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Table 1 PKHD1 variants details

From: Use of patient derived urine renal epithelial cells to confirm pathogenicity of PKHD1 alleles

Variant Molecular consequence db SNP ID Accession number (ClinVar or HGMD) Clinical significance on ClinVar/HGMD Allele frequency (GnomADe) SIFT
[28]
PolyPhen
[29]
CADD
[30]
REVEL
[31]
References
c.6900C > T; (p.Asn2300=) synonymous rs776060304 VCV000558073 Uncertain significance T = 0.000016 (4/251312) N/A N/A 9 (likely benign) N/A [32,33,34]
c.7964A > C; p.(His2655Pro) missense rs748196998 CM163038 Likely disease-causing C = 0.000004 (1/251258) 0
(deleterious)
0.994 (probably damaging) 24 (likely benign) 0.819 (likely disease causing) [35]
c.6900C > G; (p.Asn2300Lys) missense rs776060304 VCV000552623 Uncertain significance N/A 0
(deleterious)
0.999 (probably damaging) 22 (likely benign) 0.489 (likely benign) [36]
c.7964A > G; p.(His2655Arg) missense N/A CM1612097 Pathogenic N/A 0
(deleterious)
0.990 (probably damaging) 24 (likely benign) 0.786 (likely disease causing) [36]
  1. Molecular consequence, db SNP ID, variant accession number, clinical significance, allele frequency and pathogenicity prediction values according to a range of different algorithms for the two variants identified in the proband (c.6900C > T (p.Asn2300=); 7964A > C; p.(His2655Pro), in bold) and two different variants described in the literature that change the same nucleotides (c.6900C > G (p.Asn2300Lys); c.7964A > G; p.(His2655Arg))