Carnitine deficiency: genes and variants

Genes linked to Carnitine deficiency

• SLC22A5: Organic cation/carnitine transporter 2

  It imports carnitine into cells and reabsorbs filtered carnitine in the kidney, maintaining the stores required for mitochondrial long-chain fatty-acid oxidation. Biallelic loss-of-function variants cause primary carnitine deficiency with hypoketotic hypoglycemia, skeletal weakness, or cardiomyopathy.

  22 disease-causing and 17 uncertain variants in SLC22A5 are linked to Carnitine deficiency.

Where Carnitine deficiency variants cluster

• SLC22A5 Cytoplasmic (positions 1–20): 3 of 22 disease-causing changes, 3.8× more than its size predicts.
• SLC22A5 Transmembrane (positions 463–483): 3 of 22 disease-causing changes, 3.6× more than its size predicts.

Known disease-causing variants in Carnitine deficiency

Which prediction tools work for Carnitine deficiency

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

• CATVariant: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• REVEL: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• CADD: 100 out of 100
• PolyPhen-2: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• SIFT: 100 out of 100
• phyloP: 96 out of 100

Same protein, different disease

• Renal carnitine transport defect is also caused by SLC22A5 variants; they fall partly in the same places as the Carnitine deficiency variants (79 disease-causing).

Diseases related to Carnitine deficiency

• Renal carnitine transport defect, also linked to SLC22A5

Frequently asked questions

Which genes are linked to Carnitine deficiency?

In CATVariant, Carnitine deficiency is linked to 1 analyzed protein: SLC22A5 (Organic cation/carnitine transporter 2).

How many genetic variants are linked to Carnitine deficiency?

39 variants: 22 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 17 are of uncertain significance or have conflicting reports.

Which uncertain variants in Carnitine deficiency 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 deficiency?

Among tools not trained on clinical labels, CADD separates this disease's known disease-causing variants from harmless ones best (AUROC 1.00, based on 20 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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