Carnitine palmitoyl transferase II deficiency, neonatal form: genes and variants

Genes linked to Carnitine palmitoyl transferase II deficiency, neonatal form

• 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.

  9 disease-causing and 69 uncertain variants in CPT2 are linked to Carnitine palmitoyl transferase II deficiency, neonatal form.

Known disease-causing variants in Carnitine palmitoyl transferase II deficiency, neonatal form

Which prediction tools work for Carnitine palmitoyl transferase II deficiency, neonatal form

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

• CATVariant: 89 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• PolyPhen-2: 84 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• SIFT: 66 out of 100

Same protein, different disease

• Carnitine palmitoyltransferase II deficiency is also caused by CPT2 variants; they fall mostly in different places as the Carnitine palmitoyl transferase II deficiency, neonatal form variants (15 disease-causing).
• Carnitine palmitoyl transferase II deficiency, myopathic form is also caused by CPT2 variants; they fall mostly in different places as the Carnitine palmitoyl transferase II deficiency, neonatal form 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 palmitoyl transferase II deficiency, neonatal form variants (11 disease-causing).
• Encephalopathy, acute, infection-induced, susceptibility to, 4 is also caused by CPT2 variants; they fall mostly in different places as the Carnitine palmitoyl transferase II deficiency, neonatal form variants (8 disease-causing).

Diseases related to Carnitine palmitoyl transferase II deficiency, neonatal form

• Carnitine palmitoyltransferase II deficiency, also linked to CPT2
• Carnitine palmitoyl transferase II deficiency, severe infantile form, also linked to CPT2
• Carnitine palmitoyl transferase II deficiency, myopathic 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 palmitoyl transferase II deficiency, neonatal form?

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

How many genetic variants are linked to Carnitine palmitoyl transferase II deficiency, neonatal form?

92 variants: 9 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 69 are of uncertain significance or have conflicting reports.

Which uncertain variants in Carnitine palmitoyl transferase II deficiency, neonatal form look disease-causing?

None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.

Which variant effect predictor works best for Carnitine palmitoyl transferase II deficiency, neonatal form?

Among tools not trained on clinical labels, SIFT separates this disease's known disease-causing variants from harmless ones best (AUROC 0.66, based on 9 disease-causing and 10 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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