CPT2
protein-codingcarnitine palmitoyltransferase 2
Gene summary
The protein encoded by this gene is a nuclear protein which is transported to the mitochondrial inner membrane. Together with carnitine palmitoyltransferase I, the encoded protein oxidizes long-chain fatty acids in the mitochondria. Defects in this gene are associated with mitochondrial long-chain fatty-acid (LCFA) oxidation disorders. [provided by RefSeq, Jul 2008]
- CPT1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009704
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0012136
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0015515
Submitter: Myriad Women's Health
Inheritance Pattern: AR
Disease ID:MONDO:0010914
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0012136
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0015515
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:0015515
Submitter: ClinGen
Inheritance Pattern: Unknown
Disease ID:MONDO:0013633
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Cardiovascular; Gastrointestinal; Musculoskeletal; Neurologic; Renal
Intervention: Biochemical; Musculoskeletal; Pharmacogenomic; Renal
Rationale: There are diverse presentations, including a severe infantile hepatocardiomuscular and myopathic forms, and optimal treatment may vary according to the phenotype; Severe, life-threatening rhabdomyolytic episodes can be precipitated by illness, prolonged exercise, dehydration, or fasting, and medical therapy (eg, with fibrates), along with avoidance of these precipitating factors (and interventions such as IV glucose in the instance of acute episodes) can be beneficial; Dietary measures (high-carbohydrate/low-fat diet) and medications (eg, carnitine, triheptanoin) can be beneficial; Certain medications should be avoided, including valproate, general anesthesia, ibuprofen, and high-dose diazepam
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CPT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000098.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 10 | 365 | 1 | 376 | ||
| missense | 8 | 44 | 400 | 27 | 2 | 481 |
| nonsense | 24 | 29 | 1 | 54 | ||
| start loss | 0 | |||||
| frameshift | 61 | 90 | 5 | 156 | ||
| splice donor/acceptor (+/-2bp) | 3 | 7 | 10 | |||
| Total | 96 | 170 | 416 | 392 | 3 | 1077 |
Highest pathogenic variant AF is 0.0016730893
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000089.1 | 5 | MANE Select | |
| Ensembl | ENSP00000360541.3 | 5 | MANE Select | |
| RefSeq | NP_001317518.1 | 5 | Standard | |
| Ensembl | ENSP00000490867.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Thermogenesis - Homo sapiens (human)
- Fatty acid degradation - Homo sapiens (human)
- PPAR signaling pathway - Homo sapiens (human)
- Long chain acyl-CoA dehydrogenase deficiency (LCAD)
- Trifunctional protein deficiency
Biological Process
- fatty acid beta-oxidation
- carnitine shuttle
- regulation of lipid metabolic process
- positive regulation of cold-induced thermogenesis
Molecular Function
- carnitine O-palmitoyltransferase activity
Cellular Component
- nucleoplasm
- nucleolus
- mitochondrion
- mitochondrial inner membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000371486
- Coding exons
- 5
- Length
- 17769
- Individuals with no LoFs
- 125613
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 135
- Defined
- 125748
- p
- 0.000537
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.397 | 337 | 358 | 0.941 | 0.0000200 | 4322 |
| Missense (PolyPhen) | 125 | 139.84 | 0.8939 | 1652 | ||
| Synonymous | -1.17 | 165 | 147 | 1.12 | 0.00000831 | 1330 |
| Loss of Function | 0.946 | 17 | 21.8 | 0.781 | 0.00000118 | 234 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00037 | rare |
| Latino/Admixed American | 0.00032 | 0.00032 | rare |
| Ashkenazi Jewish | 0.0049 | 0.0049 | notable |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0.00018 | 0.00018 | rare |
| European (Non-Finnish) | 0.00042 | 0.00042 | rare |
| South Asian | 0.00033 | 0.00033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Disease
- DISEASE: Carnitine palmitoyltransferase 2 deficiency, myopathic, stress-induced (CPT2D) [MIM:255110]: An autosomal recessive disorder of mitochondrial long-chain fatty acid oxidation, characterized by recurrent myoglobinuria, episodes of muscle pain, stiffness, and rhabdomyolysis. These symptoms are exacerbated by prolonged exercise, fasting, cold, or viral infection. CPT2DM affects most frequently children or young adults, and severity of attacks is highly variable. Myoglobinuria can cause kidney failure and death. {ECO:0000269|PubMed:10090476, ECO:0000269|PubMed:11477613, ECO:0000269|PubMed:14605500, ECO:0000269|PubMed:14615409, ECO:0000269|PubMed:1528846, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15622536, ECO:0000269|PubMed:7711730, ECO:0000269|PubMed:8358442, ECO:0000269|PubMed:8651281, ECO:0000269|PubMed:9600456, ECO:0000269|PubMed:9758712, ECO:0000269|Ref.13, ECO:0000269|Ref.17}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Carnitine palmitoyltransferase 2 deficiency, infantile (CPT2DI) [MIM:600649]: An autosomal recessive disorder of mitochondrial long-chain fatty acid oxidation, characterized by hepatic or hepato-cardio-muscular manifestations with onset in infancy. Clinical features include hypoketotic hypoglycemia, lethargy, seizures, hepatomegaly, liver dysfunction, cardiomegaly and dilated cardiomyopathy. {ECO:0000269|PubMed:1528846, ECO:0000269|PubMed:8651281}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Carnitine palmitoyltransferase 2 deficiency, lethal neonatal (CPT2DLN) [MIM:608836]: An autosomal recessive disorder of mitochondrial long-chain fatty acid oxidation with fatal outcome, presenting shortly after birth. It is characterized by respiratory distress, seizures, altered mental status, hepatomegaly, cardiomegaly, cardiac arrhythmia, and, in many cases, dysmorphic features, renal dysgenesis, and migration defects. recessive. {ECO:0000269|PubMed:11477613}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Encephalopathy, acute, infection-induced, 4 (IIAE4) [MIM:614212]: A severe neurologic complication of an infection. It manifests within days in otherwise healthy children after common viral infections, without evidence of viral infection of the brain or inflammatory cell infiltration. In affected children, high- grade fever is accompanied within 12 to 48 hours by febrile convulsions, often leading to coma, multiple-organ failure, brain edema, and high morbidity and mortality. The infections are usually viral, particularly influenza, although other viruses and even mycoplasma have been found to cause the disorder. {ECO:0000269|PubMed:15811315, ECO:0000269|PubMed:21697855}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. CPT2 polymorphic variants do not cause classical carnitine palmitoyltransferase 2 deficiency, and patients harboring any of them are asymptomatic most of the time. However, they are prone to viral infection (high fever)-related encephalopathy (PubMed:21697855). {ECO:0000269|PubMed:21697855}.;
Recessive Scores
- pRec
- 0.101
Intolerance Scores
- LoFtool
- 0.131
- RVIS EVS
- 0.51
- RVIS percentile EVS
- 80.31
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.763
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |