Carnitine palmitoyltransferase II deficiency: genes and variants

Genes linked to Carnitine palmitoyltransferase II deficiency

• CPT2: Carnitine O-palmitoyltransferase 2, mitochondrial

  It converts long-chain acylcarnitines back to acyl-CoA inside mitochondria, allowing long-chain fatty acids to undergo beta-oxidation. Biallelic deficiency causes a spectrum from lethal neonatal disease to recurrent exercise- or fasting-triggered rhabdomyolysis.

  15 disease-causing and 265 uncertain variants in CPT2 are linked to Carnitine palmitoyltransferase II deficiency.

Known disease-causing variants in Carnitine palmitoyltransferase II deficiency

Uncertain variants in Carnitine palmitoyltransferase II deficiency that look disease-causing

Which prediction tools work for Carnitine palmitoyltransferase II deficiency

How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).

• CATVariant: 92 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• REVEL: 90 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• PolyPhen-2: 90 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• CADD: 87 out of 100
• SIFT: 79 out of 100
• phyloP: 71 out of 100

Same protein, different disease

• Carnitine palmitoyl transferase II deficiency, myopathic form is also caused by CPT2 variants; they fall mostly in different places as the Carnitine palmitoyltransferase II deficiency variants (11 disease-causing).
• Carnitine palmitoyl transferase II deficiency, severe infantile form is also caused by CPT2 variants; they fall mostly in different places as the Carnitine palmitoyltransferase II deficiency variants (11 disease-causing).
• Carnitine palmitoyl transferase II deficiency, neonatal form is also caused by CPT2 variants; they fall mostly in different places as the Carnitine palmitoyltransferase II deficiency variants (9 disease-causing).
• Encephalopathy, acute, infection-induced, susceptibility to, 4 is also caused by CPT2 variants; they fall mostly in different places as the Carnitine palmitoyltransferase II deficiency variants (8 disease-causing).

Diseases related to Carnitine palmitoyltransferase II deficiency

• Carnitine palmitoyl transferase II deficiency, severe infantile form, also linked to CPT2
• Carnitine palmitoyl transferase II deficiency, myopathic form, also linked to CPT2
• Carnitine palmitoyl transferase II deficiency, neonatal form, also linked to CPT2
• Encephalopathy, acute, infection-induced, susceptibility to, 4, also linked to CPT2

Frequently asked questions

Which genes are linked to Carnitine palmitoyltransferase II deficiency?

In CATVariant, Carnitine palmitoyltransferase II deficiency is linked to 1 analyzed protein: CPT2 (Carnitine O-palmitoyltransferase 2, mitochondrial).

How many genetic variants are linked to Carnitine palmitoyltransferase II deficiency?

338 variants: 15 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 265 are of uncertain significance or have conflicting reports.

Which uncertain variants in Carnitine palmitoyltransferase II deficiency look disease-causing?

1 uncertain variants reach the likely-pathogenic range of the ACMG/AMP points scale on computable evidence, for example CPT2 R296Q. These are leads for expert review, not diagnoses.

Which variant effect predictor works best for Carnitine palmitoyltransferase II deficiency?

Among tools not trained on clinical labels, CADD separates this disease's known disease-causing variants from harmless ones best (AUROC 0.87, based on 9 disease-causing and 9 harmless variants).

About this data

Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.

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