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

BMC Nephrology

Table 1 PKHD1 variants details

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]

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))

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