Renal carnitine transport defect: genes and variants

Genes linked to Renal carnitine transport defect

• 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.

  79 disease-causing and 344 uncertain variants in SLC22A5 are linked to Renal carnitine transport defect.

Where Renal carnitine transport defect variants cluster

• SLC22A5 Cytoplasmic (positions 1–20): 10 of 79 disease-causing changes, 3.5× more than its size predicts.
• SLC22A5 Cytoplasmic (positions 219–232): 7 of 79 disease-causing changes, 3.5× more than its size predicts.
• SLC22A5 Transmembrane (positions 21–41): 8 of 79 disease-causing changes, 2.7× more than its size predicts.
• SLC22A5 Transmembrane (positions 463–483): 8 of 79 disease-causing changes, 2.7× more than its size predicts.
• SLC22A5 Cytoplasmic (positions 164–172): 4 of 79 disease-causing changes, 3.1× more than its size predicts.

Known disease-causing variants in Renal carnitine transport defect

Showing 60 of 79.

Uncertain variants in Renal carnitine transport defect that look disease-causing

Which prediction tools work for Renal carnitine transport defect

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

• REVEL: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• PolyPhen-2: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• CATVariant: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• SIFT: 99 out of 100
• CADD: 97 out of 100
• phyloP: 92 out of 100

Diseases related to Renal carnitine transport defect

• Carnitine deficiency, also linked to SLC22A5

Frequently asked questions

Which genes are linked to Renal carnitine transport defect?

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

How many genetic variants are linked to Renal carnitine transport defect?

433 variants: 79 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 344 are of uncertain significance or have conflicting reports.

Which uncertain variants in Renal carnitine transport defect look disease-causing?

9 uncertain variants reach the likely-pathogenic range of the ACMG/AMP points scale on computable evidence, for example SLC22A5 G15E, SLC22A5 R83P, SLC22A5 G12D, SLC22A5 C50W and SLC22A5 A214V. These are leads for expert review, not diagnoses.

Which variant effect predictor works best for Renal carnitine transport defect?

Among tools not trained on clinical labels, SIFT separates this disease's known disease-causing variants from harmless ones best (AUROC 0.99, based on 75 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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