Polycystic kidney disease, adult type: genes and variants

Genes linked to Polycystic kidney disease, adult type

• PKD1: Polycystin-1

  Together with polycystin-2, it participates in tubular signaling, mechanosensation, and maintenance of renal epithelial architecture. Loss-of-function variants are the most common cause of autosomal dominant polycystic kidney disease.

  61 disease-causing and 1,129 uncertain variants in PKD1 are linked to Polycystic kidney disease, adult type.

• PKD2: Polycystin-2

  It provides calcium-permeable polycystin channel activity and forms signaling complexes with polycystin-1 in renal epithelial cells. Loss-of-function variants cause autosomal dominant polycystic kidney disease, generally with a milder average course than PKD1-associated disease.

  1 disease-causing and 0 uncertain variants in PKD2 are linked to Polycystic kidney disease, adult type.

Weakly linked (only a few uncertain records): PLP1.

Where Polycystic kidney disease, adult type variants cluster

• PKD1 PLAT (positions 3118–3233): 7 of 61 disease-causing changes, 4.3× more than its size predicts.
• PKD1 Extracellular (positions 3687–3901): 8 of 61 disease-causing changes, 2.6× more than its size predicts.
• PKD1 REJ (positions 2146–2833): 16 of 61 disease-causing changes, 1.6× more than its size predicts.
• PKD1 WSC (positions 177–271): 4 of 61 disease-causing changes, 3.0× more than its size predicts.
• PKD1 PKD 14 (positions 1807–1890): 3 of 61 disease-causing changes, 2.5× more than its size predicts.

Known disease-causing variants in Polycystic kidney disease, adult type

Showing 60 of 62.

Which prediction tools work for Polycystic kidney disease, adult type

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

• CATVariant: 90 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• REVEL: 90 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• CADD: 88 out of 100
• MetaLR: 88 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• SIFT: 86 out of 100
• PolyPhen-2: 83 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• phyloP: 74 out of 100

Same protein, different disease

• Autosomal dominant polycystic kidney disease is also caused by PKD1 variants; they fall mostly in different places as the Polycystic kidney disease, adult type variants (6 disease-causing).
• Polycystic kidney disease is also caused by PKD2 variants; they fall mostly in different places as the Polycystic kidney disease, adult type variants (7 disease-causing).
• Autosomal dominant polycystic kidney disease is also caused by PKD2 variants; they fall mostly in different places as the Polycystic kidney disease, adult type variants (6 disease-causing).

Diseases related to Polycystic kidney disease, adult type

• Autosomal dominant polycystic kidney disease, also linked to PKD1 and PKD2
• Polycystic kidney disease, also linked to PKD1 and PKD2
• Kidney disorder, also linked to PKD1 and PKD2
• Meckel syndrome, also linked to PKD1 and PKD2
• Chronic kidney disease, also linked to PKD1 and PKD2

Frequently asked questions

Which genes are linked to Polycystic kidney disease, adult type?

In CATVariant, Polycystic kidney disease, adult type is linked to 2 analyzed proteins: PKD1 (Polycystin-1) and PKD2 (Polycystin-2).

How many genetic variants are linked to Polycystic kidney disease, adult type?

1,229 variants: 62 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 1,129 are of uncertain significance or have conflicting reports.

Which uncertain variants in Polycystic kidney disease, adult type 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 Polycystic kidney disease, adult type?

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 23 disease-causing and 141 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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