# Genetics of CAKUT

**Authors:** Alina C. Hilger, Rik Westland, Julia Hoefele

PMC · DOI: 10.1515/medgen-2025-2053 · Medizinische Genetik · 2026-02-18

## TL;DR

This paper reviews the genetic causes of congenital kidney and urinary tract anomalies, focusing on recent discoveries and their clinical implications.

## Contribution

The paper summarizes recent genetic findings and genotype–phenotype correlations in CAKUT over the past decade.

## Key findings

- CAKUT is caused by both monogenic variants and multifactorial influences.
- Recent studies have identified key developmental pathways and genotype–phenotype correlations.
- Emerging genetic mechanisms are informing diagnosis and clinical management.

## Abstract

Congenital anomalies of the kidney and urinary tract (CAKUT) represent a heterogeneous group of developmental disorders and are the leading cause of pediatric chronic kidney disease worldwide. The phenotypic spectrum is broad, encompassing kidney agenesis, hypodysplasia, multicystic dysplastic kidneys, vesicoureteral reflux, obstructive uropathies, and other malformations affecting the kidneys, ureters, and urethra. Advances in genetics have begun to unravel the molecular pathways underlying these diverse phenotypes, yet the complexity of CAKUT reflects contributions from both monogenic variants and multifactorial causes.

This review provides an overview of the current understanding of the genetic causes of CAKUT, beginning with fundamental principles of kidney and urinary tract development, and then focusing on major discoveries in the past ten years. We aim to summarize key genetic findings, with an emphasis on genotype–phenotype correlations and developmental pathways, highlight emerging mechanisms, and discuss their implications for diagnosis, counseling, and clinical management.

## Full-text entities

- **Genes:** Pax2 (paired box 2) [NCBI Gene 18504] {aka Opdc, Pax-2}, TBX5 (T-box transcription factor 5) [NCBI Gene 6910] {aka HOS}, Gata3 (GATA binding protein 3) [NCBI Gene 14462] {aka Gata-3, jal}, Fgf20 (fibroblast growth factor 20) [NCBI Gene 80857] {aka Fgf4a}, TSHZ3 (teashirt zinc finger homeobox 3) [NCBI Gene 57616] {aka TSH3, ZNF537}, Zmym2 (zinc finger, MYM-type 2) [NCBI Gene 76007] {aka 5830413P05Rik, FIM, MYM, RAMP, SCLL, Zfp198}, PTK7 (protein tyrosine kinase 7 (inactive)) [NCBI Gene 5754] {aka CCK-4, CCK4}, Gfra1 (glial cell line derived neurotrophic factor family receptor alpha 1) [NCBI Gene 14585] {aka GFRalpha-1}, Wdpcp (WD repeat containing planar cell polarity effector) [NCBI Gene 216560] {aka Frtz, homolog-13}, MYOCD (myocardin) [NCBI Gene 93649] {aka MGBL, MYCD}, BNC2 (basonuclin zinc finger protein 2) [NCBI Gene 54796] {aka BSN2, LUTO, bn2}, ARID3A (AT-rich interaction domain 3A) [NCBI Gene 1820] {aka BRIGHT, DRIL1, DRIL3, E2FBP1}, Itga8 (integrin alpha 8) [NCBI Gene 241226], FOXC1 (forkhead box C1) [NCBI Gene 2296] {aka ARA, ASGD3, FKHL7, FREAC-3, FREAC3, IGDA}, Bmp7 (bone morphogenetic protein 7) [NCBI Gene 12162] {aka OP1}, Six1 (sine oculis-related homeobox 1) [NCBI Gene 20471], Fgfr2 (fibroblast growth factor receptor 2) [NCBI Gene 14183] {aka Bek, Fgfr-2, Fgfr-7, Fgfr2b, Fgfr7, KGFR}, Gdnf (glial cell line derived neurotrophic factor) [NCBI Gene 14573] {aka ATF}, Wnt9b (wingless-type MMTV integration site family, member 9B) [NCBI Gene 22412] {aka Wnt14b, Wnt15, clf, clf1, wnt-14b, wnt-15}, Vangl1 (VANGL planar cell polarity 1) [NCBI Gene 229658] {aka Kitenin, Lpp2, Stb2, Stbm}, Fzd8 (frizzled class receptor 8) [NCBI Gene 14370] {aka Fz8}, Lrp4 (low density lipoprotein receptor-related protein 4) [NCBI Gene 228357] {aka 6430526J12Rik, D230026E03, Megf7, mdig}, SALL1 (spalt like transcription factor 1) [NCBI Gene 6299] {aka HEL-S-89, HSAL1, Sal-1, TBS, ZNF794}, NR6A1 (nuclear receptor subfamily 6 group A member 1) [NCBI Gene 2649] {aka CT150, GCNF, GCNF1, NR61, RTR, hGCNF}, Eya1 (EYA transcriptional coactivator and phosphatase 1) [NCBI Gene 14048] {aka bor}, SOX9 (SRY-box transcription factor 9) [NCBI Gene 6662] {aka CMD1, CMPD1, ENH13, SRA1, SRXX2, SRXY10}, Ret (ret proto-oncogene) [NCBI Gene 19713] {aka PTC, RET51, RET9, c-Ret}, GFRA1 (GDNF family receptor alpha 1) [NCBI Gene 2674] {aka GDNFR, GDNFR-alpha-1, GDNFRA, GFR-ALPHA-1, GFRalpha-1, RET1L}, Hnf1b (HNF1 homeobox B) [NCBI Gene 21410] {aka HNF-1-beta, HNF-1B, HNF-1Beta, Hnf1beta, LFB3, Tcf-2}, Wnt4 (wingless-type MMTV integration site family, member 4) [NCBI Gene 22417] {aka Wnt-4}, Bmp4 (bone morphogenetic protein 4) [NCBI Gene 12159] {aka Bmp-4, Bmp2b, Bmp2b-1, Bmp2b1}, HNF1B (HNF1 homeobox B) [NCBI Gene 6928] {aka ADTKD3, FJHN, HNF-1-beta, HNF-1B, HNF1beta, HNF2}, Foxd2 (forkhead box D2) [NCBI Gene 17301] {aka Mf2}, Wnt5a (wingless-type MMTV integration site family, member 5A) [NCBI Gene 22418] {aka 8030457G12Rik, Wnt-5a}
- **Diseases:** chronic kidney disease (MESH:D051436), multicystic dysplastic kidney (MESH:D021782), pancreatic atrophy (MESH:D010195), Ureteral anomalies (MESH:D014515), RCAD (MESH:C535520), diabetes (MESH:D003920), dysmorphic (MESH:D057215), neurogenic bladder (MESH:D001750), agenesis (MESH:C536482), Urethral anomalies (MESH:D014526), eye abnormalities (MESH:D005124), dysplasia (MESH:D015792), hypomagnesemia (OMIM:613882), autism spectrum disorder (MESH:D000067877), small hands and (MESH:D018288), growth restriction (MESH:D005317), hypoplasia (MESH:D000080344), Axenfeld-Rieger syndrome (MESH:C535679), mass reduction (MESH:C536030), anal canal stenosis (MESH:C563020), Congenital defects of the bladder (MESH:D001745), proteinuria (MESH:D011507), congenital kidney anomalies (MESH:D007680), obstructive uropathies (MESH:C536483), hearing impairment (MESH:D034381), renal hypoplasia (MESH:D006030), genetic diseases (MESH:D030342), clinodactyly (MESH:C537090), craniofacial dysmorphism (MESH:C537512), microcephaly (MESH:D008831), ureteropelvic junction obstruction (MESH:C537373), facial dysmorphic features (MESH:C536503), obesity (MESH:D009765), anterior segment dysgenesis (MESH:C537775), congenital heart defects (MESH:D006330), hydronephrosis (MESH:D006869), congenital lower urinary tract obstruction (MESH:D014552), cardiac and gastrointestinal malformations (MESH:D005767), DiGeorge/velocardiofacial syndrome (MESH:C563337), renal pelvic dilation (MESH:D002311), 22q11.2 deletions (MESH:D004062), CAKUT (MESH:C566906), congenital urethral stenosis (MESH:D014525), VUR (MESH:D014718), hypertension (MESH:D006973), renal cystic dysplasia (MESH:D052177), cystic dysplasia (MESH:C537755), dysplastic/hypoplastic nails (MESH:D009260), posterior (MESH:D001041), urethral obstruction (MESH:D014524), extrarenal abnormalities (MESH:D000014), hypocalcemia (MESH:D006996), scoliosis (MESH:D012600), ectopic ureters (MESH:D014516), Townes-Brocks syndrome (MESH:C536974), papillary atrophy (MESH:D002291), renal cysts (MESH:D003560), developmental delay (MESH:D002658), ureteral obstruction (MESH:D014517), LUTO (MESH:D014570)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606], Danio rerio (leopard danio, species) [taxon 7955], Xenopus laevis (African clawed frog, species) [taxon 8355]

## Full text

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## References

29 references — full list in the complete paper: https://tomesphere.com/paper/PMC12910339/full.md

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Source: https://tomesphere.com/paper/PMC12910339