CPT1C (carnitine palmitoyltransferase 1C)

Gene

• Entrez ID: 126129
• Gene name: Carnitine palmitoyltransferase 1C
• Gene symbol: CPT1C
• Synonyms (NCBI Gene): CATL1, CPT I-C, CPT1-B, CPT1P, CPTI-B, CPTIC, SPG73
• Chromosome: 19
• Chromosome location: 19q13.33
• Summary: This gene encodes a member of the carnitine/choline acetyltransferase family. The encoded protein regulates the beta-oxidation and transport of long-chain fatty acids into mitochondria, and may play a role in the regulation of feeding behavior and whole-b

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs786204767	C>T	Pathogenic	Missense variant, 5 prime UTR variant, coding sequence variant, non coding transcript variant
rs1486248764	G>A,T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT040222	hsa-miR-615-3p	CLASH	23622248
MIRT734074	hsa-miR-1291	Immunohistochemistry (IHC), Immunoprecipitaion (IP), Luciferase reporter assay, qRT-PCR, Western blotting	32641987

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003824	Function	Catalytic activity	IEA
GO:0004095	Function	Carnitine O-palmitoyltransferase activity	ISS
GO:0005515	Function	Protein binding	IPI	25751282
GO:0005739	Component	Mitochondrion	ISS
GO:0005783	Component	Endoplasmic reticulum	IDA	30135643
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005783	Component	Endoplasmic reticulum	ISS
GO:0005789	Component	Endoplasmic reticulum membrane	IBA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	ISS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006631	Process	Fatty acid metabolic process	IBA
GO:0006631	Process	Fatty acid metabolic process	ISS
GO:0008474	Function	Palmitoyl-(protein) hydrolase activity	IDA	30135643
GO:0008474	Function	Palmitoyl-(protein) hydrolase activity	IEA
GO:0009437	Process	Carnitine metabolic process	IBA
GO:0009437	Process	Carnitine metabolic process	ISS
GO:0016020	Component	Membrane	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016746	Function	Acyltransferase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0030424	Component	Axon	IEA
GO:0030424	Component	Axon	ISS
GO:0030425	Component	Dendrite	IEA
GO:0030425	Component	Dendrite	ISS
GO:0032281	Component	AMPA glutamate receptor complex	IEA
GO:0042995	Component	Cell projection	IEA
GO:0098734	Process	Macromolecule depalmitoylation	IEA
GO:0098794	Component	Postsynapse	IEA
GO:0098978	Component	Glutamatergic synapse	IEA
GO:0099072	Process	Regulation of postsynaptic membrane neurotransmitter receptor levels	IEA

Other IDs

• MIM: 608846
• HGNC: 18540
• e!Ensembl: ENSG00000169169

Protein

• UniProt ID: Q8TCG5
• Protein name: Palmitoyl thioesterase CPT1C (EC 3.1.2.22) (Carnitine O-palmitoyltransferase 1, brain isoform) (CPTI-B) (Carnitine palmitoyltransferase 1C) (Carnitine palmitoyltransferase I) (CPT I-C)
• Protein function: Palmitoyl thioesterase specifically expressed in the endoplasmic reticulum of neurons. Modulates the trafficking of the glutamate receptor, AMPAR, to plasma membrane through depalmitoylation of GRIA1 (PubMed:30135643). Also regulates AMPR traffi
• PDB: 2M76
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF16484	CPT_N	1 → 47	Carnitine O-palmitoyltransferase N-terminus	Domain
  PF00755	Carn_acyltransf	171 → 759	Choline/Carnitine o-acyltransferase	Family

• Tissue specificity: TISSUE SPECIFICITY: Expressed predominantly in brain and testis. Expressed in motor neurons. {ECO:0000269|PubMed:12376098, ECO:0000269|PubMed:25751282}.
• Sequence:

  MAEAHQAVGFRPSLTSDGAEVELSAPVLQEIYLSGLRSWKRHLSRFWNDFLTGVFPASPL
  SWLFLFSAIQLAWFLQLDPSLGLMEKIKELLPDWGGQHHGLRGVLAAALFASCLWGALIF
  TLHVALRLLLSYHGWLLEPHGAMSSPTKTWLALVRIFSGRHPMLFSYQRSLPRQPVPSVQ
  DTVRKYLESVRPILSDEDFDWTAVLAQEFLRLQASLLQWYLRLKSWWASNYVSDWWEEFV
  YLRSRNPLMVNSNYYMMDFLYVTPTPLQAARAGNAVHALLLYRHRLNRQEIPPTLLMGMR
  PLCSAQYEKIFNTTRIPGVQKDYIRHLHDSQHVAVFHRGRFFRMGTHSRNSLLSPRALEQ
  QFQRILDDPSPACPHEEHLAALTAAPRGTWAQVRTSLKTQAAEALEAVEGAAFFVSLDAE
  PAGLTREDPAASLDAYAHALLAGRGHDRWFDKSFTLIVFSNGKLGLSVEHSWADCPISGH
  MWEFTLATECFQLGYSTDGHCKGHPDPTLPQPQRLQWDLPDQIHSSISLALRGAKILSEN
  VDCHVVPFSLFGKSFIRRCHLSSDSFIQIALQLAHFRDRGQFCLTYESAMTRLFLEGRTE
  TVRSCTREACNFVRAMEDKEKTDPQCLALFRVAVDKHQALLKAAMSGQGVDRHLFALYIV
  SRFLHLQSPFLTQVHSEQWQLSTSQIPVQQMHLFDVHNYPDYVSSGGGFGPADDHGYGVS
  YIFMGDGMITFHISSKKSSTKTDSHRLGQHIEDALLDVASLFQAGQHFKRRFRGSGKENS
  RHRCGFLSRQTGASKASMTSTDF

• Sequence length: 803

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Hereditary spastic paraplegia 73	Pathogenic; Likely pathogenic	rs780195851, rs1568547326, rs786204767, rs2514088767, rs1186386364, rs748659009, rs1447368316, rs767517922, rs2514147270, rs566644989, rs751933977	RCV001942228 RCV001967506 RCV000169633 RCV002612089 RCV002876785 RCV003005274 RCV003590909 RCV003588420 RCV003752029 RCV003887842 RCV001256201	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AUTOIMMUNE DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL DOMINANT SPASTIC PARAPLEGIA TYPE 73	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CPT1C-related disorder	Benign; Uncertain significance; Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary spastic paraplegia	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOTHYROIDISM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MELANOMA	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-NEOPLASTIC PERIPHERAL NERVOUS SYSTEM DISEASE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PANIC DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIPHERAL NERVOUS SYSTEM DISEASES	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIPHERAL NEUROPATHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spastic paraplegia	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
SPASTIC PARAPLEGIA 73, AUTOSOMAL DOMINANT	—	CTD, HPO CTD, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPASTIC PARAPLEGIA, HEREDITARY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
AUTOIMMUNE DISEASE, MULTISYSTEM, INFANTILE-ONSET, 1	Autoimmune Diseases	GWASCAT_DG	30595370		★☆☆☆☆ Found in Text Mining only
AUTOIMMUNE DISEASE, MULTISYSTEM, INFANTILE-ONSET, 2	Autoimmune Diseases	GWASCAT_DG	30595370		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	GWASCAT_DG	30595370		★☆☆☆☆ Found in Text Mining only
Autosomal dominant spastic paraplegia type 73	Spastic Paraplegia	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Carcinoma	Breast Carcinoma	BEFREE	31128263		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	36674468	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	37078750	Associate	★☆☆☆☆ Found in Text Mining only
Distal lower limb amyotrophy	Distal lower limb amyotrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	24618825		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	24618825	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	24618825		★☆☆☆☆ Found in Text Mining only
Glomerulonephritis Membranous	Membranous glomerulonephritis	Pubtator	36674468	Associate	★☆☆☆☆ Found in Text Mining only
Henoch-Schoenlein Purpura	Henoch-Schonlein Nephritis	BEFREE	25751282, 29847346		★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	BEFREE	28472467		★☆☆☆☆ Found in Text Mining only
Hypothyroidism	Hypothyroidism	GWASCAT_DG	30595370		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung Neoplasms	Lung Neoplasms	BEFREE	21576264		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	31128263		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28334197, 29317762, 30070697		★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	CTD_human_DG	16778180		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mitochondrial Diseases	Mitochondrial disease	Pubtator	30070697	Associate	★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	BEFREE	20864405		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	21576264, 22952346, 28334197, 29317762, 30070697		★☆☆☆☆ Found in Text Mining only
Non-alcoholic Fatty Liver Disease	Non-Alcoholic Fatty Liver Disease	BEFREE	29568887		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	30448371		★☆☆☆☆ Found in Text Mining only
Papillary thyroid carcinoma	Papillary thyroid carcinoma	BEFREE	29151954		★☆☆☆☆ Found in Text Mining only
Peripheral Nervous System Diseases	Nervous System Diseases	BEFREE	20864405		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Peripheral Nervous System Diseases	Nervous System Diseases	CTD_human_DG	20864405		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Peripheral Neuropathy	Peripheral Neuropathy	BEFREE	20864405		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spastic Paraplegia	Spastic Paraplegia	HPO_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Spastic paraplegia 10, autosomal dominant	Spondylometaphyseal dysplasia	BEFREE	25751282		★☆☆☆☆ Found in Text Mining only
SPASTIC PARAPLEGIA 73, AUTOSOMAL DOMINANT	Spastic Paraplegia	UNIPROT_DG	25751282		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPASTIC PARAPLEGIA 73, AUTOSOMAL DOMINANT	Spastic Paraplegia	ORPHANET_DG	25751282		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPASTIC PARAPLEGIA 73, AUTOSOMAL DOMINANT	Spastic Paraplegia	GENOMICS_ENGLAND_DG	30564185		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPASTIC PARAPLEGIA 73, AUTOSOMAL DOMINANT	Spastic Paraplegia	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPASTIC PARAPLEGIA 73, AUTOSOMAL DOMINANT	Spastic Paraplegia	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spastic Paraplegia Hereditary	Hereditary spastic paraplegia	Pubtator	30911584, 36109173	Associate	★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	27189278	Inhibit	★☆☆☆☆ Found in Text Mining only