Table 1 Diagnostic pathogenic variants.

From: Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study

Gene

Variant

Type

ACMG classification

Individual

Previous Clinical diagnosis

Kidney biopsy

Genetic diagnosis anticipated clinically

COL4A5

c.875G>A, p.(Gly292Glu)

SNV

class 4 (p = 0.97)

Ind_924166

gout

yes

yes

c.1871G>A, p.(Gly624Asp)

SNV

class 5 (p = 1.00)

Ind_734367

hereditary disorders

no

no

c.2023G>A, p.(Gly675Ser)

SNV

class 4 (p = 0.90)

Ind_408589

hereditary disorders

no

yes

c.1871G>A, p.(Gly624Asp)

SNV

class 5 (p = 1.00)

Ind_553814

hereditary disorders

yes

no

c.1871G>A, p.(Gly624Asp)

SNV

class 5 (p = 1.00)

Ind_674188

hereditary disorders

yes

no

c.1894G>A, p.(Gly632Ser)

SNV

class 4 (p = 0.97)

Ind_523397

hereditary disorders

yes

no

c.3196G>A, p.(Gly1066Ser)

SNV

class 5 (p = 1.00)

Ind_120641

hereditary disorders

yes

no

c.3275G>A, p.(Gly1092Glu)

SNV

class 4 (p = 0.90)

Ind_320658

hereditary disorders

yes

no

chrX:g.(?_107683936)_(107918029_?)del

CNV

class 5

Ind_739404

hereditary disorders

yes

no

c.1871G>A, p.(Gly624Asp)

SNV

class 5 (p = 1.00)

Ind_276132

IgA nephropathy

yes

no

c.3508G>A, p.(Gly1170Ser)

SNV

class 5 (p = 1.00)

Ind_245000

IgA nephropathy; chronic glomerulonephritis

no

no

c.1871G>A, p.(Gly624Asp)

SNV

class 5 (p = 1.00)

Ind_768032

nephrosclerosis

yes

no

c.1871G>A, p.(Gly624Asp)

SNV

class 5 (p = 1.00)

Ind_197144

nephrosclerosis

yes

no

c.1871G>A, p.(Gly624Asp)

SNV

class 5 (p = 1.00)

Ind_905960

nephrosclerosis

yes

no

c.1871G>A, p.(Gly624Asp)

SNV

class 5 (p = 1.00)

Ind_540052

nephrosclerosis; gout

yes

no

c.1871G>A, p.(Gly624Asp)

SNV

class 5 (p = 1.00)

Ind_902111

unknown

no

no

COL4A4

c.5048G>A, p.(Cys1683Tyr)

SNV

class 4 (p = 0.90)

Ind_330223

hereditary disorders

no

yes

c.2242G>A, p.(Gly748Ser)

SNV

class 4 (p = 0.90)

Ind_203846

IgA nephropathy

yes

no

c.4832G>A, p.(Gly1611Glu)

SNV

class 4 (p = 0.90)

Ind_641864

IgA nephropathy

yes

no

c.735G>A, p.[(=);0?]

SNV

class 4 (p = 0.90)

Ind_251195

nephrosclerosis

yes

no

c.3707G>A, p.(Gly1236Glu)

SNV

class 4 (p = 0.90)

Ind_591007

nephrosclerosis; interstitial nephritis

yes

no

c.93_94del, p.(Ser32Cysfs*28)

indel

class 5 (p = 1.00)

Ind_805187

unknown

no

no

c.736G>A, p.(Gly246Ser)

SNV

class 4 (p = 0.97)

Ind_218190

unknown

no

no

c.1935_1952del, p.(Pro647_Val652del)

indel

class 4 (p = 0.99)

Ind_712115

unknown

no

no

COL4A3

c.688G>A, p.(Gly230Ser)

SNV

class 4 (p = 0.90)

Ind_800358

gout

no

no

c.1595G>A, p.(Gly532Asp)

SNV

class 4 (p = 0.97)

Ind_977173

gout; hereditary disorders

no

no

c.1559G>A, p.(Gly520Asp)

SNV

class 4 (p = 0.97)

Ind_553814

hereditary disorders

yes

no

c.4388G>C, p.(Gly1463Ala)

SNV

class 4 (p = 0.90)

Ind_458246

IgA nephropathy

yes

no

HNF1B

chr17:g.(?_34914860)_(36105069_?)dup

CNV

class 5

Ind_207310

nephrosclerosis

no

no

c.742C>G, p.(Gln248Glu)

SNV

class 4 (p = 0.90)

Ind_197144

nephrosclerosis

yes

no

c.810–1G>A, p.0?

SNV

class 5 (p = 1.00)

Ind_861194

others

no

no

chr17:g.(?_34475214)_(36504124_?)del

CNV

class 5

Ind_958149

unknown

no

no

UMOD

c.608G>A, p.(Cys203Tyr)

SNV

class 5 (p = 1.00)

Ind_725568

interstitial nephritis

no

no

c.673G>T, p.(Gly225Cys)

SNV

class 4 (p = 0.90)

Ind_395543

interstitial nephritis

yes

no

c.548G>A, p.(Cys183Tyr)

SNV

class 4 (p = 0.97)

Ind_777983

nephrosclerosis; interstitial nephritis

no

no

MT-TF

chrM:g.616T>C

SNV

class 5 (p = 0.99)

Ind_151715

unknown

no

no

  1. List of all individuals who had a (likely) pathogenic variant identified, as well as their previous diagnostic group/s and clinical anticipation of the hereditary background and whether they had a renal biopsy. Please compare Supplementary Notes for the calculation of the Bayesian p values and File S3 for detailed criteria applied in manual ACMG variant classification.
  2. Note that the calculated posterior p values indicate a pathogenic classification for some variants, but this can’t be reached with the current combination rules requiring one strong criteria for class 5.
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