Autosomal recessive hypophosphatemic bone disease: genes and variants
Autosomal recessive hypophosphatemic bone disease is linked to 1 analyzed protein (SLC34A3). 13 DNA variants are known to cause it; 171 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to Autosomal recessive hypophosphatemic bone disease
SLC34A3: Sodium-dependent phosphate transport protein 2C
It reabsorbs phosphate in the renal proximal tubule under hormonal control and is essential for maintaining serum phosphate and bone mineralization. Biallelic or dominant pathogenic variants can cause hereditary hypophosphatemic rickets with hypercalciuria.
13 disease-causing and 171 uncertain variants in SLC34A3 are linked to Autosomal recessive hypophosphatemic bone disease.
Where Autosomal recessive hypophosphatemic bone disease variants cluster
- SLC34A3 Extracellular (positions 389–445): 5 of 13 disease-causing changes, 4.0× more than its size predicts.
- SLC34A3 Transmembrane (positions 189–209): 3 of 13 disease-causing changes, 6.6× more than its size predicts.
Known disease-causing variants in Autosomal recessive hypophosphatemic bone disease
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| SLC34A3 M1I | 1 | Cytoplasmic | Disease-causing (★★) |
| SLC34A3 M1T | 1 | Cytoplasmic | Disease-causing (★★) |
| SLC34A3 S192L | 192 | Transmembrane | Disease-causing (★★) |
| SLC34A3 G196R | 196 | Transmembrane | Disease-causing (★★) |
| SLC34A3 A413E | 413 | Extracellular | Disease-causing (★★) |
| SLC34A3 G457S | 457 | Transmembrane | Disease-causing (★★) |
| SLC34A3 R468W | 468 | Cytoplasmic | Disease-causing (★★) |
| SLC34A3 S192W | 192 | Transmembrane | Disease-causing (★) |
| SLC34A3 G406V | 406 | Extracellular | Disease-causing (★) |
| SLC34A3 G404R | 404 | Extracellular | Disease-causing (★) |
| SLC34A3 G419D | 419 | Extracellular | Disease-causing (★) |
| SLC34A3 P369L | 369 | Transmembrane | Disease-causing (★) |
| SLC34A3 T425I | 425 | Extracellular | Disease-causing |
Which prediction tools work for Autosomal recessive hypophosphatemic bone disease
How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).
- CATVariant: 92 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- PolyPhen-2: 90 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- SIFT: 89 out of 100
Diseases related to Autosomal recessive hypophosphatemic bone disease
- Hypophosphataemia or rickets, also linked to SLC34A3
Frequently asked questions
Which genes are linked to Autosomal recessive hypophosphatemic bone disease?
In CATVariant, Autosomal recessive hypophosphatemic bone disease is linked to 1 analyzed protein: SLC34A3 (Sodium-dependent phosphate transport protein 2C).
How many genetic variants are linked to Autosomal recessive hypophosphatemic bone disease?
187 variants: 13 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 171 are of uncertain significance or have conflicting reports.
Which uncertain variants in Autosomal recessive hypophosphatemic bone disease look disease-causing?
None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.
Which variant effect predictor works best for Autosomal recessive hypophosphatemic bone disease?
Among tools not trained on clinical labels, SIFT separates this disease's known disease-causing variants from harmless ones best (AUROC 0.89, based on 11 disease-causing and 18 harmless variants).
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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