Table 1 Recessive variant in CYS1 in one family with cystic kidney disease.

From: Cystin genetic variants cause autosomal recessive polycystic kidney disease associated with altered Myc expression

Family

Nucleotide change

Amino acid change

Exon

(Zyg, Seg)

In silico

Severity Scores

gnomAD

(H/h/T)

Sex

Ethnic origin

PC

Clinical phenotype

B783

c.318 + 5G > A

Splice

1 (Hom, B)

CADD 17.06a

HSF 13.17b

MaxEnt 62.8%c

NNS 71.3%c

0/0/

 ~ 251,000

M

Egypt

Y

Initial Onset: 5 years, polyuria, polydipsia

Serum Studies: Cr 0.6 mg/dL

RUS: bilateral cortical and medullary cysts

Extra-renal: Mild congenital hepatic fibrosis

  1. B, both parents appropriately heterozygous; CADD, Combined Annotation-Dependent Depletion prediction score; Cr, serum creatinine; gnomAD, Genome Aggregation database; H, homozygotes in gnomAD; h, heterozygous alleles in gnomAD; Hom, homozygous zygosity; HSF, HSF splice prediction score; M, male; MaxEnt, MaxEnt splice prediction score; NNS, NNSPLICE splice-site variant prediction score; PC, parental consanguinity; RUS, renal ultrasound; Seg, segregation; T, total alleles in gnomAD; Y, yes; Zyg, zygosity.
  2. aCADD scores between 10 and 20 are in the 1–10% most deleterious substitutions possible in human genome in terms of predicted effect on the gene product.
  3. bPredicts wildtype site broken by this change.
  4. cPercentage reflects expected reduction in splicing at this donor site as consequence of change.
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