Associate	26068709	★☆☆☆☆ Found in Text Mining only
Rhabdomyosarcoma	Associate	20956521	★☆☆☆☆ Found in Text Mining only
Sacral defect and anterior sacral meningocele	Associate	28007035	★☆☆☆☆ Found in Text Mining only