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. 2017 May 31;28(10):2901–2914. doi: 10.1681/ASN.2017010043

Table 3.

Causative mutations in known genes associated with highly penetrant CAKUT phenotype

Patient Renal Phenotypea Extrarenal Phenotype Causal Gene NM_ref Nucleotide Change Protein Change PP2 Sift MT Granthamb GVDVc No. of Missense Deleterious Scores Splice Effect, % ExAC Inheritance Ref.
Rare variants in individuals with CAKUT
 K4 RH Bifid uterus HNF1B 000458 c.[(?_−30)_(*220_?)del];[=] 0 NAd 36
 K50 UMD+ No HNF1B 000458 c.[(?_−30)_(*220_?)del];[=] 0 Affected mothere
 K103 RD+ No HNF1B 000458 c.[(?_−30)_(*220_?)del];[=] 0 Affected mothere
 K124 RD+ No HNF1B 000458 c.[(?_−30)_(*220_?)del];[=] 0 De novod
 K143 RD+ No HNF1B 000458 c.[(?_−30)_(*220_?)del];[=] 0 De novod
 K172 UMD+ Diabetes plus cryptorchidy HNF1B 000458 c.[(?_−30)_(*220_?)del];[=] 0 Affected motherf
 K185 RD No HNF1B 000458 c.[(?_−30)_(*220_?)del];[=] 0 NAd
 K203 RD No HNF1B 000458 c.[(?_−30)_(*220_?)del];[=] 0 NAe
 K170 RH+ No HNF1B 000458 c.[344+2_+5del];[=] −100 0 NAd
 K72 RH Papillary excavation PAX2 003987 c.[(?_−30)_(*220_?)del];[=] 0 Germinal mosaicism/two affected childrene 37
 K62 RH Eye coloboma PAX2 003987 c.[?−30_410+?del];[=] 0 NAd
 K79 RD Papillary coloboma PAX2 003987 c.[44−?_496+?del];[=] 0 De novod
 K117 RH No PAX2 003987 c.[183C>A];[=] p.[Ser61Arg];[=] 1 0 dc 110 C0 4/5 0 De novod
 K133 RH+ Papillary coloboma PAX2 003987 c.[76del];[=] p.[Val26Cysfs*3];[=] 0 Affected motherg 38
 K146 RH+ No PAX2 003987 c.[446del];[=] p.[Pro149Glnfs*10];[=] 0 NAd
 K148 RH No PAX2 003987 c.[76dup];[=] p.[Val26Glyfs*28];[=] 0 Unaffected mother (somatic mosaicism)d 39
 K176 RH+ No PAX2 003987 c.[331G>A];[=] p.[Ala111Thr];[=] 0.998 0 dc 58 C0 4/5 0 Affected mothere 40
 K199 Oth Papillary coloboma PAX2 003987 c.[212G>A];[=] p.[Arg71Lys];[=] 0.974 0 dc 26 C0 3/5 −49 0 NAe,h 41
 K80 UKA+ Preauricular pit plus ear tag EYA1 000503 c.[557−?_1597+?del];[=] 0 Affected motheri
 K78 BKA No EYA1 000503 c.[967–1G>C ]:[=] −100 0 Affected fathere 42
 K119 RH Branchial defect plus deafness EYA1 000503 c.[1459T>C];[=] p.[Ser487Pro];[=] 0.132 0.07 dc 74 C0 2/5 0.0015% NFE Affected fatheri 43
 K135 UKA Preauricular pit EYA1 000503 c.[553C>T];[=] p.[Gln185*];[=] 0 Affected motheri 44
 K145 RH Branchial defect EYA1 000503 c.[1338_1346del];[=] p.[Asn446_Tyr448del];[=] 0 Affected fathere
 K101 UKA Ear tag plus external ear canal stenosis GATA3 001002295 c.[(?_−30)_(*220_?)del];[=] 0 Affected fatherj 45
 K167 UKA Deafness plus intellectual disability GATA3 001002295 c.[(?_−30)_(*220_?)del];[=] 0 NAd
 K48 RH+ No GATA3 001002295 c.[829C>T];[=] p.[Arg277*];[=] 0 De novod 46
 K158 BKA No ANOS1 000216 c.[?−30_255+?del] 0 Unaffected mothere 47
 K26 BKA No ANOS1 000216 c.[769C>T];[=] p.[Arg257*];[=] 0 NAd 48
 K160 UKA Deafness plus branchial defect plus colobomatous microphtalmia CHD7 017780 c.[5050G>A];[=] p.[Gly1684Ser];[=] 0.929 0 dc 56 C55 5/5 −38 0 Fatherk 49
 K73 RH+ Lissencephaly plus agenesis of corpus callosum KIF14 014875 c.[3567−?_4072+?del];[(3567-?_4072+?del)] 0 NAd
 K195 BKA Craniostenosis plus microcephaly plus agenesis of corpus callosum KIF14 014875 c.[3910C>T];[1090C>T] p.[Gln1304*];[Arg364Cys] 1 0 dc 180 C0 4/5 0 One mutation from each parente
Rare variants in individuals with branchial signs and/or ear defect without CAKUT phenotype
 BO4 No Branchial defect plus preauricular pit plus deafness EYA1 000503 c.[1081C>T];[=] p.[Arg361*];[=] 0 De novod 50
 BO5 No Branchial defect plus deafness SIX1 005982 c.[273_274insC];[=] p.[Tyr92Leufs*62];[=] 0 Affected motheri

PP2, Polyphen2; MT, MutationTaster; GVDV, Grantham variation score and Grantham difference score; RH, renal hypoplasia; NA, not available; UMD, unilateral multicystic dysplasia; RD, renal dysplasia; Oth, other; UKA, unilateral kidney agenesis; BKA, bilateral kidney agenesis; NFE, non-Finnish European population.

a

Plus indicates presence of (a) secondary CAKUT phenotype(s).

b

Considered as deleterious when ≥50.

c

Considered as deleterious when ≥C25.

d

Patient with sporadic case.

e

Patient with familial case.

f

Parent affected with diabetes without renal defect.

g

Parent affected with coloboma without renal defect.

h

Mutation transmitted to a son with coloboma without renal defect.

i

Parent affected with BO without renal defect.

j

Parent affected with deafness without renal defect.

k

Clinical information not available.