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Table 1 Clinical features and genetic alterations of the patients

From: Ultra-rare renal diseases diagnosed with whole-exome sequencing: Utility in diagnosis and management

Pt No Sex Phenotype and symptoms Age at WES (yr) Renal function Affected gene Nucleotide change Amino acid change Inheritance ACMG classification Reference Incidence (number of pts)
1 F Renal insufficiency with hyperuricemic crisis, family history of ESRD of unknown etiology 59 ESRD UMOD c.626G > T p.Gly209Val AD LP New unknown
2 M Recurrent ureter stone since the age of 30 with renal insufficiency 41 ESRD APRT c.G294A p.Trp98* AR P [14] Unknown, 1/5000–1/10000
3 F Dysmorphic face with cleft palate, short stature, scoliosis, microscopic hematuria with renal insufficiency from glomerular mesangiolysis 20 CKD Stage2 MAF c.185C > T p.Thr62Met AD P New up to 21
4 M ESRD at 4 years old with unknown etiology, short stature with a narrow chest, dense skull, family history of same clinical phenotype 18 ESRD IFT140 c.2650C > T
c.4309G > A
p.Arg884Trp
p.Glu1437Lys
AR VUS
VUS
Found in the general population up to 20
5 M Early-onset renal insufficiency with small kidneys 11 CKD
Stage 3
PAX2 c.124_139del p.Val42Argfs*36 AD P New up to 60
6 M Early-onset renal insufficiency with small kidneys 10 CKD
Stage 2
PAX2 c.686-1G > T Splice site variant AD P New up to 60
7 F Nephrocalcinosis, hypercalciuria with persistent nephrocalcinosis 9 Normal CYP24A1 c.376C > T p.Pro126Ser AR VUS New unknown
8 F Neonatal hypocalcemia, hypomagnesemia with tetany 7 Normal TRPM6 c.1421A > G
c.4917_4918delAA
p.Tyr474Cys
p.Lys1639Ansfs*4
AR LP
P
New unknown
9 F Both renal hypoplasia with multiple cysts, anuria after 17 days of birth 0.2 ESRD PAX2 c.76dupG p.Val26Glyfs*28 AD P [20] up to 60
  1. Pt, patient; WES, whole-exome sequencing; Ref, reference; AR, autosomal recessive; AD, autosomal dominant; ESRD, end-stage renal disease; CKD, chronic kidney disease; ACMG, American College of Medical Genetics and Genomics; LP, likely pathogenic; P, pathogenic; VUS, variant of unknown significance
  2. *Nonsense mutation
  3. Variant was not found in NCBI (National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov), gnomAD (Genome Aggregation Database, https://gnomad.broadinstitute.org), UCSC Genome Browser (University of California, Santa Cruz Genome Browser, https://genome.ucsc.edu), or HGMD (The Human Gene Mutation Database, http://www.hgmd.cf.ac.uk)