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Aliases for CPT1C Gene

Aliases for CPT1C Gene

  • Carnitine Palmitoyltransferase 1C 2 3 4 5
  • Carnitine O-Palmitoyltransferase I, Brain Isoform 3 4
  • EC 4 58
  • CPT1-B 3 4
  • CPTI-B 3 4
  • CATL1 3 4
  • Carnitine O-Palmitoyltransferase 1, Brain Isoform 3
  • Carnitine Palmitoyltransferase I Related C 3
  • CPT IC 4
  • CPT1P 3
  • CPTIC 3
  • SPG73 3

External Ids for CPT1C Gene

Previous GeneCards Identifiers for CPT1C Gene

  • GC19P050852
  • GC19P050562
  • GC19P054870
  • GC19P054886
  • GC19P050195
  • GC19P046571
  • GC19P050199
  • GC19P050207

Summaries for CPT1C Gene

Entrez Gene Summary for CPT1C Gene

  • 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-body energy homeostasis. Alternatively spliced transcript variants encoding multiple protein isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]

GeneCards Summary for CPT1C Gene

CPT1C (Carnitine Palmitoyltransferase 1C) is a Protein Coding gene. Diseases associated with CPT1C include Spastic Paraplegia 73, Autosomal Dominant. Among its related pathways are Fatty acid metabolism and Glucagon signaling pathway. GO annotations related to this gene include transferase activity, transferring acyl groups and carnitine O-palmitoyltransferase activity. An important paralog of this gene is CPT1A.

UniProtKB/Swiss-Prot for CPT1C Gene

  • May play a role in lipid metabolic process.

Additional gene information for CPT1C Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CPT1C Gene

Genomics for CPT1C Gene

Regulatory Elements for CPT1C Gene

Enhancers for CPT1C Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19H048958 2.1 FANTOM5 Ensembl ENCODE dbSUPER 21.2 -726.8 -726849 10.2 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 ZC3H11A NFYC MEF2D NUP62 PRR12 ENSG00000269321 RUVBL2 PPP1R15A TSKS ENSG00000268047 IRF3 PIH1D1 CPT1C
GH19H048780 1.6 Ensembl ENCODE dbSUPER 26 -909.2 -909168 2.9 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B ZNF766 ZNF143 FOS SP5 PRR12 SNRNP70 PIH1D1 GRWD1 SNORD35A CYTH2 IRF3 SNORD35B ENSG00000268093 KDELR1
GH19H050678 1.3 Ensembl ENCODE 30.7 +988.6 988599 1.2 HDGF PKNOX1 ATF1 ZNF133 SIN3A YBX1 GLI4 BRCA1 TCF12 GLIS2 ZNF175 NUP62 POLD1 ENSG00000267808 CPT1C ADM5 ENSG00000268047 PTOV1-AS2 ZNF473 PTOV1
GH19H049494 2 FANTOM5 Ensembl ENCODE dbSUPER 15.1 -191.8 -191835 9.7 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D SSRP1 GLIS1 PRR12 RPS11 PIH1D1 RPL13A ALDH16A1 SNORD35A IRF3 SNORD35B SNRNP70 RPL18
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CPT1C on UCSC Golden Path with GeneCards custom track

Promoters for CPT1C Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000110938 222 1001 ZBTB10 MXI1 TAF1 REST ZNF501 ZFHX2 POLR2A ZBTB33 PRDM4 ZBTB20

Genomic Locations for CPT1C Gene

Genomic Locations for CPT1C Gene
22,854 bases
Plus strand

Genomic View for CPT1C Gene

Genes around CPT1C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CPT1C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CPT1C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CPT1C Gene

Proteins for CPT1C Gene

  • Protein details for CPT1C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Carnitine O-palmitoyltransferase 1, brain isoform
    Protein Accession:
    Secondary Accessions:
    • A8K0Z8
    • Q5K6N5
    • Q8N6Q9
    • Q8NDS6
    • Q8TE84

    Protein attributes for CPT1C Gene

    803 amino acids
    Molecular mass:
    90989 Da
    Quaternary structure:
    • Peripherally associated with AMPAR complex. AMPAR complex consists of an inner core made of 4 pore-forming GluA/GRIA proteins (GRIA1, GRIA2, GRIA3 and GRIA4) and 4 major auxiliary subunits arranged in a twofold symmetry. One of the two pairs of distinct binding sites is occupied either by CNIH2, CNIH3 or CACNG2, CACNG3. The other harbors CACNG2, CACNG3, CACNG4, CACNG8 or GSG1L. This inner core of AMPAR complex is complemented by outer core constituents binding directly to the GluA/GRIA proteins at sites distinct from the interaction sites of the inner core constituents. Outer core constituents include at least PRRT1, PRRT2, CKAMP44/SHISA9, FRRS1L and NRN1. The proteins of the inner and outer core serve as a platform for other, more peripherally associated AMPAR constituents, including CPT1C. Alone or in combination, these auxiliary subunits control the gating and pharmacology of the AMPAR complex and profoundly impact their biogenesis and protein processing (By similarity). Interacts with ATL1 (PubMed:25751282).
    • Sequence=BAB85068.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAD38561.2; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CPT1C Gene

    Alternative splice isoforms for CPT1C Gene


neXtProt entry for CPT1C Gene

Selected DME Specific Peptides for CPT1C Gene


Post-translational modifications for CPT1C Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for CPT1C Gene

Gene Families for CPT1C Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for CPT1C Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the carnitine/choline acetyltransferase family.
  • Belongs to the carnitine/choline acetyltransferase family.
genes like me logo Genes that share domains with CPT1C: view

Function for CPT1C Gene

Molecular function for CPT1C Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Palmitoyl-CoA + L-carnitine = CoA + L-palmitoylcarnitine.
UniProtKB/Swiss-Prot Function:
May play a role in lipid metabolic process.

Enzyme Numbers (IUBMB) for CPT1C Gene

Phenotypes From GWAS Catalog for CPT1C Gene

Gene Ontology (GO) - Molecular Function for CPT1C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004095 carnitine O-palmitoyltransferase activity IEA --
GO:0005515 protein binding IPI 25751282
GO:0016740 transferase activity IEA --
GO:0016746 transferase activity, transferring acyl groups IEA --
genes like me logo Genes that share ontologies with CPT1C: view
genes like me logo Genes that share phenotypes with CPT1C: view

Human Phenotype Ontology for CPT1C Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CPT1C Gene

MGI Knock Outs for CPT1C:

miRNA for CPT1C Gene

miRTarBase miRNAs that target CPT1C

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for CPT1C Gene

Localization for CPT1C Gene

Subcellular locations from UniProtKB/Swiss-Prot for CPT1C Gene

Mitochondrion outer membrane; Multi-pass membrane protein. Cell junction, synapse. Cell projection, dendrite. Cell projection, axon. Endoplasmic reticulum. Note=Localized in the soma and dendritic and axonal projections. {ECO:0000269 PubMed:25751282}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CPT1C gene
Compartment Confidence
endoplasmic reticulum 5
mitochondrion 4
peroxisome 3
plasma membrane 2
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CPT1C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005741 mitochondrial outer membrane IEA --
GO:0005783 endoplasmic reticulum ISS --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with CPT1C: view

Pathways & Interactions for CPT1C Gene

genes like me logo Genes that share pathways with CPT1C: view

UniProtKB/Swiss-Prot Q8TCG5-CPT1C_HUMAN

  • Pathway: Lipid metabolism; fatty acid beta-oxidation.

SIGNOR curated interactions for CPT1C Gene

Is activated by:

Gene Ontology (GO) - Biological Process for CPT1C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006631 fatty acid metabolic process IEA --
GO:0006635 fatty acid beta-oxidation IEA --
GO:0009437 carnitine metabolic process IEA --
genes like me logo Genes that share ontologies with CPT1C: view

Drugs & Compounds for CPT1C Gene

(2) Drugs for CPT1C Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Carnitine Approved Pharma 0
Coenzyme A Nutra 0

(3) Additional Compounds for CPT1C Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (+)-palmitoylcarnitine
  • (3S)-3-hexadecanoyloxy-4-(trimethylammonio)butanoate
  • (3S)-3-hexadecanoyloxy-4-(trimethylammonio)butanoic acid
  • (3S)-3-palmitoyloxy-4-(trimethylammonio)butanoate
  • (3S)-3-palmitoyloxy-4-(trimethylammonio)butanoic acid
  • Hexadecanoyl CoA
  • Hexadecanoyl Coenzyme A
  • Palmitoyl CoA
  • Palmitoyl coenzyme a
  • Palmitoyl-CoA
genes like me logo Genes that share compounds with CPT1C: view

Transcripts for CPT1C Gene

Unigene Clusters for CPT1C Gene

Carnitine palmitoyltransferase 1C:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CPT1C Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^
SP1: - - - - - -
SP2: - - - - - - - -
SP3: - - - - - - - -
SP4: - - - -
SP6: - - - - - -
SP7: - - - - -
SP8: - - - - -
SP13: -

ExUns: 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^ 20a · 20b · 20c ^ 21a · 21b · 21c ^ 22a · 22b · 22c · 22d
SP1: - - - -
SP2: - - - - -
SP3: - - - - -
SP5: - - - -
SP10: - -
SP11: -
SP12: -

Relevant External Links for CPT1C Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CPT1C Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CPT1C Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CPT1C Gene

This gene is overexpressed in Breast (33.5), Retina (16.9), and Testis (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CPT1C Gene

Protein tissue co-expression partners for CPT1C Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CPT1C Gene:


SOURCE GeneReport for Unigene cluster for CPT1C Gene:


mRNA Expression by UniProt/SwissProt for CPT1C Gene:

Tissue specificity: Expressed predominantly in brain and testis. Expressed in motor neurons.

Evidence on tissue expression from TISSUES for CPT1C Gene

  • Nervous system(4.7)
  • Eye(4.2)
  • Kidney(4)
  • Muscle(2.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CPT1C Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
Head and neck:
  • brain
  • head
  • foot
  • lower limb
  • upper limb
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with CPT1C: view

No data available for mRNA differential expression in normal tissues for CPT1C Gene

Orthologs for CPT1C Gene

This gene was present in the common ancestor of animals.

Orthologs for CPT1C Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CPT1C 34
  • 100 (a)
(Canis familiaris)
Mammalia CPT1C 33 34
  • 87.96 (n)
(Bos Taurus)
Mammalia CPT1C 33 34
  • 87.7 (n)
(Mus musculus)
Mammalia Cpt1c 33 16 34
  • 81.7 (n)
(Rattus norvegicus)
Mammalia Cpt1c 33
  • 81.27 (n)
(Monodelphis domestica)
Mammalia CPT1C 34
  • 55 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 44 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 57 (a)
(Danio rerio)
Actinopterygii zgc:112484 34
  • 53 (a)
fruit fly
(Drosophila melanogaster)
Insecta whd 34
  • 43 (a)
(Caenorhabditis elegans)
Secernentea cpt-1 34
  • 41 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 44 (a)
Species where no ortholog for CPT1C was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for CPT1C Gene

Gene Tree for CPT1C (if available)
Gene Tree for CPT1C (if available)

Paralogs for CPT1C Gene

Paralogs for CPT1C Gene

genes like me logo Genes that share paralogs with CPT1C: view

Variants for CPT1C Gene

Sequence variations from dbSNP and Humsavar for CPT1C Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs786204767 Pathogenic, Spastic paraplegia 73, autosomal dominant (SPG73) [MIM:616282] 49,692,361(+) GCCTG(C/T)GCTCC nc-transcript-variant, reference, missense, utr-variant-5-prime
rs1000151538 -- 49,703,421(+) GGTCT(C/T)GACCT intron-variant
rs1000231962 -- 49,703,785(+) GTGCC(C/T)CTAAG intron-variant
rs1000388855 -- 49,691,481(+) GCATG(A/C)GCAGT intron-variant, downstream-variant-500B, upstream-variant-2KB, utr-variant-5-prime
rs1000880518 -- 49,695,729(+) CAGGC(A/G)TGTGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CPT1C Gene

Variant ID Type Subtype PubMed ID
nsv9739 CNV gain+loss 18304495
nsv953600 CNV deletion 24416366
nsv833865 CNV gain+loss 17160897
nsv833864 CNV gain 17160897
nsv817854 CNV gain 17921354
nsv7308 OTHER inversion 18451855
nsv470150 CNV gain 18288195
nsv469715 CNV gain+loss 16826518
nsv1160655 CNV deletion 26073780
nsv1148469 CNV insertion 26484159
esv1580543 CNV insertion 17803354
esv1209349 CNV insertion 17803354
dgv1796n106 CNV deletion 24896259

Variation tolerance for CPT1C Gene

Residual Variation Intolerance Score: 4.89% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.18; 39.40% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CPT1C Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CPT1C Gene

Disorders for CPT1C Gene

MalaCards: The human disease database

(1) MalaCards diseases for CPT1C Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, and GeneCards

Disorder Aliases PubMed IDs
spastic paraplegia 73, autosomal dominant
  • hereditary spastic paraplegia 73
- elite association - COSMIC cancer census association via MalaCards
Search CPT1C in MalaCards View complete list of genes associated with diseases


  • Spastic paraplegia 73, autosomal dominant (SPG73) [MIM:616282]: A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. {ECO:0000269 PubMed:25751282}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for CPT1C

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CPT1C: view

No data available for Genatlas for CPT1C Gene

Publications for CPT1C Gene

  1. A novel brain-expressed protein related to carnitine palmitoyltransferase I. (PMID: 12376098) Price N … Zammit V (Genomics 2002) 2 3 4 60
  2. Mutation in CPT1C Associated With Pure Autosomal Dominant Spastic Paraplegia. (PMID: 25751282) Rinaldi C … Fischbeck KH (JAMA neurology 2015) 3 4 60
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 45 60
  4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 45 60
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60

Products for CPT1C Gene

Sources for CPT1C Gene

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