Carnitine palmitoyl transferase II deficiency, neonatal form: genes and variants
Explore variant evidence for Carnitine palmitoyl transferase II deficiency, neonatal form across 1 analyzed protein (CPT2). Linked ClinVar records include 9 pathogenic or likely pathogenic variants, 52 variants of uncertain significance and 17 with conflicting classifications.
Coverage includes proteins already analyzed in CATVariant, not every gene involved in this condition. Database links are associations, not an assessment of clinical gene–disease validity. Computable evidence prioritizes variants for expert review and does not reclassify them. Counts refer to the selected disease label.
Data updated 2026-10-10. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
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 ClinVar pathogenic / likely pathogenic and 69 uncertain variants in CPT2 have source records linked to Carnitine palmitoyl transferase II deficiency, neonatal form. Association strength is not clinical gene validity.
ClinVar pathogenic and likely pathogenic variants linked to Carnitine palmitoyl transferase II deficiency, neonatal form
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| CPT2 R151Q | 151 | Mitochondrial matrix | Pathogenic / likely pathogenic (★★) |
| CPT2 R503C | 503 | Mitochondrial matrix | Pathogenic / likely pathogenic (★★) |
| CPT2 Y479C | 479 | Mitochondrial matrix | Pathogenic / likely pathogenic (★★) |
| CPT2 I502T | 502 | Mitochondrial matrix | Pathogenic / likely pathogenic (★★) |
| CPT2 S113L | 113 | Mitochondrial matrix | Pathogenic / likely pathogenic (★★) |
| CPT2 R631C | 631 | Mitochondrial matrix | Pathogenic / likely pathogenic (★★) |
| CPT2 F383Y | 383 | Mitochondrial matrix | Pathogenic / likely pathogenic (★★) |
| CPT2 Y628S | 628 | Mitochondrial matrix | Pathogenic / likely pathogenic (★★) |
| CPT2 G345R | 345 | Mitochondrial matrix | Pathogenic / likely pathogenic (★) |
Which prediction tools work for Carnitine palmitoyl transferase II deficiency, neonatal form
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- 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 also has ClinVar records linked to CPT2 variants; they fall mostly in different places as the Carnitine palmitoyl transferase II deficiency, neonatal form variants (15 pathogenic / likely pathogenic).
- Carnitine palmitoyl transferase II deficiency, myopathic form also has ClinVar records linked to CPT2 variants; they fall mostly in different places as the Carnitine palmitoyl transferase II deficiency, neonatal form variants (11 pathogenic / likely pathogenic).
- Carnitine palmitoyl transferase II deficiency, severe infantile form also has ClinVar records linked to CPT2 variants; they fall mostly in different places as the Carnitine palmitoyl transferase II deficiency, neonatal form variants (11 pathogenic / likely pathogenic).
- Encephalopathy, acute, infection-induced, susceptibility to, 4 also has ClinVar records linked to CPT2 variants; they fall mostly in different places as the Carnitine palmitoyl transferase II deficiency, neonatal form variants (8 pathogenic / likely pathogenic).
Diseases related to Carnitine palmitoyl transferase II deficiency, neonatal form
- Carnitine palmitoyltransferase II deficiency, also linked to CPT2
- Carnitine palmitoyl transferase II deficiency, myopathic form, also linked to CPT2
- Carnitine palmitoyl transferase II deficiency, severe infantile form, also linked to CPT2
- Encephalopathy, acute, infection-induced, susceptibility to, 4, also linked to CPT2
Frequently asked questions
Which genes have records linked to Carnitine palmitoyl transferase II deficiency, neonatal form?
This view contains 1 analyzed proteins: CPT2. Links come from clinical records and association databases. They do not imply that every listed gene is a validated cause, and missing genes may not yet be analyzed.
What do the clinical classifications mean?
Linked records include 9 pathogenic or likely pathogenic variants, 52 variants of uncertain significance and 17 with conflicting classifications. Labels summarize source records; multi-condition records may not make a separate assertion for this disease. Check the original record and review status.
Does the evidence score change a VUS classification?
No. 0 VUS or conflicting variants reach the likely-pathogenic points range on the computable criteria available here. This is a research prioritization signal, not a clinical classification. Patient, family and other required evidence may be missing.
Can I download the variant evidence?
Download the CSV for all 92 variants in the selected disease scope, including clinical labels, review status, evidence criteria, predictor scores, functional measurements and population frequency where available.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from eligible public CATVariant analyses 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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