Disease Mechanisms of Monogenic Congenital Anomalies of the Kidney and Urinary Tract American Journal of Medical Genetics Part C

Abstract

Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) is a developmental disorder of the kidney and/or genito-urinary tract, which results in end stage kidney disease (ESKD) in up to 50% of children. Despite the congenital nature of the disease, CAKUT accounts for almost 10% of adult onset ESKD. Multiple lines of evidence suggest that CAKUT is a Mendelian disorder including the observation of familial clustering of CAKUT. Pathogenesis in CAKUT is embryonic in origin with disturbances of kidney and urinary tract development resulting in a heterogenous range of disease phenotypes. Despite polygenic and environmental factors being implicated, a significant proportion of CAKUT is monogenic in origin with studies demonstrating single gene defects in 10–20% of patients with CAKUT. Here we review monogenic disease causation with emphasis on the etiological role of gene developmental pathways in CAKUT.

Introduction

Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) is a developmental disorder of the kidney and/or genito-urinary tract. It has an estimated prevalence of 1 in every 500 live birth and constitutes 20% of all congenital malformation (Talati et al., 2019). CAKUT is the most common reason for end stage kidney disease (ESKD) in the first three decades of life, accounting for almost 50% of pediatric and 7% for adult onset ESKD (Talati et al., 2019). In adulthood CAKUT is thought to predispose to early onset hypertension and cardiovascular disease (Song & Yosypiv, 2011).

Classification of the CAKUT phenotype

CAKUT is defined as any abnormality in the size, shape, position, number, or function of either the kidney(s) and/ or genitourinary tract. The CAKUT phenotypes can be classified based on anatomic position or by the functional defects observed (Table 1). Histological classification, as seen in other subcategories of kidney disease are largely avoided, as histological diagnosis is generally not required to confirm the diagnosis. More recently it has been suggested that reduced nephron number according to the Barker hypothesis (Hales & Barker, 2001) is part of the phenotypic spectrum of patients with CAKUT, especially in those who present in later life (Murugapoopathy & Gupta, 2020).

Table 1.

Major CAKUT phenotypes based on anatomical position listed from a cranial to caudal position

Kidney phenotypes

Renal agenesis

Renal hypodysplasia

Multicystic-dysplastic kidney

Horseshoe kidney

Duplex kidney

Ureteric phenotypes

Hydronephrosis

Uteropelvic junction obstruction

Hydroureter/ Megaureter

Duplex/ Bifid ureter (partial or complete)

Utero-vesical junction obstruction

Vesico-urethral reflux

Lower urinary tract phenotypes

Bladder exstrophy

Bladder agenesis

Posterior urethral valve

Urethral agenesis

Genito-urinary phenotypes

Cryptorchidism

Diagnosis of CAKUT

With increasing availability of pre-natal ultrasound, many cases of CAKUT are now being diagnosed during the second trimester anatomic examination, where defects in either the kidney and/or genito-urinary tract are observed. Alternatively, the consequence of reduced urinary output, name oligohydramnios, can be observed raising the suspicion of a developmental defect in the kidneys. CAKUT, in particular the reduced nephron dose phenotype, may have a delayed diagnosis into adulthood, especially if prior imaging of the urinary tract has not been performed. Often these patients present with hypertension and chronic kidney disease with subsequent imaging of the kidneys revealing a CAKUT phenotype.

Although ultrasound imaging has a high yield in confirming a diagnosis, certain subtypes of CAKUT particularly involving the lower urinary tract may require additional imaging modalities to confirm the diagnosis. For example, in posterior urethral valve, cystoscopy is the gold standard for diagnosis, although the secondary consequence of the phenotype, namely obstruction with hydronephrosis, may still be detected on ultrasound examination of the kidneys (Nasir et al., 2011).

Prognosis in CAKUT

Prognosis in CAKUT is largely dependent on the age at presentation and type of anomaly present (Sanna-Cherchi et al., 2009). Favorable outcomes have been observed in patients with isolated uni- or bilateral hydronephrosis detected on prenatal ultrasound, whereas high risk features such as oligohydramnios and bilateral anomalies are associated with an increased need of surgery and/or chronic kidney disease (Nef et al., 2016).

Familial Clustering in CAKUT

Familial clustering in CAKUT has been characterized in many studies. For example, a Turkish study of 218 patients with CAKUT revealed familial clustering in over half of cases, following ultrasonographic confirmation of CAKUT in first degree relatives of affected individuals (Bulum et al., 2013). Overall it is estimated that anywhere between 10% to 50% of children with CAKUT will report a family history of kidney or urinary tract anomalies consistent with the diagnosis of CAKUT (Bulum et al., 2013; Connaughton et al., 2015).

Screening for CAKUT

Routine screening for CAKUT is controversial and there are currently no consensus guidelines on who and when to screen. There is however mounting evidence that certain risk factors should prompt consideration of post-natal ultrasound (USS) screening for CAKUT. For example, a recent prospective study from China of 4,877 infants identified 268 cases (5.5%) of CAKUT by primary screening and 92 cases (1.9%) by tertiary screening. This study devised a predictive model incorporating high risk factors, namely male gender, preterm birth, antenatal abnormal ultrasound findings, gestational hypothyroidism, and oligohydramnios all which increase the risk of CAKUT (Liu et al., 2022).

Routine screening in asymptomatic family members is not currently recommended, however studies increasingly show that familial screening maybe beneficial. For example, in first-degree relatives of children with non-syndromic CAKUT, the incidence of CAKUT is 6% (9 out of 149 family members), which is significantly higher than the risk in the general population. Interestingly, most of the CAKUT phenotypes detected in biologically related individuals were discordant to the index case (88.8%) (Viswanathan et al., 2021). In another study, familial occurrence of CAKUT was noted in 7.9% of the 138 families using either renal ultrasonogram, radionuclide diuretic renogram or micturating cystourethrogram in family members of the index case (Manoharan et al., 2020). In a retrospective review, Gok et al. found a frequency of familial CAKUT of 14.4%, with the highest rate in those with renal agenesis (Suman Gök et al., 2020).

Given the non-invasive nature of USS screening and the high likelihood of familial occurrence of CAKUT, all patients with CAKUT should at minimum have extended pedigree analysis performed with ultrasonography in at risk individuals. In addition, because of the association with extra-renal manifestations of disease (A. van der Ven et al., 2018), patients with CAKUT should have a comprehensive multi-system clinical examination with specialist referral as indicated clinically.

Depending on the associated clinical features, chromosomal microarray should be offered if there is a suspicion for multi-system involvement with syndromic features. If negative, sequencing analysis can be performed either through gene panel testing or whole exome/ genome analysis looking for monogenic causes of disease. In all cases, trio analysis should be considered particularly if both parents are asymptomatic given the potential for de novo disease. However, given the high prevalence of incomplete penetrance and variable expressivity, ultrasonographic examination in nominally unaffected family members should be considered.

Embryonic development of the kidney and genito-urinary tract

CAKUT arises following disturbances of the normal development of the kidney and/or urinary tract. The upper urinary system, the gonads and sexual ducts arises from two structures; the nephric ducts (ND) and the nephric cord (NC), both of which arise from the intermediate mesoderm (Figure 1A).

Figure 1. Diagrammatic representation of embryonic development of the kidney.

A. Nephric duct elongation and induction of the metanephric mesenchyme.

The nephric ducts (ND) and the nephric cord (NC) arise from the intermediate mesoderm. The ND elongates caudally and fuses with the cloaca. The metanephric mesenchyme (MM) expresses GDNF which provides the signal to the ND to induce the ureteric bud (UB).

B. Ureteric bud outgrowth/ Induction of cap mesenchyme.

The UB is an outgrowth of the ND, that sprouts in the direction of the MM. The MM forms the cap mesenchyme (CM).

C. Ureteric bud branching morphogenesis.

Following induction from the UB, a portion of the CM then undergoes mesenchymal to epithelial transition (MET) progresses through various morphological stages including the comma-shaped body followed by the S-shaped body to form a nephron. The S-shaped body ultimately fuses with the collecting ducts. The UB tips continue to branch whilst the renal vesicle continues to mature into a nephron.

The ND is an epithelial tube from which an epithelial outgrowth called the ureteric bud (UB) arises (Figure 1B). The ND itself elongates caudally and ultimately fuses with the cloacal epithelium, which is a precursor of the urinary bladder. The metanephric mesenchyme (MM) arises from mesenchymal cells in the posterior intermediate mesoderm. At the early stages of kidney development, a subset of cell in the MM provides signaling to the ND to induce the UB. The UB then invades the adjacent MM and later forms the collecting duct system. The UB induces nephron formation. The portion of the MM that come in closest proximity to the UB forms the cap mesenchyme (CM) (Figure 1B). Following induction from the UB, a portion of the CM then undergoes mesenchymal to epithelial transition (MET) with formation of the renal vesicle (Figure 1C). The remainder of the cells in the CM continues to proliferate, thereby providing a pool of progenitor cells throughout kidney development that are required for nephron induction (Kagan et al., 2022).

The renal vesicle progresses through various morphologically distinct stages including comma- and S-shaped bodies to generate all epithelial components of the nephron: The Bowman’s capsule (including podocytes) at the proximal end and the distal tubular system (proximal and distal tubule and intervening loop of Henle) (Figure 1C). Throughout nephrogenesis the UB repeatedly branches largely stimulated by the MM-derived signal (branching morphogenesis), a process which is maintained by the reciprocal induction between the MM and the UB. The bladder is primarily derived from the cloaca, which in early embryonic development (approximately 4 weeks gestation) divides into two sections, the rectum and urogenital sinus, that latter which ultimately forms the bladder and part of the infra-vesical urethra. The distal aspect of the UB and its surrounding mesenchyme proliferate and differentiate into the urothelium, the specialized epithelium of the urinary drainage system, and a fibromuscular wall capable of peristaltic contractions, respectively. Connectivity of the ureter with the bladder is achieved in a complex developmental program. Following caudal extension of the ND and fusion with the cloaca, the distal portion of the ND (the so-called common ND) is eliminated by apoptosis. The distal aspect of the ureter lies down on the bladder and is eliminated by apoptosis as well ultimately resulting in insertion of the distal ureter into the anterior aspect of the dorsal bladder wall (Uetani & Bouchard, 2009). This entire process is governed by a number of developmental genes, which if defective, can result in a CAKUT phenotype as described below (A. T. van der Ven et al., 2018).

Molecular basis of CAKUT

The molecular basis of CAKUT is hypothesized to range from monogenic to polygenic with environmental factors during embryogenesis also implicated in the pathogenesis (Dart et al., 2015; Groen In ‘t Woud et al., 2016; Hsu et al., 2014; Lee et al., 2012; Nicolaou et al., 2015; Parikh et al., 2002; Ven et al., 2018).

Here we focus on monogenic causation, however knowledge of potential environmental factors can provide insights into monogenic disease causation and potential gene developmental pathways. For example, Vitamin A exposure during embryogenesis has been implicated as an environmental factor in CAKUT pathogenesis (Das et al., 2014; Lee et al., 2012). Interestingly, retinoic acid, the active metabolite of Vitamin A has been implicated in abnormal murine kidney development (Batourina et al., 2002; Batourina et al., 2001; Batourina et al., 2005; Chia et al., 2011; Mendelsohn et al., 1999; Rosselot et al., 2010). It is hypothesized that during embryonic development retinoic acid regulates the insertion of the ND into the cloaca and later branching morphogenesis of the UB (Batourina et al., 2001; Chia et al., 2011; A. T. van der Ven et al., 2018). Mouse models with mutations in genes regulating intracellular retinoic acid, namely Retinol Dehydrogenase 10 (Rdh10) (Rhinn et al., 2011), Aldehyde Dehydrogenase 1 Family Member A2 (Ald1a2) (Rosselot et al., 2010), Cytochrome P450 Family 26 Subfamily A Member 1 (Cyp26a1) (Abu-Abed et al., 2001; Sakai et al., 2001), develop phenotypes in the CAKUT disease spectrum. In humans, heterozygous truncating mutations in the gene Nuclear Receptor Interacting Protein 1 (NRIP1) have been detected in patients with CAKUT (Vivante, Mann, et al., 2017; Zheng et al., 2022). Interestingly, NRIP1 encodes a nuclear receptor transcriptional cofactor that directly interacts with the retinoic acid receptors to modulate retinoic acid transcriptional signaling (Vivante, Mann, et al., 2017).

Monogenic causation in CAKUT

With the expansion of next generation sequencing technology, now 45 monogenic causes of isolated CAKUT (Table 2) and over 150 monogenic causes of syndromic CAKUT (Table 3) have been described (Connaughton & Hildebrandt, 2019; Connaughton et al., 2019; Ven et al., 2018). Monogenic causation of CAKUT has long been suspected as evidenced by a) monogenic mouse models which exhibit CAKUT phenotypes, b) familial clustering of CAKUT, c) the fact that CAKUT occurs in conjunction with multi-organ syndromes, d) the involvement of developmental gene pathways in CAKUT pathogenesis, e) the congenital nature of CAKUT (Vivante & Hildebrandt, 2016; Vivante et al., 2014). CAKUT due to single gene disorders follows a Mendelian pattern of inheritance with either an autosomal dominant, autosomal recessive, and X-linked pattern of inheritance. Mutations in the transcription factors PAX2 and HNF1B represent the most prevalent forms of monogenic CAKUT (Ahn et al., 2020; Hwang et al., 2014). However with the ever-expanding use of next-generation sequencing technology in clinical medicine, other single gene disorder are increasingly identified in cohorts with CAKUT phenotypes (Kagan et al., 2022). Moreover, significant clinical and genetic heterogenicity exists with both intra- and interfamilial variability. Despite reports suggesting gene-phenotype correlation for some subtypes of CAKUT (i.e. PAX2 and renal hypoplasia (Sanyanusin et al., 1995)), emerging data now suggests that even identical variants in the CAKUT causing genes can result in varying CAKUT phenotypes with intra-individual and even intra-familial variability (Ven et al., 2018).

Table 2.

45 genes that represent monogenic causes of human isolated CAKUT, if mutated. (Sorted alphabetically by mode of inheritance).

Gene	Protein	Reference	Mode of inheritance	Phenotype	OMIM #
ACE	Angiotensin I-converting enzyme	Gribouval Nat Genet 37:964, 2005	AR	Renal tubular dysgenesis	# 267430
AGT	Angiotensinogen	Gribouval Nat Genet 37:964, 2005	AR	Renal tubular dysgenesis	# 267430
AGTR1	Angiotensin II receptor, type 1	Gribouval Nat Genet 37:964, 2005	AR	Renal tubular dysgenesis	# 267430
CHRM3	Muscarinic acetylcholine receptor M3	Weber AJHG 19:634, 2011	AR	Prune belly syndrome	# 100100
ETV4	ETS translocation variant 4, E1A enhancer binding protein	Chen IJPCH 4:61, 2016	AR	NA	* 600711
FRAS1	Extracellular matrix protein FRAS1	Kohl JASN 25:1917, 2014	AR	Fraser syndrome 1	# 219000
FREM1	FRAS1 related extracellular matrix protein 1	Kohl JASN 25:1917, 2014	AR	Manitoba oculotrichoanal syndrome	# 248450
FREM2	FRAS1 related extracellular matrix protein 2	Kohl JASN 25:1917, 2014	AR	Fraser syndrome 2	# 617666
FOXA2	Forkhead Box A2	Zheng NDT 2021 online ahead of print doi:10.1093/ndt/gfab253	AR	Horseshoe Kidney	* 600288
GRIP1	Glutamate receptor interacting protein 1	Kohl JASN 25:1917, 2014	AR	Fraser syndrome 3	# 617667
HOXA11	Homobox A11	Saygili Clin. Genet. 93(4):390, 2020	AR	CAKUT	* 1429958
HPSE2	Heparanase 2 (Inactive)	Bulum Nephron 130:54, 2015	AR	Urofacial syndrome 1	# 236730
ITGA8	Integrin α8	Humbert AJHG 189:1260, 2014	AR	Renal hypodysplasia/ aplasia 1	# 191830
NPNT	Nephronectin	Al-Hamed Clin. Genetics. Online ahead print	AT	Bilateral renal hypodysplasia	* 610306
REN	Renin	Gribouval Nat Genet 37:964, 2005	AR	Renal tubular dysgenesis	# 267430
TRAP1	Heat-shock protein 75 (also known as TNF receptor-associated protein 1)	Saisawat Kid Int 85:880, 2014	AR	NA	* 606219
FGF20	Fibroblast Growth Factor 20	Barak Dev Cell 22:1191, 2012	AR	Renal hypodysplasia/ aplasia 2	# 615721
WNT9B	Wingless Type MMTV Integration Site Family	Lemire AJMG 185(10):2005,2021	AR	Bilateral renal agenesis/ hypoplasia/ dysplasia	* 602864
BMP4	Bone morphogenic protein 4	Weber JASN 19:891, 2008	AD	Microphthalmia, syndromic 6	# 607932
CHD1L	Chromodomain helicase DNA binding protein 1-like	Brockschmidt NDT 27:2355, 2012	AD	NA	* 613039
CRKL	CRK Like Proto-Oncogene, adaptor protein	Lopez-Rivera NEJM 376:742, 2017	AD	NA	* 602007
DSTYK	Dual serine/threonine and tyrosine protein kinase	Sanna-Cherchi NEJM 369:621, 2013	AD	Congenital anomalies of kidney and urinary tract 1	# 610805
EYA1	Eyes absent homolog 1	Abdelhak Nat Genet 15:157, 1997	AD	Branchiootorenal syndrome 1, with or without cataracts	# 113650
FOXC1	Forkhead Box C1	Wu Genet. Med. 22(10):1673, 2020	AD	CAKUT	* 601090
FOXA3	Forkhead Transcription Factor 3	Zheng NDT 2021 online ahead of print doi:10.1093/ndt/gfab253	AD	Uretero-pelvic junction obstruction	* 602295
FOXL2	Forkhead Transcription Factor 2	Zheng NDT 2021 online ahead of print doi:10.1093/ndt/gfab253	AD	Uretero-pelvic junction obstruction and eyelid abnormalities	* 605597
GATA3	GATA binding protein 3	Pandolfi Nat Genet 11:40, 1995; Van Esch Nature 406:419, 2000	AD	Hypoparathyroidism, sensorineural deafness, and renal dysplasia	# 146255
GREB1L	Growth Regulation By Estrogen In Breast Cancer 1 Like	Brophy Genetics 207:215, 2017, Sanna-Cherchi AJHG 101:1034, 2017	AD	Renal hypodysplasia/ aplasia 3	# 617805
HNF1B	HNF homeobox B	Lindner Hum Mol Genet 24:263, 1999	AD	Renal cysts and diabetes syndrome	# 137920
MUC1	Mucin 1	Kirby Nat Genet 45:299, 2013	AD	Medullary cystic kidney disease 1	# 174000
NRIP1	Nuclear Receptor Interacting Protein 1	Vivante JASN 28:2364, 2107	AD	NA	* 602490
PAX2	Paired box 2	Sanyanusin Hum Mol Genet 4:2183, 1995	AD	Papillorenal syndrome	# 120330
PBX1	PBX Homeobox 1	Heidet JASN 28:2901, 2017	AD	Congenital anomalies of kidney and urinary tract syndrome with or without hearing loss, abnormal ears, or developmental delay	# 617641
RET	Proto-oncogene tyrosine-protein kinase receptor Ret	Skinner AJHG 82:344, 2008	AD	Multiple OMIM classifications	* 164761
ROBO2	Roundabout, axon guidance receptor, homolog 2 (Drosophila)	Hwang Hum Genet 134:905, 2015; Lu AJHG 80:616, 2007	AD	Vesicoureteral reflux 2	# 610878
SALL1	Sal-like protein 1 (also known as spalt-like transcription factor 1)	Kohlhase Nat Genet 18:81, 1998	AD	Townes-Brocks syndrome 1	# 107480
SIX1	SIX homeobox 1	Ruf PNAS 101: 8090, 2004	AD	Branchio-otic syndrome 3	# 608389
SIX2	SIX homeobox 2	Weber JASN 19:891, 2008	AD	NA	* 604994
SIX5	SIX homeobox 5	Hoskins AJHG 80:800, 2007	AD	Branchiootorenal syndrome 2	# 610896
SLIT2	Slit homolog 2	Hwang Hum Genet 134:905, 2015	AD	NA	* 603746
SOX17	Transcription factor SIX-17	Gimelli Hum Mut 31:1352, 2010	AD	Vesicoureteral reflux 3	# 613674
SRGAP1	SLIT-ROBO Rho GTPase activating protein 1	Hwang Hum Genet 134:905, 2015	AD	NA	* 606523
TBX18	T-Box transcription factor	Vivante AJHG 97:291, 2015	AD	Congenital anomalies of kidney and urinary tract 2	# 143400
TNXB	Tenascin XB	Gbadegesin JASN 24:1313, 2013	AD	Vesicoureteral reflux 8	# 615963
UPK3A	Uroplakin 3A	Jenkins JASN 16:2141, 2005	AD	NA	* 611559
WNT4	Protein Wnt-4	Biason-Lauber NEJM 351:792, 2004; Mandel AJHG 82:39, 2008; Vivante JASN 24:550, 2013	AD	Mullerian aplasia and hyperandrogenism	# 158330
KAL1	Anosmin 1	Hardelin PNAS 89:8190, 1992	XL	Hypogonadotropic hypogonadism 1 with or without anosmia (Kallmann syndrome 1)	# 308700

AR, autosomal recessive; AD, autosomal dominant; NA, not available; OMIM, Online Mendelian Inheritance in Man; XL; X-linked

^#,phenotype MIM number

^*gene/ locus MIM number if not phenotype MIM number available.

Table 3.

155 genes that represent monogenic causes of human syndromic CAKUT, if mutated. (Sorted alphabetically by mode of inheritance).

Gene	Protein	Reference	Mode of inheritance	Phenotype	OMIM number
B3GALTL	Beta 3-Glucosyltransferase	Lesnik Oberstein AJHG 79:562, 2006	AR	Peters-plus syndrome	# 261540
BSCL2	BSCL2, Seipin Lipid Droplet Biogenesis Associated	Haghighi Clin Genet 89: 434, 2016	AR	Multiple classifications	# 608594 # 269700 # 600794 # 615924 # 270685
CD151	CD151 Molecule (Raph Blood Group)	Karamatic Blood 104:2217, 2004	AR	NA	* 602243
CD96	CD96 Molecule	Kaname AJHG 81:835, 2007	AR	C syndrome	# 211750
CHRNG	Cholinergic Receptor Nicotinic Gamma Subunit	Vogt J Med Genet 49:21, 2012	AR	Escobar syndrome	# 265000
CISD2	CDGSH Iron Sulfur Domain 2	Amr AJHG 81:673, 2007	AR	Wolfram syndrome 2	# 604928
CTU2	Cytosolic Thiouridylase, subunit 2	Shaheen AJMG 170:3222, 2016	AR	Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome	# 618142
CYP21	Cytochrome P450 Family 21	Martul Arch Dis Child 55:324, 1980	AR	Hyperandrogenism, nonclassic type, due to 21-hydroxylase deficiency	# 201910
DACH1	Dachshund Family Transcription Factor 1	Schild NDT 28:227, 2013	AR	NA	* 603803
DHCR7	7-Dehydrocholesterol Reductase	Löffler AJHG 13;95:174, 2000	AR	Smith-Lemli-Opitz syndrome	# 270400
DIS3L2	DIS3 Like 3’–5’ Exoribonuclease 2	Astuti Nat Genet 5;44:277, 2012	AR	Perlman syndrome	# 267000
EMG1	EMG1, N1-Specific Pseudouridine Methyltransferase	Armistead AJHG 84:728, 2009	AR	Bowen-Conradi syndrome	# 211180
ERCC8	Excision repair cross-complementing, group 8	Bertola J Hum Genet 51:701, 2006	AR	Cockayne syndrome, type A	# 216400
ESCO2	Establishment Of Sister Chromatid Cohesion N-Acetyltransferase 2	Vega J Med Genet 47:30, 2010	AR	Roberts syndrome	# 268300
ETFA	Electron Transfer Flavoprotein Alpha Subunit	Lehnert Eur J Pediatr 139:56, 1982	AR	Glutaric acidemia IIA	# 231680
ETFB	Electron Transfer Flavoprotein Beta Subunit	Lehnert Eur J Pediatr 139:56, 1982	AR	Glutaric acidemia IIB	# 231680
ETFDH	Electron Transfer Flavoprotein Dehydrogenase	Lehnert Eur J Pediatr 139:56, 1982	AR	Glutaric acidemia IIC	# 231680
FANCA	Fanconi Anemia Complementation Group A	Joenje & Patel Nat Rev Genet 2:466, 2001	AR	Fanconi anemia, complementation group A	# 227650
FANCB	Fanconi Anemia Complementation Group B	McCauley AJMG 155A:2370, 2011	AR	Fanconi anemia, complementation group B	# 300514
FANCD2	Fanconi Anemia Complementation Group D2	Kalb AJHG 80:895, 2007	AR	Fanconi anemia, complementation group D2	# 227646
FANCE	Fanconi Anemia Complementation Group E	Wegner Clin Genet 50:479, 1996	AR	Fanconi anemia, complementation group E	# 600901
FANCI	Fanconi Anemia Complementation Group I	Savage AJMG 170A:386, 2015	AR	Fanconi anemia, complementation group I	# 609053
FANCL	Fanconi Anemia Complementation Group L	Vetro Hum Mutat 36:562, 2015	AR	Fanconi anemia, complementation group L	# 614083
FAT4	FAT Atypical Cadherin 4	Alders Hum Genet 133:1161, 2014	AR	Van Maldergem syndrome 2	# 615546
FOXP1	Forkhead Box P1	Bekheirnia Genet Med 19:412, 2017	AR	NA	* 605515
HES7	Hes Family BHLH Transcription Factor 7	Sparrow Hum Mol Genet 17:3761, 2008	AR	NA	* 608059
HYLS1	HYLS1, Centriolar And Ciliogenesis Associated	Paetau J Neuropathol Exp Neurol 67:750, 2008	AR	Hydrolethalus syndrome	# 236680
ICK	Intertinal cell kinase	Lahiry AJHG 84:822, 2009	AR	NA	* 612325
IFT46	Intraflagellar Transport 46	Lee Dev Biol 400:248, 2015	AR	Short-rib thoracic dysplasia 16 with or without polydactyly	# 617102
IFT74	Intraflagellar Transport 74	Cevik PLoS GeneT 9:e1003977, 2013	AR	Bardet-Biedl syndrome 20	# 617119
ITGA3	Integrin Subunit Alpha 3	Yalcin Hum Mol Genet 24:3679, 2015	AR	Interstitial lung disease, nephrotic syndrome, and epidermolysis bullosa, congenital	# 614748
JAM3	Junctional Adhesion Molecule 3	Mochida AJHG 10;87:882, 2010	AR	Hemorrhagic destruction of the brain, subependymal calcification, and cataracts	# 613730
LMNA	Lamin A/C	Klupa Endocrine 36:518, 2009	AR	Multiple OMIM classification	* 150330
LRIG2	Leucione rich repeats and immunoglobulin like domains containing protein 2	Stuart AJHG 92:259, 2013	AR	Urofacial syndrome 2	# 615112
LRP2	LDL Receptor Related Protein 2	Kantarci Nat Genet 39:957, 2007	AR	Donnai-Barrow syndrome	# 222448
LRP4	LDL Receptor Related Protein 4	Li Am J Hum Genet 86:696, 2010	AR	Cenani-Lenz syndactyly syndrome	# 212780
MESP2	Mesoderm Posterior BHLH Transcription Factor 2	George-Abraham AJMG A 158A:1971, 2012	AR	NA	* 605195
MKS3	Meckel Syndrome Type 3 Protein	Baala AJHG 80:186, 2007	AR	Meckel syndrome 3	# 607361
PEX5	Peroxisomal Biogenesis Factor 5	Sundaram Nat Clin Pract Gastroenterol Hepatol 5:456, 2008	AR	Peroxisome biogenesis disorder 2A (Zellweger)	# 214110
PMM2	Phosphomannomutase 2	Horslen Arch Dis Child 66:1027, 1991	AR	Congenital disorder of glycosylation, type Ia	# 212065
POC1A	POC1 centriolar protein	Shaheen AJHG 91:330, 2012	AR	Short stature, onychodysplasia, facial dysmorphism, and hypotrichosis	# 614813
PROK2	Prokineticin 2	Madan Mol Genet Metab Rep 12:57, 2017	AR	Hypogonadotropic hypogonadism 4 with or without anosmia	# 610628
RECQL4	RecQ Like Helicase 4	Siitonen Eur J Hum Genet 17:151, 2009	AR	Baller-Gerold syndrome	# 218600
ROR2	Receptor Tyrosine Kinase Like Orphan Receptor 2	Wiens Clin Genet 37:481, 1990	AR	Robinow syndrome	# 268310
RPS19	Ribosomal Protein S19	Hoefele Pediatr Nephrol 25:1255, 2010	AR	NA	* 603474
SCARF2	Scavenger Receptor Class F Member 2	Anastasio AJHG 87:553, 2010	AR	Van den Ende-Gupta syndrome	# 600920
STRA6	Stimulated By Retinoic Acid 6	Golzio AJHG 80:1179, 2007	AR	Microphthalmia, syndromic 9 Microphthalmia, isolated, with coloboma 8	# 601186
TMCO1	Transmembrane And Coiled-Coil Domains 1	Xin PNAS 107:258, 2010	AR	Craniofacial dysmorphism, skeletal anomalies, and mental retardation syndrome	# 213980
UBR1	Ubiquitin Protein Ligase E3 Component N-Recognin 1	Vanlieferinghen Genet Couns 14:105, 2003	AR	Johanson-Blizzard syndrome	# 243800
PEX1	Peroxisomal Biogenesis Factor 1	Crane Hum Mutat 26:167, 2005	AR	Peroxisome biogenesis disorder 1A (Zellweger)	# 214100
PIGL	Phosphatidylinositol Glycan Anchor Biosynthesis Class L	Schnur AJMG 72:24, 1997	AR	CHIME syndrome	# 280000
PIGO	Phosphatidylinositol Glycan Anchor Biosynthesis Class O	Krawitz AJHG 91:146, 2012	AR	Hyperphosphatasia with mental retardation syndrome 2	# 614749
PIGN	Phosphatidylinositol Glycan Anchor Biosynthesis Class N	Ohba Neurogenetics 15:85, 2014	AR	Multiple congenital anomalies-hypotonia-seizures syndrome 1	# 614080
PIGT	Phosphatidylinositol Glycan Anchor Biosynthesis Class T	Nakashima Neurogenetics 15:193, 2014	AR	Multiple congenital anomalies-hypotonia-seizures syndrome 3	# 615398
PIGV	Phosphatidylinositol Glycan Anchor Biosynthesis Class V	Horn Eur J Hum Genet 22:762, 2014	AR	NA	* 610274
PIGY	Phosphatidylinositol Glycan Anchor Biosynthesis Class Y	Ilkovski Hum Mol Genet 24:6146, 2015	AR	Hyperphosphatasia with mental retardation syndrome 6	# 616809
PTF1A	Pancreas Specific Transcription Factor, 1a	Gurung Mol Med Rep 12:1579, 2015	AR	NA	* 607194
ROBO1	Roundabout Guidance Receptor 1	Kidney Int. S0085–2538(22) 157–0, 2022	AR	Kidney and genitourinary defects, neurodevelopmental defects, eye anomalies, and cardiac defects.	* 602430
WFS1	Wolframin ER Transmembrane Glycoprotein	Salih Acta Paediatr Scand 80:567, 1991	AR	Wolfram syndrome 1	# 222300
WNT3	Wnt Family Member 3	Niemann AJHG 74:558, 2004	AR	Tetra-amelia syndrome 1	# 273395
ZMPSTE24	Zinc Metallopeptidase STE24	Chen AJMG A 149A:1550, 2009	AR	Restrictive dermopathy, lethal	# 275210
ACTB	Actin Beta	Rivière Nat Genet 44:440, 2012	AD	Baraitser-Winter syndrome 1	# 243310
ACTG1	Actin Gamma 1	Rivière Nat Genet 44:440, 2012	AD	Baraitser-Winter syndrome 1	# 243310
AIFM3	Apoptosis Inducing Factor, Mitochondria Associated 3	Lopez-Rivera NEJM 376:742, 2017	AD	NA	* 617298
ARID1B	AT-Rich Interaction Domain 1B	Levy J Med Genet 28, 1991	AD	Coffin-Siris syndrome 1	# 135900
ATXN10	Ataxin 10	Matsuura Nat Genet 26:191, 2000	AD	Spinocerebellar ataxia 10	# 603516
BICC1	BicC Family RNA Binding Protein 1	Kraus Hum Mutat 33:86, 2012	AD	Renal cystic/ dysplasia	# 601331
BMP7	Bone Morphogenetic Protein 7	Hwang Kidney Int 85:1429, 2014	AD	NA	* 112267
BRAF	B-Raf Proto-Oncogene, Serine/Threonine Kinase	Sarkozy Hum Mutat 30:695, 2009	AD	Cardiofaciocutaneous syndrome	# 115150
CDC5L	Cell Division Cycle 5 Like	Groenen Genomics 49:218, 1998	AD	NA	* 602868
CREBBP	CREB Binding Protein	Kanjilal J Med Genet 29:669, 1992	AD	Rubinstein-Taybi syndrome 1	# 180849
DACT1	Dishevelled Binding Antagonist Of Beta Catenin 1	Webb Hum Mutat 38:373, 2017	AD	Townes-Brocks syndrome 2	# 617466
EP300	E1A Binding Protein P300	Roelfsema AJHG 76:572, 2005	AD	Rubinstein-Taybi syndrome 2	# 613684
ESRRG	Estrogen Related Receptor Gamma	Harewood PLoS One 5:e12375, 2010	AD	NA	* 602969
FBN1	Fibrillin 1	Tokhmafshan Pediatr Nephrol 32:565, 2017	AD	Marfan syndrome	# 154700
FGFR1	Fibroblast growth factor receptor 1	Farrow AJHG 140A:537, 2006	AD	Multiple OMIM classifications	# 615465 # 147950 # 123150 # 166250 # 101600 # 190440
FGFR3	Fibroblast growth factor receptor 3	Rohmann Nat Genet 38:495, 2006	AD	LADD syndrome	# 149730
FGF10	Fibroblast Growth Factor 10	Milunsky Clin Genet 69:349, 2006; Bamforth AJMG 43:932, 1992	AD	LADD syndrome	# 149730
FGF8	Fibroblast Growth Factor 8	Falardeau J Clin Invest 118:2822 2008	AD	Hypogonadotropic hypogonadism 6 with or without anosmia	# 612702
FGFR2	Fibroblast Growth Factor Receptor 2	LeHeup Eur J Pediatr 154:130, 1995	AD	Multiple OMIM classifications	* 176943
FGFRL2	Forkhead Box C1	LeHeup Eur J Pediatr 154:130, 1995	AD	Antley-Bixler syndrome without genital anomalies or disordered steroidogenesis	# 207410
FMN1	Formin 1	Dimitrov J Med Genet 47:569, 2010	AD	NA	* 136535
FOXF1	Forkhead Box F1	Hilger Hum Mutat 36:1150, 2015	AD	Alveolar capillary dysplasia with misalignment of pulmonary veins	# 265380
GDF3	Growth Differentiation Factor 3	Karaca AJMG A 167A:2795, 2015	AD	Klippel-Feil syndrome 3	# 613702
GDNF	Glial cell line derived neurotrophic factor	Pini Prato Medicine (Baltimore) 88:83, 2009	AD	Susceptibility Hirschsprung Disease	# 613711
GFRA1	GDNF Family Receptor Alpha 1	Chatterjee Hum Genet 131:1725, 2013	AD	NA	* 601496
GLI2	GLI Family Zinc Finger 2	Carmichael J Urol 190:1884, 2013	AD	Culler-Jones syndrome, Holoprosencephaly 9	# 615849 # 610829
HOXA13	Homeobox A13	Halal AJMG 30:793, 1998	AD	Hand-foot-uterus syndrome	# 140000
HOXD13	Homeobox D13	Garcia-Barceló AJMG A146A:3181, 2008	AD	NA	* 142989
JAG1	Jagged 1	Kamath Nat Rev Nephrol 9:409, 2013	AD	Alagille syndrome 1	# 118450
KAT6B	Lysine Acetyltransferase 6B	Campeau AJMG 90:282, 2012	AD	Genitopatellar syndrome	# 606170
KCTD1	Potassium Channel Tetramerization Domain Containing 1	Marneros AJMG 92:621, 2013	AD	Scalp-ear-nipple syndrome	# 181270
KCNH2	Potassium Voltage-Gated Channel Subfamily H Member 2	Caselli AJMG 146A:1195, 2008	AD	Scalp-ear-nipple syndrome	* 152427
KRAS	KRAS Proto-Oncogene, GTPase	Schubbert Nat Gene 38:331, 2006	AD	Noonan syndrome 3	# 609942
LMX1B	LIM Homeobox Transcription Factor 1 Beta	Dreyer Nat Genet 19:47, 1998	AD	Nail-patella syndrome	# 161200
LPP	LIM Domain Containing Preferred Translocation Partner In Lipoma	Hernández-García AJMG A 158A:1785, 2012	AD	NA	* 600700
MAP2K1	Mitogen-activated protein kinase kinase 1	Schulz Clin Genet 73:62, 2007	AD	Cardiofaciocutaneous syndrome 3	# 615279
MAP2K2	Mitogen-activated protein kinase kinase 2	Schulz Clin Genet 73:62, 2007	AD	Cardiofaciocutaneous syndrome 4	# 615280
MLL2/ KMT2D	Myeloid/Lymphoid Or Mixed-Lineage Leukemia Protein 2	Banka Eur J Hum Genet 20:381, 2012	AD	Kabuki syndrome 1	# 147920
MYCN	Feingold Syndrome	Marcelis Hum Mut 29:1125, 2006	AD	Feingold syndrome 1	# 164280
NOTCH2	Notch 2	Kamath Nat Rev Nephrol 9:409, 2013	AD	Alagille syndrome 2, Hajdu-Cheney syndrome	# 610205 # 102500
PKD1	Polycystin 1, Transient Receptor Potential Channel Interacting	Rossetti JASN 18:2143, 2007	AD	Polycystic kidney disease 1	# 173900
PKD2	Polycystin 2, Transient Receptor Potential Cation Channel	Rossetti JASN 18:2143, 2007	AD	Polycystic kidney disease 2	# 613095
PROKR2	Prokineticin Receptor 2	Sarfati Front Horm Res 39:121, 2010	AD	Hypogonadotropic hypogonadism 3 with or without anosmia	# 244200
PTPN11	Protein Tyrosine Phosphatase, Non-Receptor Type 11	Bertola AJMG 130A:378, 2004	AD	LEOPARD syndrome 1	# 151100
RAF1	Raf-1 Proto-Oncogene, Serine/Threonine Kinase	Razzaque Nat Genet 39:1013, 2007	AD	Noonan syndrome 5	# 611553
RAI1	Retinoic Acid Induced 1	Vilboux PLoS One 6:e22861, 2011	AD	Smith-Magenis syndrome	# 182290
SALL4	Spalt Like Transcription Factor 4	Kohlhase GeneReviews®Book Section, 1993	AD	Duane-radial ray syndrome	# 607323
SEMA3A	Semaphorin 3A	Young Hum Reprod 27:1460, 2012	AD	Hypogonadotropic hypogonadism 16 with or without anosmia	# 614897
SEMA3E	Semaphorin 3E	Lalani J Med Genet 41:e94, 2004	AD	CHARGE syndrome	# 214800
SETBP1	SET Binding Protein 1	Schinzel AJMG 1:361, 1978	AD	Schinzel-Giedion midface retraction syndrome	# 269150
SHH	Sonic Hedgehog	Lurie AJMG 35:286, 1990	AD	Holoprosencephaly 3	# 142945
SF3B4	Splicing Factor 3b Subunit 4	Bernier AJMG 90:925, 2012	AD	Acrofacial dysostosis 1, Nager type	# 154400
SNAP29	Synaptosome Associated Protein 29	Lopez-Rivera NEJM 376:742, 2017	AD	Di George syndrome	* 604202
SOS1	SOS Ras/Rac Guanine Nucleotide Exchange Factor 1	Ferrero Eur J Med Genet 51:566, 2008	AD	Noonan syndrome 4	# 610733
SOX9	SRY-Box 9	Airik Hum Mol Genet 19:4918, 2010	AD	Campomelic dysplasia	# 114290
SRCAP	Snf2 Related CREBBP Activator Protein	Hood AJHG 90:308, 2012	AD	Floating-Harbor syndrome	# 136140
TBX1	T-Box 1	Kujat AJMG A 140:1601, 2006	AD	Di George syndrome	# 188400
TBX3	T-Box 3	Meneghini Eur J Med Genet 49:151, 2006	AD	Ulnar-mammary syndrome	# 181450
TBX6	T-Box 3	Yang Kidney Int. 98(4):1020, 2020	AD	CAKUT	* 602427
TFAP2A	Transcription Factor AP-2 Alpha	Milunsky AJHG 82:1171, 2008	AD	Branchiooculofacial syndrome	# 113620
TP63	Tumor Protein P63	Celli Cell 99:143, 1999	AD	Multiple OMIM classifications	* 603273
TRPS1	Zinc finger transcription factor; Trichorhinophalangeal syndrome	Tasic Ren Fail 36:619, 2014	AD	Trichorhinophalangeal syndrome	# 190350 # 190351
TSC1	Tuberous Sclerosis 1	Curatolo Lancet 372:657, 2008	AD	Tuberous sclerosis-1	# 191100
TSC2	Tuberous Sclerosis 2	Kumar Hum Mol Genet 4:1471, 1995	AD	Tuberous sclerosis-2	# 613254
TWIST2	Twist Family BHLH Transcription Factor 2	Stevens AJMG 107:30, 2002	AD	Ablepharon-macrostomia syndrome	# 200110
WNT5A	Wnt Family Member 5A	Roifman Clin Genet 87:34, 2015; Person Dev Dyn 239:327, 2010	AD	Robinow syndrome	# 180700
ZMYM2	Zinx finger MYM-type 2	Connaughton AJHG 10794):727, 2020	AD/ de novo	Neurodevelopmental-craniofacial syndrome with variable renal and cardiac anomalies	# 619522
GDF6	Growth Differentiation Factor 6	Tassabehji Hum Mutat 29:1017, 2008	AD/ AR	Multiple OMIM classifications	* 601147
GLI3	GLI Family Zinc Finger 3	Cain PLoS One 4:e7313, 2009	AD/ AR	Multiple OMIM classifications	* 165240
PCSK5	Proprotein Convertase Subtilisin & Kexin Type 5	Nakamura BMC Res Notes 8:228, 2015	AD/ AR	NA	* 600488
PTEN	Phosphatase And Tensin Homolog	Reardon J Med Genet 38:820, 2001	AD/ AR	Multiple OMIM classifications	* 601728
RPS24	Ribosomal Protein S24	Yetgin Turk J Pediatr 36:239, 1994	AD/ AR	Aase-Smith syndrome	* 602412
VANGL1	VANGL Planar Cell Polarity Protein 1	Bartsch Mol Syndromol 3:76, 2012	AD/ AR	Caudal regression syndrome	# 600145
AXIN1	Axin 1	Oates AJHG 79:155, 2006	De novo	Caudal duplication anomaly	# 607864
H19	H19, Imprinted Maternally Expressed Transcript (Non-Protein Coding)	Hur PNAS 113:10938, 2016	De novo	Beckwith-Wiedemann syndrome	# 130650
KCNQ1OT1	KCNQ1 Opposite Strand & Antisense Transcript 1 (Non-Protein Coding)	Chiesa Hum Mol Genet 21:10, 2012	De novo	Beckwith-Wiedemann syndrome	# 130650
NIPBL	NIPBL, Cohesin Loading Factor	Rohatgi AJMG 152A:1641, 2010	De novo	Cornelia de Lange syndrome 1	# 122470
CDKN1C	Cyclin Dependent Kinase Inhibitor 1C	Mussa Pediatr Nephrol 27:397, 2012	De novo	Beckwith-Wiedemann syndrome	# 130650
CHD7	Chromodomain Helicase DNA Binding Protein 7	Janssen Hum Mutat 33:1149 2012	De novo	CHARGE syndrome	# 214800
AMER1	APC Membrane Recruitment Protein 1	Pellegrino AJMG 16:159, 1997	XL	Osteopathia striata with cranial sclerosis	# 300373
ATP7A	ATPase Copper Transporting Alpha	Vulpe Nat Genet 3:7, 1993	XL	Menkes disease	# 309400
BCOR	BCL6 Corepressor	Ng Nat Genet 36:411, 2004	XL	Microphthalmia, syndromic 2	# 300166
DLG3	Disc large, drosphilia, homologue of 3	Philips Orphanet J Rare Dis 9:49, 2014	XL	Mental retardation, X-linked 90	# 300850
FAM58A	Family With Sequence Similarity 58 Member A	Green J Med Genet 33:594, 1996; Unger Nat Genet 40:287, 2008	XL	STAR syndrome	# 300707
FLNA	Filamin A	Robertson AJMG A 140:1726, 2006	XL	Multiple OMIM classifications	* 300017
GPC3	Glypican 3	Cottereau AJMG C Semin Med Genet 163:92, 2013	XL	Simpson-Golabi-Behmel syndrome, type 1	# 312870
MID1	Midline 1	Preiksaitiene Clin Dysmorphol 24:7, 2015	XL	Opitz GBBB syndrome, type I	# 300000
NSDHL	NAD(P) Dependent Steroid Dehydrogenase-Like	König J Am Acad Dermatol 46:594, 2002	XL	CHILD syndrome	# 308050
PIGA	Phosphatidylinositol Glycan Anchor Biosynthesis Class A	Johnston AJHG 90:295, 2012	XL	Multiple congenital anomalies-hypotonia-seizures syndrome 2	# 300868
PORCN	Porcupine O-Acyltransferase	Suskan Pediatr Dermatol 7:283, 1990	XL	Focal dermal hypoplasia	# 305600
SMC1A	Structural Maintenance Of Chromosomes 1A	Deardorff GeneReviews® Book Section Seattle(WA), 1993	XL	Cornelia de Lange syndrome 2	# 300590
UPF3B	UPF3B, Regulator Of Nonsense Mediated MRNA Decay	Lynch Eur J Med Genet 55:476, 2012	XL	NA	* 300298
ZIC3	Zic Family Member 3	Chung AJMG 155:1123, 2011	XL	VACTERL association	# 314390
OSR1	Odd-Skipped Related Transciption Factor 1	Zhang Hum Mol Genet 20:4167, 2011	Unknown	NA	* 608891
SH2B1	SH2B Adaptor Protein 1	Sampson AJMG 152:2618, 2010	Unknown	NA	* 608937

AR, autosomal recessive; AD, autosomal dominant; NA, not available; OMIM, Online Mendelian Inheritance in Man; XL; X-linked

^#,phenotype MIM number; Unknown, mode of inheritance not clearly characterized;

^*gene/ locus MIM number if not phenotype MIM number available.

Recent studies demonstrate an estimated prevalence of monogenic causation in CAKUT between 10% to 20% (Ahn et al., 2020; Capone et al., 2017; Kagan et al., 2022; Ven et al., 2018) however prevalence can vary depending on the population under study, the CAKUT subtypes included in the analysis, and the method of analysis. For example, in a population of fetuses with bilateral kidney anomalies, high through-put next generation sequencing, identified a monogenic cause in 11 of 56 (20%) (Rasmussen et al., 2018). In a pediatric cohort of 100 children with renal hypodysplasia, Weber detected a monogenic cause in 17% of affected individuals (Weber et al., 2006). In a heterogenous pediatric cohort of 232 families encompassing a variety of subtypes of CAKUT, monogenic causation was observed in 14% (Ven et al., 2018). In a Korean population of children with CAKUT, targeted exome sequencing identified genetic causes in 13.8% of the 94 pathogenic variants in either HNF1B, PAX2, EYA1, UPK3A, and FRAS1 (Ahn et al., 2020). More recently, we demonstrated that in a large cohort of 731 families with CAKUT a single-gene cause for CAKUT was identified in 11.4% of families (Seltzsam et al., 2022). Copy number variants (CNVs) result from either deletions or duplications of chromosomal regions. The resulting change in gene dosage can result in CAKUT if the involved genes are known to be pathogenic in CAKUT. For example, pathogenic CNVs in HNF1B, EYA1, and CHD1L, have been described in patients with CAKUT (Ahn et al., 2020; Sanna-Cherchi et al., 2012). It is estimated that a further ~10–15% of cases of CAKUT are due to CNVs. Recent data demonstrates that the detection rate may be significantly higher in patients with syndromic CAKUT, where a detection rate of 29.4% was observed in patients with renal hypodysplasia and extra-renal features (i.e. non-isolated RHD) versus patients with isolated RHD (9.7% detection rate, p=0.060) (Cai et al., 2020).

Renal agenesis and the GDNF-RET signaling pathway

Renal agenesis is defined as absence of one (unilateral) or both (bilateral) kidneys. Despite the obvious similarities, these CAKUT phenotypes carry a vastly different prognosis: bilateral agenesis is often detected on pre-natal ultrasonography and is largely incompatible with life while unilateral renal agenesis may be entirely asymptomatic with many cases only detected as an incidental finding following abdominal imaging. The incidence of bilateral renal agenesis is estimated at 0.1–0.3 per 100 births while unilateral agenesis is estimated at 1 per 1000 live births. Renal agenesis is hypothesized to develop due to defects in ND formation, establishment of the MM, or disturbed GDNF expression and/or signaling (Figure 1) (Davis et al., 2014; Ichikawa et al., 2002; Schedl, 2007; Short & Smyth, 2016).

This process is tightly regulated by the GDNF-RET signaling pathway. GDNF is initially released from the MM and binds to its co-receptor GDNF Family Receptor Alpha 1 (GFRα1) (Chia et al., 2011; Davis et al., 2014). RET is a tyrosine kinase receptor that is expressed in the UB (Davis et al., 2014; A. T. van der Ven et al., 2018), that is activated by this GDNF-GFRα1-RET complex through phosphorylation of specific tyrosine residues. Mutations in genes that function either up-stream or downstream of the GDNF-GFRα1-RET pathway have been implicated in both human and murine CAKUT. For example, mutations in RET have been implicated in patients with CAKUT specifically those with renal agenesis (Chatterjee et al., 2012; Skinner et al., 2008). Mutations in GDNF regulatory genes EYA1 (Abdelhak et al., 1997), SIX1 (Ruf et al., 2004) and SIX5 (Hoskins et al., 2007) have also, been implicated in patients with syndromic CAKUT namely Brachio–Oto–Renal syndrome (OMIM #113650) (Krug et al., 2011), which is characterized by defects in branchial arch, ear and renal development. Regulation of both, the level and expression of GDNF, have also been associated with CAKUT with mutations in transcription factors PAX2, GATA3, and SALL1 implicated in disease pathogenesis. Heterozygous mutations in SALL1 are implicated in Townes–Brocks syndrome (OMIM # 107480), characterized by external ear anomalies with sensorineural hearing loss, limb anomalies, and renal and anorectal malformations (Kohlhase et al., 1998), while heterozygous mutations in GATA3 have been described in patients with DiGeorge-like phenotype (OMIM #146255) that includes hypoparathyroidism, heart defects, immune deficiency, deafness and renal malformations (Hwang et al., 2014; Van Esch et al., 2000).

Renal Hypodysplasia (RHD)

Both quantitative and qualitative abnormal development of the kidneys can result in a kidney(s) of reduced size (renal hypoplasia) with/without abnormal renal tissue (renal dysplasia). RHD can again, be unilateral or bilateral occurring a frequency of 1 in 1,000 and 1 in 5,000, respectively (Winyard & Chitty, 2008). One of the proposed pathways for the development of RHD is, as described above, abnormal interaction between RET, a receptor in UB and its ligand GDNF. This interaction is critical for the initial induction and out sprouting of the UB from the ND. GDNF acts a chemotactic factor for the UB, and is governed by several transcription factors many of which have been implicated in renal hypodysplasia (PAX2, EYA1, HOXD11 and SIX2) (Kagan et al., 2022; Vivante & Hildebrandt, 2016). Most notably, heterozygous mutations in the transcription factor, Paired-Box gene 2 (PAX2), are known to cause monogenic CAKUT (Thomas et al., 2011) and are described in families with Renal Coloboma Syndrome (OMIM # 120330) (Sanyanusin et al., 1995).

Multicystic dysplastic kidney (MCDK)

Multicystic dysplastic kidney is characterized by multiple irregular cysts randomly distributed in a dysplastic kidney (Spence, 1955). MCDK is often classified within the category of renal cystic disease (RCD) however due to the developmental origin, it falls within the CAKUT spectrum of disease (Raina et al., 2021). For the purpose of this review, we have excluded other forms of renal cystic disease including polycystic kidney disease, ciliopathies including nephronophthisis and cystic disease in cancer syndrome as the etiology and pathogenesis does not fall within the CAKUT spectrum. MCDK is a form of dysplasia of the kidney with cyst developing as a results of abnormal kidney development, which contrast from other forms of renal cystic disease which result from a primary ciliary disorder (nephronophthisis and polycystic kidney disease). MCDK has an incidence of 1 in 4,300 and is frequently associated with other CAKUT phenotypes such as VUR (Schreuder et al., 2009). Multiple genes have been implicated in the MCDK phenotype, including Hepatocyte nuclear factor 1-beta (HNF1B) and PAX2, however many of the genes implicated in CAKUT (Table 2 and Table 3) have also been implicated in this subtype of CAKUT. Heterozygous mutations in HNF1B have been identified in patients with renal cysts and diabetes syndrome (OMIM #137920) and maturity-onset diabetes of the young type 5 (OMIM #606391). Equally, HNF1B associated disease can present with multiple CAKUT phenotypes including renal agenesis, RHD and MCDK. The reason for the cystic phenotype may be related to abnormal interaction between HNF1B and the PKHD1 gene, which when mutated causes autosomal recessive polycystic kidney disease (OMIM #263200). HNF1B, which is a transcription factor, binds to the proximal promoter of the PKHD1 gene to stimulate gene transcription (Hiesberger et al., 2004). Copy number variants on chromosome 17 which involve the HNF1B gene, including whole gene deletions, have also been described in patient with CAKUT and diabetes since the HNF1B gene is located on chromosome 17 (Mefford et al., 2007; Sanna-Cherchi et al., 2012). Together mutations in the transcription factors PAX2 or HNF1B, both of which are associated with an autosomal dominant mode of inheritance, constitute the most common mutations found in patients with CAKUT (Thomas et al., 2011).

Vesico-ureteric reflux (VUR)

VUR is a functional disorder of the bladder ureter connectivity which results in retrograde passage of urine from the bladder to the ureter and/or kidneys. Both genetic and environmental triggers are hypothesized to contribute to defective function of this valve. Valvular function is regulated by both the anatomical structure of the valve, such as the length of the submucosal ureter, the width of the ureteric opening, the muscles of the trigone and ureter, and ureteric peristalsis (Tokhmafshan et al., 2017; Williams et al., 2008). Ultimately this retrograde flow of urine can result in chronic infections and scarring of the kidney tissue which is often referred to as “reflux nephropathy”. In utero abnormal interaction between the UB and MM are again implicated in VUR (Figure 1B) (Bertoli-Avella et al., 2008), with mutations in genes such as ROBO2 implicated in VUR in both mice and humans (Lu et al., 2007). For example, heterozygous mutations in ROBO2, with subsequent reduction in ROBO2 gene dosage have been detected in patients with VUR (Hwang et al., 2014). ROBO2 is a transmembrane receptor that binds to its SLIT2 ligand and together have been implicated in regulating GDNF-RET signaling pathway (Bertoli-Avella et al., 2008; Hwang et al., 2015).

Hydronephrosis and bladder pathology

Hydronephrosis can result from any pathology that results in the impedance of normal urinary flow in either the upper or lower urinary tract and subsequent backpressure on the kidney and urinary tract. The clinical manifestation in most cases is ultrasonographic evidence of either hydronephrosis or hydroureter. The primary sites of obstruction within the urinary tract are either the ureter-pelvic or ureter-bladder junction. Both structural malformations and functional abnormalities in the ureteric smooth muscle can lead to obstruction within the urinary tract. Ureter-pelvic junction obstruction (UPJO) is one of the primary causes of hydronephrosis particularly in the neonatal period and is hypothesized to be caused by congenital absence of peristaltic contraction ability within the ureter. Loss of this peristaltic contractility is thought to be related to inappropriate smooth muscle difference in the ureteral wall (Bohnenpoll & Kispert, 2014). TBX18, a transcription factor expressed in undifferentiated mesenchymal cells surrounding the distal ureter stalk. Defects in this gene have been implicated in abnormal smooth muscle differentiation in the ureteral wall, thus leading to UPJO. In fact, heterozygous Tbx18 mice have been shown to develop UPJO while in human with heterozygous mutations in TBX18 have UPJO with hydronephrosis (Airik et al., 2006; Vivante et al., 2015).

The other source of obstruction within the genitourinary tract is the bladder. Recently, Mann et al. demonstrated that disruption of the neural pathways innervating the bladder can lead to bladder dysfunction ultimately leading to hydronephrosis (N Mann et al., 2019). Genes involved in the regulation of smooth muscle formation and contraction, neuronal patterning, and synaptic neuronal transmission in the bladder such as CHRM3 (Weber et al., 2011), ACTG2 (Thorson et al., 2014), ACTA2 (Milewicz et al., 2010), MYH11 (Kloth et al., 2019), MYLK (Halim et al., 2017), HPSE2 (Bulum et al., 2015), LRIG2 (Stuart et al., 2013) and most recently CHRNA3 (N Mann et al., 2019) have been shown to cause ureteral and bladder dysfunction leading to obstructive changes in the urinary tract.

Syndromic CAKUT and the Fraser Complex

CAKUT may occur in isolation as a monogenic disorder or as part of a syndromic disorder. For example, Fraser Syndrome (OMIM # 219000) is a rare autosomal recessive form of CAKUT characterized by renal anomalies with extra-renal features including syndactyly, cryptophthalmos, and abnormalities of the respiratory tract (van Haelst et al., 2008). The Fraser Complex (FC) is an extracellular matrix complex composed of a group of related protein, which include FRAS1, FREM2, FREM1 and GRIP1. The function of the FC once assembled is to stabilizes interaction between the UB and the MM (Figure 1). Both the assembly and maintenance of FC is governed by FC genes (FRAS1, FREM2 FREM1 and GRIP1) (Kiyozumi et al., 2006; Pavlakis et al., 2011; Takamiya et al., 2004) and have already been described in patients with CAKUT (Jadeja et al., 2005; McGregor et al., 2003; Nathanson et al., 2013; Slavotinek et al., 2006; Takamiya et al., 2004; van Haelst et al., 2008). Interestingly the FC gene developmental pathway has also been shown to regulate GDNF expression in the MM, which as outlined above is important in the GDNF-RET signaling pathway, demonstrating the link between various developmental pathways during kidney development. The loss of integrity of the FC due to pathogenic mutations in FRAS1, FREM2, FREM1 and GRIP1 can therefore lead to impaired interaction between the UB and MM (Pitera et al., 2008). In addition, the cytosolic protein GRIP1 has been shown to interact with FRAS1 facilitating appropriate trafficking and targeting in the UB (Takamiya et al., 2004).

Nephronectin (Npnt) is an extracellular matrix protein which is expressed during kidney development including the UB. The FC once assembled at the epithelial-mesenchymal interface of the UB, directly interacts with Npnt. Very recently, a pathologic homozygous frameshift variant in NPNT was detected in a family with 3 cases of bilateral renal agenesis. Pathogenicity was confirmed of this biallelic loss-of-function variant in a knock-in mouse model (Dai et al., 2021). At the UB, Npnt serves as an adaptor for other proteins expressed in the MM such as Integrin Subunit Alpha 8 (ITGA8) and Integrin Subunit Beta 1 (ITGB1) (Brandenberger et al., 2001; Kiyozumi et al., 2012; Linton et al., 2007), the former which has also been implicated in human disease (OMIM # 191830) (Humbert et al., 2014; Kohl S, 2014). ITGA8 is also an upstream activator of GDNF, which again, as outlined above is involved in the tyrosine kinase signaling pathway (Kiyozumi et al., 2012; Linton et al., 2007).

Another regulator in the interaction between the UB and MM, which occurs at the level of the extra-cellular matrix are the heparin sulphate proteoglycans (HSPGs) (Bonnans et al., 2014; Patel et al., 2017; Steer et al., 2004). HPSE2 encodes the Heparanase 2 enzyme which is an endoglycosidase that degrades heparin sulphate proteoglycans (Levy-Adam et al., 2010). Uro-facial syndrome (also known as Ochoa syndrome, OMIM # 236730) is an autosomal recessive disorder due to mutations in HPSE2 and is characterized by syndromic facial features, where there is a crying facial expression when attempting to smile along with features of the CAKUT disease spectrum including hydronephrosis, hydroureter, and posterior urethral valve (Vivante, Hwang, et al., 2017).

VACTERL association

VACTERL association or VATER syndrome describes a sequence of anomalies that includes Vertebral anomalies, Anorectal malformations, Cardiac defects, Trachea-esophageal fistula and/or Esophageal atresia, Renal anomalies, and Limb defects. This is a rare disease entity with an estimated prevalence of between 1 in 10,000 to 1 in 40,000 births. Genetic causation in VACTERL similar to CAKUT, is suspected due to a number of factors: a) familial cluster of the disease with increased prevalence in first degree relative of affected individuals, b) high concordance between monozygotic twins and, c) the existence of murine knock-out models of disease (Reutter et al., 2016). Both chromosomal anomalies and single gene disorder have been detected in patients with VACTERL with mutations in the genes TRAP1 and ZIC3 implicated in human disease (Chung et al., 2011; Saisawat et al., 2014). A recent exome sequencing study in 21 families with VACTERL, revealed a candidate variant in 6 families (21%). The variants included biallelic and X-chromosomal hemizygous variants in the following genes: B9D1, FREM1, ZNF157, SP8, ACOT9, and TTLL11 (Kolvenbach et al., 2021), however further work is still required to confirm if these possible candidate genes are indeed disease causing.

Conclusion

Current data indicates that when a patient presents with CAKUT, genetic testing will reveal a monogenic cause of disease in 10 to 20% of individuals (N. Mann et al., 2019; Rasmussen et al., 2018; Seltzsam et al., 2022; Ven et al., 2018; Weber et al., 2006). This percentages increases in the presence of extra-renal features of disease and patients with so-called syndromic CAKUT. Ongoing novel gene discovery has led to the identification of almost 200 monogenic causes of both isolated and syndromic CAKUT (Table 2 and Table 3). With the ever-expanding use of high through-put sequencing techniques, many of the newly identified genes have started to converge on overlapping signaling pathways, such as the GDNF-RET signaling pathway, the Fraser complex pathways and more recently the retinoic acid metabolism pathway (A. T. van der Ven et al., 2018). Mutations in implicated genes are hypothesized to lead to various levels of disruptions in the interaction between the ureteric bud and the metanephric mesenchyme or subsequent branching morphogenesis and nephrogenesis in utero. Further work is necessary to determine the exact interplay between these signaling pathways in CAKUT pathogenesis.