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 (6 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	76	9	89
missense		1	130	12	2	145
nonsense	4	1	1			6
start loss		1				1
frameshift	2		3			5
inframe indel						0
splice donor/acceptor (+/-2bp)		2				2
splice region			6	12	1	19
non coding			2	26	5	33
Total	6	5	140	114	16

Highest pathogenic variant AF is 0.0000131

Variants in CPT1C

This is a list of pathogenic ClinVar variants found in the CPT1C region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-49692254-T-G		Hereditary spastic paraplegia 73	Likely pathogenic (Aug 18, 2020)
19-49692273-C-T		Hereditary spastic paraplegia 73	Likely benign (Sep 03, 2020)
19-49692278-G-A		Hereditary spastic paraplegia 73	Uncertain significance (Oct 17, 2023)
19-49692285-A-T		Hereditary spastic paraplegia 73	Likely benign (Jun 16, 2022)
19-49692291-G-A		Hereditary spastic paraplegia 73	Likely benign (Mar 23, 2022)
19-49692299-C-T		not specified	Uncertain significance (Mar 24, 2023)
19-49692303-C-A		Hereditary spastic paraplegia 73	Uncertain significance (Oct 13, 2023)
19-49692307-G-A		Hereditary spastic paraplegia 73 • not specified	Uncertain significance (May 02, 2024)
19-49692308-C-T		Hereditary spastic paraplegia 73	Uncertain significance (Sep 23, 2022)
19-49692322-A-G		Hereditary spastic paraplegia 73	Uncertain significance (Jul 17, 2023)
19-49692359-T-G		Hereditary spastic paraplegia 73	Uncertain significance (Sep 01, 2022)
19-49692361-C-T		Hereditary spastic paraplegia 73	Pathogenic (Mar 09, 2015)
19-49692362-G-A		Hereditary spastic paraplegia 73	Uncertain significance (Nov 03, 2022)
19-49692363-C-T		Hereditary spastic paraplegia 73	Likely benign (Jan 29, 2024)
19-49692374-G-C		Hereditary spastic paraplegia 73	Uncertain significance (Oct 06, 2023)
19-49692391-T-C		not specified	Uncertain significance (Jan 26, 2022)
19-49692403-G-A		Hereditary spastic paraplegia 73	Benign (May 15, 2023)
19-49692412-C-T		Hereditary spastic paraplegia 73	Likely benign (Jan 05, 2024)
19-49697330-A-T		Hereditary spastic paraplegia 73	Uncertain significance (Sep 26, 2021)
19-49697340-C-T		Hereditary spastic paraplegia 73	Likely benign (Sep 22, 2023)
19-49697341-G-A		Hereditary spastic paraplegia 73	Uncertain significance (Aug 04, 2021)
19-49697364-C-T		Hereditary spastic paraplegia 73	Likely benign (Jan 13, 2023)
19-49697380-T-G		Hereditary spastic paraplegia 73 • not specified	Uncertain significance (May 24, 2023)
19-49697384-G-A		Hereditary spastic paraplegia 73 • not specified	Uncertain significance (Oct 14, 2023)
19-49697387-C-T		Hereditary spastic paraplegia 73	Uncertain significance (Oct 08, 2021)

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