CPT2

protein-coding

carnitine 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]

Previous symbols:
  • CPT1

MANE transcript

NM_000098.3

Inheritance

AR

ClinVar variants

P:266U:416B:395

Top phenotype

Carnitine palmitoyltransferase II deficiency, myopathic, stress-induced; Carnitine palmitoyltransferaseII deficiency, infantile

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr1:53,196,792-53,214,197

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~17.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

carnitine palmitoyl transferase II deficiency, myopathic formSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009704

Submitter: Orphanet

carnitine palmitoyl transferase II deficiency, neonatal formSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012136

Submitter: Labcorp Genetics (formerly Invitae)

carnitine palmitoyltransferase II deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0015515

Submitter: Myriad Women's Health

carnitine palmitoyl transferase II deficiency, severe infantile formSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010914

Submitter: Orphanet

carnitine palmitoyl transferase II deficiency, neonatal formSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0012136

Submitter: Orphanet

carnitine palmitoyltransferase II deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0015515

Submitter: Natera

carnitine palmitoyltransferase II deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0015515

Submitter: ClinGen

encephalopathy, acute, infection-induced, susceptibility to, 4LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0013633

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Carnitine palmitoyltransferase II deficiency, myopathic, stress-induced; Carnitine palmitoyltransferaseII deficiency, infantileAR

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

Refs: 5416202; 123038; 187736; 736528; 272487; 2748260; 2712755; 1999498; 1940982; 1528846; 8358442; 8201482; 8651281; 8786066; 8682496; 11389301; 11477613; 11595519; 12410208; 12673791; 15363638; 15642848; 15622536; 18471680; 18550408; 18925671; 19228633; 19335026; 20661589; 20301431; 20505667; 20543534; 20810031; 21641254; 21913903; 23184072; 23326270; 33610471Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CPT2 variants in ClinVar

27 Conditions Cataloged
Carnitine palmitoyltransferase II deficiencyTotal: 1003
Carnitine palmitoyl transferase II deficiency, severe infantile formTotal: 262
Encephalopathy, acute, infection-induced, susceptibility to, 4Total: 242
Carnitine palmitoyl transferase II deficiency, neonatal formTotal: 230
Carnitine palmitoyl transferase II deficiency, myopathic formTotal: 224
not providedTotal: 211
not specifiedTotal: 105
Inborn genetic diseasesTotal: 78

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.

EffectPLPVUSLBBSum
synonymous
10
clinvar
365
clinvar
1
clinvar
376
missense
8
clinvar
44
clinvar
400
clinvar
27
clinvar
2
clinvar
481
nonsense
24
clinvar
29
clinvar
1
clinvar
54
start loss
0
frameshift
61
clinvar
90
clinvar
5
clinvar
156
splice donor/acceptor (+/-2bp)
3
clinvar
7
clinvar
10
Total9617041639231077

Highest pathogenic variant AF is 0.0016730893

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000098.3RefSeqNP_000089.15MANE Select
ENST00000371486.4EnsemblENSP00000360541.35MANE Select
NM_001330589.2RefSeqNP_001317518.15Standard
ENST00000635862.1EnsemblENSP00000490867.16Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.3973373580.9410.00002004322
Missense (PolyPhen)125139.840.89391652
Synonymous-1.171651471.120.000008311330
Loss of Function0.9461721.80.7810.00000118234

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000370.00037rare
Latino/Admixed American0.000320.00032rare
Ashkenazi Jewish0.00490.0049notable
East Asian0.000380.00038rare
Finnish0.000180.00018rare
European (Non-Finnish)0.000420.00042rare
South Asian0.000330.00033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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