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Homozygous Loss-of-Function Variant in SLC20A1 Coding for Ubiquitous Phosphate Transporter PiT1 Is Associated With

Eugénie Koumakis1,2, Céline Huber1, Wendy Chung3

  • 1Paris Cité University, INSERM UMR 1163, Imagine Institute, Paris, France.

Clinical Genetics
|March 30, 2026
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Summary
This summary is machine-generated.

Biallelic loss of function in SLC20A1 causes a new multisystem developmental disorder. This phosphate transporter (PiT1) deficiency leads to severe congenital anomalies and developmental delays in affected individuals.

Keywords:
PIT1SLC20A1ciliopathydevelopmental disorderhuman diseasepolydactylyrenal agenesistetralogy of Fallot

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Area of Science:

  • Genetics
  • Developmental Biology
  • Human Physiology

Background:

  • SLC20A1 encodes the phosphate transporter PiT1, crucial for phosphate homeostasis.
  • PiT1 also regulates cell proliferation, differentiation, apoptosis, and embryonic development.
  • Heterozygous SLC20A1 variants are linked to urinary tract malformations, but biallelic loss-of-function effects were unknown.

Purpose of the Study:

  • To investigate the impact of biallelic loss-of-function variants in SLC20A1.
  • To characterize the clinical phenotype associated with SLC20A1 deficiency.
  • To explore the molecular mechanisms underlying this disorder.

Main Methods:

  • Case report of a child with biallelic SLC20A1 variant and congenital anomalies.
  • Analysis of PiT1 expression in patient-derived fibroblasts.
  • Transcriptome analysis of patient fibroblasts to identify dysregulated pathways.
  • Population screening for carrier frequency.

Main Results:

  • First human case of biallelic homozygous predicted loss-of-function SLC20A1 variant (c.674_675delAA; p.K225TfsX34) identified.
  • Patient presented with multiple congenital anomalies: tetralogy of Fallot, renal agenesis, polydactyly, growth impairment, and developmental delay.
  • Decreased PiT1 expression and dysregulation of PI3K-Akt, Wnt, MAPK, and BMP signaling pathways observed in patient fibroblasts.
  • Carrier frequency of 1:432 identified in Ashkenazi Jewish population.

Conclusions:

  • Biallelic PiT1 deficiency causes a previously unrecognized multisystem developmental disorder.
  • The findings expand the known phenotypic spectrum of SLC20A1-related diseases.
  • SLC20A1 is essential for normal embryonic development and organogenesis.