Carnitine palmitoyl transferase II deficiency, myopathic form: genes and variants
Carnitine palmitoyl transferase II deficiency, myopathic form is linked to 1 analyzed protein (CPT2). 11 DNA variants are known to cause it; 64 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to Carnitine palmitoyl transferase II deficiency, myopathic 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.
11 disease-causing and 64 uncertain variants in CPT2 are linked to Carnitine palmitoyl transferase II deficiency, myopathic form.
Where Carnitine palmitoyl transferase II deficiency, myopathic form variants cluster
- CPT2 Mitochondrial matrix (positions 26–178): 5 of 11 disease-causing changes, 1.9× more than its size predicts.
Known disease-causing variants in Carnitine palmitoyl transferase II deficiency, myopathic form
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| CPT2 R151Q | 151 | Mitochondrial matrix | Disease-causing (★★) |
| CPT2 R151W | 151 | Mitochondrial matrix | Disease-causing (★★) |
| CPT2 P50H | 50 | Mitochondrial matrix | Disease-causing (★★) |
| CPT2 Y120C | 120 | Mitochondrial matrix | Disease-causing (★★) |
| CPT2 P227L | 227 | Mitochondrial matrix | Disease-causing (★★) |
| CPT2 I502T | 502 | Mitochondrial matrix | Disease-causing (★★) |
| CPT2 S113L | 113 | Mitochondrial matrix | Disease-causing (★★) |
| CPT2 R631C | 631 | Mitochondrial matrix | Disease-causing (★★) |
| CPT2 F383Y | 383 | Mitochondrial matrix | Disease-causing (★★) |
| CPT2 Y628S | 628 | Mitochondrial matrix | Disease-causing (★★) |
| CPT2 F448L | 448 | Mitochondrial matrix | Disease-causing |
Which prediction tools work for Carnitine palmitoyl transferase II deficiency, myopathic form
How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).
- REVEL: 91 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- CATVariant: 89 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- CADD: 88 out of 100
- PolyPhen-2: 87 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- phyloP: 76 out of 100
- SIFT: 73 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, myopathic form variants (15 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, myopathic form 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 palmitoyl transferase II deficiency, myopathic form 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 palmitoyl transferase II deficiency, myopathic form variants (8 disease-causing).
Diseases related to Carnitine palmitoyl transferase II deficiency, myopathic 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, 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 palmitoyl transferase II deficiency, myopathic form?
In CATVariant, Carnitine palmitoyl transferase II deficiency, myopathic 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, myopathic form?
91 variants: 11 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 64 are of uncertain significance or have conflicting reports.
Which uncertain variants in Carnitine palmitoyl transferase II deficiency, myopathic 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, myopathic form?
Among tools not trained on clinical labels, CADD separates this disease's known disease-causing variants from harmless ones best (AUROC 0.88, based on 10 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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