CPT1C

carnitine palmitoyltransferase 1C

Basic information

Region (hg38): 19:49690898-49713731

Links

ENSG00000169169

∙ NCBI:126129 ∙ OMIM:608846 ∙ HGNC:18540 ∙ Uniprot:Q8TCG5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

hereditary spastic paraplegia 73 (Limited), mode of inheritance: AD
hereditary spastic paraplegia 73 (Supportive), mode of inheritance: AD
hereditary spastic paraplegia 73 (Strong), mode of inheritance: AD
hereditary spastic paraplegia (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spastic paraplegia 73, autosomal dominant	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	25751282

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CPT1C gene.

Hereditary_spastic_paraplegia_73 (304 variants)
not_specified (94 variants)
not_provided (37 variants)
CPT1C-related_disorder (13 variants)
Hereditary_spastic_paraplegia (3 variants)
Spastic_paraplegia (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPT1C gene is commonly pathogenic or not. These statistics are base on transcript: NM_001199753.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	85 clinvar	6 clinvar	95
missense	1 clinvar	1 clinvar	184 clinvar	18 clinvar	2 clinvar	206
nonsense	4 clinvar	2 clinvar	2 clinvar			8
start loss		1				1
frameshift	3 clinvar		5 clinvar			8
splice donor/acceptor (+/-2bp)		3 clinvar				3
Total	8	7	195	103	8

Highest pathogenic variant AF is 0.0000111536

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPT1C	protein_coding	protein_coding	ENST00000392518	18	22834

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.19e-9	1.00	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	419	502	0.835	0.0000324	5177
Missense in Polyphen		165	197.12	0.83705		1990
Synonymous	-0.690	233	220	1.06	0.0000149	1662
Loss of Function	3.20	22	45.2	0.486	0.00000246	438

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000912	0.0000905
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000272	0.000272
Finnish	0.000247	0.000231
European (Non-Finnish)	0.000277	0.000273
Middle Eastern	0.000272	0.000272
South Asian	0.000460	0.000457
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: May play a role in lipid metabolic process. {ECO:0000269|PubMed:25751282}.;
Pathway: Adipocytokine signaling pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Fatty acid degradation - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);AMP-activated Protein Kinase (AMPK) Signaling;PPAR signaling pathway;mitochondrial L-carnitine shuttle;FOXA2 and FOXA3 transcription factor networks (Consensus)

Intolerance Scores

loftool: 0.0663
rvis_EVS: -0.71
rvis_percentile_EVS: 14.78

Haploinsufficiency Scores

pHI: 0.204
hipred: Y
hipred_score: 0.674
ghis: 0.570

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.798

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Cpt1c
Phenotype: growth/size/body region phenotype; muscle phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process: fatty acid beta-oxidation;carnitine metabolic process;long-chain fatty acid transport;regulation of postsynaptic membrane neurotransmitter receptor levels
Cellular component: mitochondrion;mitochondrial outer membrane;endoplasmic reticulum;cell junction;integral component of endoplasmic reticulum membrane;axon;dendrite;AMPA glutamate receptor complex;postsynapse;glutamatergic synapse
Molecular function: carnitine O-palmitoyltransferase activity;protein binding