The definition of congenital anomalies of the kidney and urinary tract (CAKUT) refers to the disease of structural malformations in the kidney and/or urinary tract [1]. CAKUT covers renal agenesis, renal hypodysplasia, multicystic dysplastic kidney, hydronephrosis, ureteropelvic junction obstruction, megaureter, ureter duplex, posterior urethral valves and vesicoureteral reflux (VUR) [1]. It's frequency and morbidity is relatively high because it can occur in about 1:500 live born children and account about 40%–50% of children with chronic kidney disease [23]. Among the whole feature of CAKUT, VUR has been traditionally considered the most important phenotype for urinary tract infection (UTI) and kidney damage, with possibly serious long-term consequences, such as hypertension and decreased renal function causing reflux nephropathy [4]. It is controversial, however, that the pathogenesis of reflux nephropathy is “congenital” or “acquired.” Some studies hypothesized that patients with VUR showed congenital renal scar before birth [56]. It could be caused by the progression to “congenital” reflux nephropathy and renal failure, although UTI and associated kidney inflammation is absent [56]. Others believe that the pathogenesis of “acquired” reflux nephropathy is the high pressure caused by the refluxing urinary stream and recurrent UTI which injure the kidney parenchyma [78]. Like VUR or reflux nephropathy, the pathogenesis of CAKUT remains unclear, and it is not well understood why only some patients progress to develop chronic kidney disease. The cause of most CAKUT cases is unknown, therefore, many studies searching for the genes are attempted. In this article, we will review on genetic causes of VUR and CAKUT.

Understanding the genetic architecture of CAKUT is difficult due to the phenotypic heterogeneity and multifactorial genetic penetrance [9]. Until recently, more than 20 human single-gene causes for CAKUT have been identified [10111213]. Understanding the genetic basis of CAKUT can be helpful to know about the kidney development. Kidney development consists of the following developmental stages: ureteric budding, metanephric kidney, mesenchymalto-epithelial transition (MET), and nephron patterning and elongation (which include proximal and distal tubule morphogenesis and glomerulogenesis) [11415161718]. These developmental stages are controlled by a large number of genes and signaling pathways and defects in these steps can lead to the clinical phenotypes of CAKUT (Table 1).

VUR can be induced by multiple birth defects affecting the urinary tract development: ureteric budding, ureter differentiation and elongation, peristalsis, UVJ formation, and bladder and urethra development [19]. The ectopic ureteric orifice is related to “Bud theory” stage, which is abnormal development of the embryonic ureteric bud [20]. This theory hypothesizes that the site at which the ureteric bud grows out from the mesonephric duct is essential for development of normal kidney and urinary tract. Actually, many early development genes involved in the ureteric budding stage lead to VUR and CAKUT. This hypothesis is closely correlated to analysis of duplex kidneys which showed that a more severe hypoplasia and dysplasia were closely associated with mal-displacement of the ureteral orifice.

In fact, ureteric budding is related to signaling mechanisms including transcription factors such as RET, PAX2, EYA1, SALL1, SIX1, SIX2, BMP4, and GATA3 [2122232425262728293031323334353637]. They have been recognized to be mutated with CAKUT and present several extrarenal manifestations [2122232425262728293031323334353637].

The RET proto-oncogene provides instructions for producing a protein that is involved in signaling within cells and mutations in the RET gene cause several diseases [38]. For example, translocations in the gene were correlated with papillary thyroid cancer [21] and multiple endocrine neoplasia (MEN) 2A and 2B syndromes [22]. RET mutation is also frequently showed in humans with renal diseases, because ureteric budding is promoted through receptor RET by Glial cell-derived neurotrophic factor (GDNF) signaling [23]. Therefore, RET mutations were subsequently reported to develop CAKUT in fetuses with bilateral renal hypodysplasia/agenesis [24].

Paired box gene 2 (PAX2) plays a key role in the development and proliferation of multiple cell lines and development of organs [39]. Therefore, PAX2 mutations in kidney can develop some disease spectrum of CAKUT, including VUR, renal hypodysplasia, renal cysts, and multicystic dysplastic kidneys [25].

Eyes absent homolog 1 (EYA1) encodes the eyes absent (EYA) family of proteins. The protein may play important roles in the development of eye, ear, branchial arches and kidney. EYA1 mutations have been related with branchiootic (BO) syndrome and congenital cataracts [2627].

Sal-like 1 (SALL1) is one of the human orthologues of the spalt (sal) gene known in Drosophila [40]. SALL1 mutations are a cause of Townes-Brocks syndrome (TBS) and branchio-oto-renal (BOR) syndrome [2829]. TBS is an autosomal dominant syndrome containing following features: renal abnormalities (multicystic kidneys, dysplastic kidney, hypoplastic kidneys), abnormalities of the external ears (dysplastic ears, sensorineural hearing loss or deafness), anorectal malformations (rectovaginal fistula, anal stenosis, imperforate anus/absence of an anal opening), heart abnormalities (ventricular septum defects and Tetralogy of Fallot) and hand and foot abnormalities (hypoplastic or fingerlike thumbs, syndactyly, fusion of the wrist bones, overlapping foot and/or toe bones) [2829].

SIX1 and SIX2 genes are similar genes each other known as the SIX gene family. Genes in this family encode proteins that bind to DNA and control the activity of other genes [3031]. When the SIX1 is mutated, it impairs the normal development of tissues at fetal stage and develops the major signs and symptoms of BOR/BO syndrome similar to phenotypes resulting from EYA1 or SALL1 mutations [3031].

Bone morphogenetic protein 4 (BMP4) produces a member of the transforming growth factor-β superfamily protein [32]. Some studies hypothesize about the role of BMP4 that it implicates in several aspects of embryonic development by regulating cell proliferation, differentiation, and apoptosis [323334]. BMP4 is further continuously expressed beyond the stage of ureteric budding throughout the embryonic development of the kidney and urinary system [323334].

Trans-acting T-cell-specific transcription factor GATA-3 (GATA3) gene encodes a transcription factor of the Gata protein family that is expressed in the ureteric buds. It is regulated by the PAX2 gene and involved in the Wolffian duct morphogenesis [35]. GATA3 mutation can cause hydroureter, ectopic ureteric budding, vas deferens hyperplasia, duplex kidney, uterine agenesis as well as Hypoparathyroidism, sensorineural Deafness, and Renal disease syndrome (including renal dysplasia, unilateral kidney agenesis, and VUR) [3637].

The metanephric kidney is formed after interaction between the ureteric bud and the metanephric mesenchyme. It starts at 4 weeks of gestation in humans, and it is regulated by Slit homolog 2 (SLIT2) and Roundabout homolog 2 (ROBO2) when the genes are expressed as a ligand and transmembrane receptor [41]. SLIT2-ROBO2 signaling has been shown to play a role after initiating ureteric budding [41].

ROBO2 encodes a protein as an “immunoglobulin receptor” for the Slit protein and functions in axon guidance and cell migration. ROBO2 mutations are related with VUR [41].

SLIT2 encodes Slit protein which is a member of secreted glycoproteins. This protein acts as “ligands” for the Robo family. SLIT2 may associated with guiding commissural axons in the forebrain by acting as a repulsive signal preventing inappropriate midline crossing of axons projecting from the olfactory bulb [42]. Therefore, SLIT2 can affect the formation and maintenance in the nervous system [43]. In the uretero-renal system, SLIT2 mutations also can cause duplicated collecting system, unilateral renal agenesis, and cystic dysplastic kidneys [4144].

SLIT-ROBO Rho GTPase-activating protein 1 (SRGAP1), as the gene name shows, is a small GTPase activating protein associated with the pathway mediating the repulsive signaling of Robo and Slit proteins in the cell migration process [45]. In 2015, Hwang et al. [44] identified 2 heterozygous mutations in SRGAP1 in 2 unrelated families and described it as a novel monogenic candidate gene as causes of CAKUT in humans.

After metanephric kidney stage, there are 3 steps left to complete the whole kidney development. Several genes involved in CAKUT have been described for the following process: (1) WNT4 and FGF20 for MET, (2) AGT, REN, ACE, and AGTR1 for renin-angiotensin system, and (3) Uromodulin (UMOD) for nephron patterning and elongation.

Not only genes described above, following genes are also known as a leading cause of CAKUT in several studies: TRAP1, PKHD1, KAL1, HOXA13, and NIPBL. Their pathogenesis of CAKUT especially associated with kidney development process, however, are not clearly revealed.

Tumor Necrosis Factor Receptor-associated Protein 1 (TRAP1) encodes a mitochondrial chaperone protein that is member of the heat shock protein 90 family. The protein has ATPase activity and may function in regulating cellular stress responses [60]. Mutations of TRAP1 can develop many kinds of CAKUT phenotypes or CAKUT in VACTERL syndrome (combination of at least three of the following congenital anomalies: vertebral defects (V), anorectal malformations (A), cardiac defects (C), tracheoesophageal fistula with or without esophageal atresia (TE), renal malformations (R), and limb defects (L) [61].

Polycystic kidney and hepatic disease 1 (PKHD1) provides instructions for making a protein called fibrocystin. Fibrocystin exists on the cell membrane of kidney cells as a receptor and interacts with molecules and signals outside of the cell [62]. More than 270 mutations in the PKHD1 gene have been identified in human with autosomal recessive polycystic kidney disease (ARPKD) [59].

Kallman syndrome 1 (KAL1) gene encodes a protein called anosmin-1. Anosmin-1 is expressed in the fetal certain regions of the brain, respiratory tract, digestive system and kidneys [63]. But the precise function of anosmin-1 in kidney is not well known. It is also unclear how KAL1 gene mutations lead to signs of Kallmann syndrome, including unilateral renal agenesis [6465].

Homeobox protein Hox-A13 (HOXA13) is a part of homeobox gene family, which appears to play a key role for the formation and development of the limbs (particularly the hands and feet), urinary tract, and reproductive system. At least 14 HOXA13 gene mutations have been found in hand-foot-genital syndrome, which can have features of VUR [6667].

Nipped-B-like protein (NIPBL) makes a protein named delangin, which helps the activity of chromosomes during cell division and controls human development [68]. NIPBL gene mutations have been identified in people with Cornelia de Lange syndrome which is a developmental disorder affecting many parts of the body. In this syndrome, sometimes VUR is also found [6970].

Nowadays, there are many attempts and technological developments to find out additional CAKUT related genes: linkage studies, targeted next-generation sequencing (NGS), copy number variation (CNV) analysis, whole genome sequencing (WGS) and genome-wide association studies (GWAS).

Linkage analyses have been successful for mapping genetic markers by analyzing a disease in a family-based approach in insulin-dependent diabetes mellitus, Alzheimer disease, breast cancer [717273]. The majority of published linkage studies on CAKUT have been about familial VUR, which occurs in ~1% of children [74]. However, linkage analysis is not sufficient tool to detect small effect sized loci [9].

Analysis of multiple genes using NGS in patients with CAKUT has demonstrated that <10% patients with CAKUT carry variants in previously implicated genes, such as HNF1B, PAX2, EYA1, SIX5, and RET. Therefore, the causative genes are not yet identified in most of CAKUT cases even though NGS technique was applied [757677].

Another aspect of CAKUT is CNVs [78]. It can be identified by high-resolution microarrays, such as the array comparative genomic hybridization (array-CGH) and single nucleotide polymorphism (SNP) microarrays [79].

Currently, genetic studies in unexplained diseases are shifting from whole exome sequencing or CNV analysis to WGS [9]. Also, GWAS, which is known as a high-throughput genotyping technologies, makes the rapid genotyping of >1 million SNPs throughout the whole genome. GWAS can also identify associated loci that confer risk of CAKUT with large sample size [8081].

Because morbidity of CAKUT may not manifest until later in life, early detection of these patients is important. CAKUT is a genetically heterogeneous group of disorders that are caused by mutations in genes related to the kidney development process. The malformation phenotypes due to gene mutations diverse from normally structured kidneys with intact kidney function to severe hypodysplasia and end stage renal failure. Although primary VUR is one of the most common phenotype of CAKUT, its prevalence can be underestimated until it shows symptoms such as fever.

However, some studies have pointed that CAKUT always has to be considered when the patient develops small phenotypes of anomalies related to urinary tract and kidney [910111213]. The advancement in sequencing and bioinformatics technologies will show us the additional CAKUT-related genes and more relevant etiologies of disease entities than can be identified by imaging study tools or histopathology alone. Newly advancing bioinformatics technologies will show us the additional CAKUT-related genes and more relevant etiologies of disease entities. Moreover, these genetic findings will provide an opportunity to develop an ideal diagnostic CAKUT genetic test in clinical practice to facilitate early diagnosis, better management of the disease, and familial genetic counselling [9]. When the price of GWAS gets lower than that of these days and it becomes more popular, we will be able to apply genetic tests to suspected patients. Using these new tools, we could identify the patients with high risks of having the deformities in kidneys before it is too late. Understanding of CAKUT and VUR genetic bases will help the management of this condition in children.