GENE REFERENCE / HGNC:2330

CPT2

carnitine palmitoyltransferase 2

protein-coding gene1p32.3Gene information

What does this gene do?

The CPT2 gene provides instructions for making an enzyme called carnitine palmitoyltransferase 2. This enzyme is essential for fatty acid oxidation, a multistep process that breaks down (metabolizes) fats and converts them into energy. Fatty acids are a major source of energy for the heart and muscles. During periods of fasting, fatty acids are also an important energy source for the liver and other tissues.

Within liver cells, fatty acid oxidation takes place within mitochondria, which are the energy-producing centers in cells. Before they can enter mitochondria, a group of fats called long-chain fatty acids must first attach to a compound called carnitine. Once inside mitochondria, carnitine palmitoyltransferase 2 removes the carnitine from these fatty acids and adds a substance called coenzyme A. Long-chain fatty acids must be joined to coenzyme A before they can be metabolized to produce energy.

Source: MedlinePlus, National Library of Medicine. Source publication: 2025-03-17. Source review: 2025-03.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
carnitine palmitoyltransferase II deficiencyMONDO:0015515 · Evaluated 2018-03-27	Autosomal recessive	DefinitiveFatty Acid Oxidation Disorders Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 1,201
Submissions for variants in or overlapping this gene: 2,959
Submissions explicitly reporting this gene: 2,918
Alleles reported pathogenic / likely pathogenic: 261
VariationIDs with uncertain significance: 418
VariationIDs with conflicting classifications: 83

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about CPT2?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 261 alleles in CPT2 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in CPT2.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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