# A Novel SLC9A3R1 Mutation as a Rare Cause of Infantile Hypercalcemia

**Authors:** Padala Ravi Kumar, Ankeet Biswas, Deepak K Dash, Debasish Patro, D. Sai Madhav Reddy

PMC · DOI: 10.7759/cureus.102923 · Cureus · 2026-02-03

## TL;DR

A rare infant case of hypercalcemia was caused by a new mutation in the SLC9A3R1 gene, showing how genetic testing can help diagnose and treat rare conditions early.

## Contribution

A novel SLC9A3R1 mutation is identified as a rare cause of infantile hypercalcemia and NPHLOP2.

## Key findings

- A two-month-old infant with hypercalcemia was found to have a heterozygous SLC9A3R1 missense variant.
- The patient showed clinical improvement after treatment with zoledronic acid and dietary adjustments.
- Genetic testing confirmed a diagnosis of hypophosphatemic nephrolithiasis/osteoporosis-2 (NPHLOP2).

## Abstract

Hypercalcemia in infants is a rare but potentially serious condition characterized by elevated serum calcium levels. We report a case of a two-month-old female presenting with poor feeding, lethargy, irritability, and failure to thrive, and she was found to have hypercalcemia. On examination, she had a weight of 3.1 kg (-3.94 SDS) with normal facial features. Laboratory investigations revealed elevated serum calcium, low phosphate, suppressed parathyroid hormone (PTH), and high 1, 25-dihydroxyvitamin D levels. Renal ultrasonography revealed bilateral medullary nephrocalcinosis. Clinical exome sequencing identified a heterozygous missense variant in the SLC9A3R1 gene, leading to a diagnosis of hypophosphatemic nephrolithiasis/osteoporosis-2 (NPHLOP2). She was initially managed with calcium restricted diet, intravenous fluid rehydration, and administration of zoledronic acid. On follow-up at one month, the patient showed significant symptomatic improvement with normalization of serum calcium levels along with weight gain. This case highlights the role of genetic testing to identify rare genetic causes of hypercalcemia during infancy. Early diagnosis and appropriate management of NPHLOP2 can significantly improve an individual's outcomes and quality of life.

## Linked entities

- **Genes:** NHERF1 (NHERF family PDZ scaffold protein 1) [NCBI Gene 9368]
- **Chemicals:** zoledronic acid (PubChem CID 68740), 1,25-dihydroxyvitamin D (PubChem CID 5280453)
- **Diseases:** hypercalcemia (MONDO:0001566), hypophosphatemic nephrolithiasis/osteoporosis-2 (MONDO:0012851), NPHLOP2 (MONDO:0012851)

## Full-text entities

- **Genes:** CYP24A1 (cytochrome P450 family 24 subfamily A member 1) [NCBI Gene 1591] {aka CP24, CYP24, HCAI, HCINF1, P450-CC24}, PTH (parathyroid hormone) [NCBI Gene 5741] {aka FIH1, PTH1}, NHERF1 (NHERF family PDZ scaffold protein 1) [NCBI Gene 9368] {aka EBP50, NHE-RF, NHERF, NHERF-1, NPHLOP2, SLC9A3R1}, ACE (angiotensin I converting enzyme) [NCBI Gene 1636] {aka ACE1, CD143, DCP, DCP1}, RDX (radixin) [NCBI Gene 5962] {aka DFNB24}, PTHLH (parathyroid hormone like hormone) [NCBI Gene 5744] {aka BDE2, HHM, PLP, PTHR, PTHRP}, CYP3A4 (cytochrome P450 family 3 subfamily A member 4) [NCBI Gene 1576] {aka CP33, CP34, CYP3A, CYP3A3, CYPIIIA3, CYPIIIA4}, AP2B1 (adaptor related protein complex 2 subunit beta 1) [NCBI Gene 163] {aka ADTB2, AP105B, AP2-BETA, CLAPB1}, TRPV5 (transient receptor potential cation channel subfamily V member 5) [NCBI Gene 56302] {aka CAT2, ECAC1, OTRPC3}, SLC34A1 (solute carrier family 34 member 1) [NCBI Gene 6569] {aka FRTS2, HCINF2, NAPI-3, NPHLOP1, NPT2, NPTIIa}, ALB (albumin) [NCBI Gene 213] {aka FDAHT, HSA, PRO0883, PRO0903, PRO1341}, CTNNB1 (catenin beta 1) [NCBI Gene 1499] {aka CTNNB, EVR7, MRD19, NEDSDV, armadillo}
- **Diseases:** cardiac arrhythmias (MESH:D001145), weight gain (MESH:D015430), granulomatous disorders (MESH:D006105), Williams syndrome (MESH:D018980), diarrhea (MESH:D003967), Addison's disease (MESH:D000224), renal phosphate wasting (MESH:D019282), PHPT (MESH:D049950), hypophosphatemic nephrolithiasis (MESH:C567363), renal (MESH:D006030), seizure (MESH:D012640), vomiting (MESH:D014839), nephrocalcinosis (MESH:D009397), stone formation (MESH:D058426), nephrolithiasis (MESH:D053040), gastrointestinal symptoms (MESH:D012817), IHH (MESH:C562999), tertiary hyperparathyroidism (MESH:D006961), malignancy (MESH:D009369), Congenital syndromes (MESH:D008209), irritability (MESH:D001523), renal failure (MESH:D051437), blue diaper syndrome (MESH:C536239), abdominal pain (MESH:D015746), abdominal discomfort (MESH:D000007), inborn errors of metabolism (MESH:D008661), hypercalciuria (MESH:D053565), familial hypocalciuric hypercalcemia (MESH:C537145), thyrotoxicosis (MESH:C566386), tuberculosis (MESH:D014376), constipation (MESH:D003248), hypophosphatasia (MESH:D007014), pheochromocytoma (MESH:D010673), overdose (MESH:D062787), hypocalcemia (MESH:D006996), hypotonia (MESH:D009123), hypertension (MESH:D006973), failure to thrive (MESH:D005183), sarcoidosis (MESH:D012507), endocrine disorders (MESH:D004700), Hypophosphatemia (MESH:D017674), congenital hypothyroidism (MESH:D003409), murmur (MESH:D006337), NPHLOP2 (MESH:C567362), osteoporosis type 2 (MESH:D010024), phosphaturia (MESH:D007015), dehydration (MESH:D003681), bone loss (MESH:D001847), Hypercalcemia (MESH:D006934), renal tubular acidosis (MESH:D000141), lethargy (MESH:D053609)
- **Chemicals:** zoledronic acid (MESH:D000077211), pamidronate (MESH:D000077268), thiazide (MESH:D049971), Vitamin D (MESH:D014807), NaCl (MESH:D012965), Phosphate (MESH:D010710), Ketoconazole (MESH:D007654), triazole (MESH:D014230), Fluconazole (MESH:D015725), 1,25(OH)2D3 (MESH:D002117), 1, 25-dihydroxyvitamin D (MESH:C097949), calcium (MESH:D002118), creatinine (MESH:D003404), glucose (MESH:D005947), magnesium (MESH:D008274), bisphosphonates (MESH:D004164), phosphate wasting (-), sodium (MESH:D012964), 25-hydroxyvitamin D (MESH:C104450), potassium (MESH:D011188), urea (MESH:D014508), Rifampicin (MESH:D012293), TMP (MESH:D013938)
- **Species:** Homo sapiens (human, species) [taxon 9606]
- **Mutations:** c.722A>G, c.328C>G, c.616T>C, C206R, rs119486097, p.Pro256Ser, g.74766944C>T, rs41282065, c.766C>T

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## References

16 references — full list in the complete paper: https://tomesphere.com/paper/PMC12962878/full.md

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Source: https://tomesphere.com/paper/PMC12962878