CLPTM1 (CLPTM1 regulator of GABA type A receptor forward trafficking)

Gene

• Entrez ID: 1209
• Gene name: CLPTM1 regulator of GABA type A receptor forward trafficking
• Gene symbol: CLPTM1
• Synonyms (NCBI Gene): -
• Chromosome: 19
• Chromosome location: 19q13.32

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT050963	hsa-miR-17-5p	CLASH	23622248
MIRT047428	hsa-miR-10b-5p	CLASH	23622248
MIRT044966	hsa-miR-186-5p	CLASH	23622248
MIRT897726	hsa-miR-1224-3p	CLIP-seq
MIRT897727	hsa-miR-1260	CLIP-seq
MIRT897728	hsa-miR-1260b	CLIP-seq
MIRT897729	hsa-miR-1280	CLIP-seq
MIRT897730	hsa-miR-4707-5p	CLIP-seq
MIRT897731	hsa-miR-532-3p	CLIP-seq
MIRT2202004	hsa-miR-3126-5p	CLIP-seq
MIRT2202005	hsa-miR-3191	CLIP-seq
MIRT2202006	hsa-miR-4278	CLIP-seq
MIRT2202007	hsa-miR-4485	CLIP-seq
MIRT2202008	hsa-miR-4716-3p	CLIP-seq
MIRT2202009	hsa-miR-887	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	21903422, 33961781
GO:0005886	Component	Plasma membrane	TAS	9828125
GO:0009897	Component	External side of plasma membrane	IEA
GO:0009897	Component	External side of plasma membrane	ISS
GO:0012505	Component	Endomembrane system	IBA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IBA
GO:0016020	Component	Membrane	IEA
GO:0030154	Process	Cell differentiation	IEA
GO:0033081	Process	Regulation of T cell differentiation in thymus	IEA
GO:0033081	Process	Regulation of T cell differentiation in thymus	ISS
GO:0050811	Function	GABA receptor binding	IEA

Other IDs

• MIM: 604783
• HGNC: 2087
• e!Ensembl: ENSG00000104853

Protein

• UniProt ID: O96005
• Protein name: Putative lipid scramblase CLPTM1 (Cleft lip and palate transmembrane protein 1)
• Protein function: Involved in GABAergic but not glutamatergic transmission. Binds and traps GABAA receptors in the endoplasmic reticulum (ER). Modulates postsynaptic GABAergic transmission, and therefore inhibitory neurotransmission, by reducing the plasma membra
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF05602	CLPTM1	57 → 497	Cleft lip and palate transmembrane protein 1 (CLPTM1)	Family

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:9828125}.
• Sequence:

  MAAAQEADGARSAVVAAGGGSSGQVTSNGSIGRDPPAETQPQNPPAQPAPNAWQVIKGVL
  FRIFIIWAISSWFRRGPAPQDQAGPGGAPRVASRNLFPKDTLMNLHVYISEHEHFTDFNA
  TSALFWEQHDLVYGDWTSGENSDGCYEHFAELDIPQSVQQNGSIYIHVYFTKSGFHPDPR
  QKALYRRLATVHMSRMINKYKRRRFQKTKNLLTGETEADPEMIKRAEDYGPVEVISHWHP
  NITINIVDDHTPWVKGSVPPPLDQYVKFDAVSGDYYPIIYFNDYWNLQKDYYPINESLAS
  LPLRVSFCPLSLWRWQLYAAQSTKSPWNFLGDELYEQSDEEQDSVKVALLETNPYLLALT
  IIVSIVHSVFEFLAFKNDIQFWNSRQSLEGLSVRSVFFGVFQSFVVLLYILDNETNFVVQ
  VSVFIGVLIDLWKITKVMDVRLDREHRVAGIFPRLSFKDKSTYIESSTKVYDDMAFRYLS
  WILFPLLGCYAVYSLLYLEHKGWYSWVLSMLYGFLLTFGFITMTPQLFINYKLKSVAHLP
  WRMLTYKALNTFIDDLFAFVIKMPVMYRIGCLRDDVVFFIYLYQRWIYRVDPTRVNEFGM
  SGEDPTAAAPVAEVPTAAGALTPTPAPTTTTATREEASTSLPTKPTQGASSASEPQEAPP
  KPAEDKKKD

• Sequence length: 669

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
ALZHEIMER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CLPTM1-related disorder	Uncertain significance; Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IGA GLOMERULONEPHRITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PANCREATIC NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alzheimer Disease	Alzheimer disease	Pubtator	33947463, 40631452	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Alzheimer`s Disease	Alzheimer disease	GWASDB_DG	21460841		★☆☆☆☆ Found in Text Mining only
Alzheimer`s Disease	Alzheimer disease	GWASCAT_DG	29777097, 30617256		★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	23368278, 24535780, 27062701, 28789383		★☆☆☆☆ Found in Text Mining only
Cleft Lip with or without Cleft Palate	Cleft Lip With Or Without Cleft Palate	BEFREE	20020508		★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	37577761	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	23368278, 24535780, 27062701, 28789383		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	CTD_human_DG	26098869		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	20597107		★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	25457634		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	16243817		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	22675468, 24175795, 29033187		★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasm	Pancreatic Neoplasm	CTD_human_DG	26098869		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic Neoplasms	LHGDN	16102578		★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	30635792	Associate	★☆☆☆☆ Found in Text Mining only