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Year : 2020  |  Volume : 3  |  Issue : 1  |  Page : 31-33

Novel pathogenic variant causing familial hypomagnesemia with hypercalciuria and nephrocalcinosis

Department of Pediatrics, Division of Pediatric Nephrology, All India Institute of Medical Sciences, New Delhi, India

Date of Submission04-Apr-2020
Date of Decision24-Apr-2020
Date of Acceptance05-May-2020
Date of Web Publication27-Jun-2020

Correspondence Address:
Arvind Bagga
Department of Pediatrics, Division of Pediatric Nephrology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/AJPN.AJPN_11_20

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Nephrocalcinosis in children can arise due to a variety of metabolic conditions and appropriate diagnosis can lead to specific management and has implications in prognosis. Familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC) is a rare disease with varied manifestations which is caused by mutations in CLDN16 and CLDN19, and has a high rate of progression to kidney failure in the second to third decades of life. Early diagnosis aids in retardation of the progression to kidney failure. We present two unrelated patients presenting with nephrocalcinosis and deranged renal function, who had a novel pathogenic variation (c.685C > T; p.Q229X), leading to the diagnosis of FHHNC. Genetic testing is crucial in patients presenting with nephrocalcinosis for diagnosis and prognostication.

Keywords: Claudin, hypomagnesemia, nephrocalcinosis

How to cite this article:
Mathew G, Khandelwal P, Thergaonkar R, Sinha A, Hari P, Bagga A. Novel pathogenic variant causing familial hypomagnesemia with hypercalciuria and nephrocalcinosis. Asian J Pediatr Nephrol 2020;3:31-3

How to cite this URL:
Mathew G, Khandelwal P, Thergaonkar R, Sinha A, Hari P, Bagga A. Novel pathogenic variant causing familial hypomagnesemia with hypercalciuria and nephrocalcinosis. Asian J Pediatr Nephrol [serial online] 2020 [cited 2022 Jul 7];3:31-3. Available from: https://www.ajpn-online.org/text.asp?2020/3/1/31/288147

  Introduction Top

Familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC) is a rare disorder of renal magnesium transport caused by mutations in CLDN16 and CLDN19 genes.[1] Clinical presentation is usually with polyuria, polydipsia, failure to thrive, nephrolithiasis or nephrocalcinosis, and varying renal dysfunction. Patients with CLDN19 mutations also show ocular involvement (glaucoma, myopia, retinal changes, and loss of vision) and hearing loss; extrarenal manifestations are infrequent in CLDN16 mutations. We report two patients with FHHNC and renal dysfunction, associated with a novel variation in CLDN16.

  Case Reports Top

Case #1

A 5-year-old boy presented with polyuria (2–2.5 L/m 2/day), polydipsia, and failure to gain weight since infancy. He was the third-born of four siblings, born to non-consanguineous parents with no family history. There was no history of antenatal polyhydramnios; birth weight was 3 kg. Weight and height were 14 kg (−1.2 standard deviation score [SDS]) and 99 cm (−1.7 SDS), respectively. Blood pressure was at the 95th percentile. Blood pH ranged from 7.35 to 7.40, bicarbonate 24–26 mEq/L, sodium 138–142 mEq/L, potassium 4.2–4.4 mEq/L, creatinine 0.9–1.3 mg/dl (estimated glomerular filtration rate [eGFR] 34–45 ml/min/1.73 m 2), phosphate 3.9 mg/dl, urate 6.3–8.1 mg/dl, calcium 9.0–9.5 mg/dl, and alkaline phosphatase 434 U/L. Level of 25-hydroxyvitamin D was 13 ng/ml (sufficient >30 ng/ml) and parathyroid hormone 188 pg/ml (normal 15–80 pg/ml). Ultrasonography showed normal-sized kidneys with dense medullary nephrocalcinosis [Figure 1]. Further evaluation showed hypercalciuria (4–9 mg/kg/day; normal <4 mg/kg/day) and proteinuria (250–300 mg/day); there was no glucosuria, aminoaciduria, and ß2-microglobulinuria (100 mg/ml; normal <300 mg/ml). Early morning urine pH was 5.8 and the minimum urine pH during the furosemide-fludrocortisone test was 6.2. Serum magnesium levels were 1.7–1.8 mg/dl (normal 1.8–2.2 mg/dl) and its fractional excretion was 16% (normal 0.5%–3%). Eye and hearing assessments were normal.
Figure 1: Patient 1. Ultrasonographic image shows dense medullary nephrocalcinosis (right kidney)

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Case #2

A 10-year-old boy was symptomatic for the past 4 years with recurrent episodes of abdominal pain. He was the second-born of four siblings to nonconsanguineous parents with no family history. Birth weight and antenatal ultrasonography records were not available. At evaluation, the weight was 24 kg (−3.9 SDS) and height 119 cm (−1.41 SDS). Investigations showed hypokalemia (2.2–2.7 mEq/l), with normal sodium 139–145 mEq/L, pH 7.35–7.40, and bicarbonate 25–26 mEq/L. Serum creatinine was 1.1–1.3 mg/dl (eGFR 40–50 ml/min/1.73 m 2), calcium 6.67.5 mg/dl (normal 9–10.5 mg/dl), phosphate 4.0–5.0 mg/dl, and alkaline phosphatase 730–760 U/L. Hypercalciuria (5–9 mg/kg/day) and hypomagnesemia (magnesium 0.8–1.0 mg/dl) were seen on multiple occasions; the fractional excretion of magnesium was 4.1%. Ultrasonography revealed bilateral medullary nephrocalcinosis and a right ureteric calculus. Eye and hearing assessments were normal. His siblings had normal renal functions and no evidence of hypercalciuria.

On clinical exome sequencing, both patients had a homozygous nonsense variation in exon 4 of the CLDN16 gene, c. 685C > T (p.Q229X), resulting in stop codon and premature termination. This novel variant is not reported in public databases (1000 Genomes, ExAC, genome Asia 100K) and was deleterious by in silico prediction (Mutation Taster, CADD score). The variant was termed pathogenic, based on the American College of Medical Genetics and Genomics classification.[2] Genomic Evolutionary Rate Profiling (GERP++) score of the variant was 5.6, suggesting the variant to be highly conserved across species. No other variants in any of the genes regulating calcium and magnesium homeostasis were observed.

  Discussion Top

We report two unrelated patients with relatively similar clinical features, hypercalciuria, and nephrocalcinosis with chronic kidney disease stage 3–4. Differential diagnosis of hypercalciuria with hypomagnesemia includes Bartter syndrome type III/IV (CLCNKB, BSND), autosomal dominant hypocalcemia (gain of function of CaSR), or FHHNC (CLDN16, CLDN19). However, the presence of CKD 3–4 at a young age ruled out most conditions, except FHHNC. Although nephrocalcinosis with kidney failure can be seen in primary hyperoxaluria, Dent's disease, cystinosis, and FHHNC, low serum magnesium with urinary wasting are not observed in any of these conditions, except FHHNC. In both our patients, a combination of both of the symptom complexes were observed, and hence, a diagnosis of FHHNC was made.

Both patients had the same novel variant that resulted in a stop codon at position 229 of CLDN16] [Figure 2]. More than 50 mutations in CLDN16 have been reported in FHHNC, spanning its five exons. Mutations are located within transmembrane regions or extracellular segments.[1] It is suggested that the first extracellular domain contains an ion selectivity filter, whereas the second domain is involved in claudin-claudin interactions and the formation of paracellular channels.[3],[4] The novel nonsense variant, in the current study, is positioned in the second extracellular domain [Figure 2] and causes protein truncation and disruption of intercellular interaction within tight junctions of thick ascending limb.
Figure 2: Model of the tight junction protein, claudin 16, consisting of four transmembrane domains, two extracellular segments, an intracellular loop, and amino- and carboxyterminal cytoplasmic tails. The affected amino acid residue (p.Q229X) in the two patients is localized to the second extracellular domain

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FHHNC is a rare renal tubular disorder with a high risk of progression to CKD. A large series showed that mean eGFR in the first decade was ~ 70–80 ml/min/1.73 m 2; approximately one-third of patients had kidney failure during the second to third decades of life.[5],[6],[7] Presentation with eGFR below 45 ml/min/1.73 m 2, similar to the present patients, has been documented in 16%–33% cases.[6],[7] Complete loss of function of claudin 16, which is expected to occur with the present novel variant, is associated with a faster decline of renal function.[1] While the reason for the early progression to CKD is not clear, various degrees of tubular atrophy, interstitial fibrosis, and segmental glomerulosclerosis has been described on renal histology.[8]

Blood levels of magnesium may be variable, even between affected siblings.[9] Despite similar genetic defects and eGFR, blood levels of magnesium in the present cases were different, suggesting genetic or epigenetic modifiers of the spectrum of clinical features. Normal blood levels of magnesium do not exclude FHHNC, and fractional excretion of magnesium helps demonstrate tubular wasting in all suspected cases. Despite reduced renal function, blood levels of magnesium may remain in low-normal range in affected patients for 1–2 years.[6]

Some patients, similar to case #1 in the present report, have features similar to incomplete distal renal tubular acidosis, with borderline low levels of magnesium and the absence of distal acidification on provocative testing. The latter defect was studied in four patients with FHHNC, who had hyperchloremic acidosis (bicarbonate 17.5–19.6 mEq/L), high urinary pH (5.7–6.0) and positive urine anion gap, and showed decreased ammonia excretion.[10] In a European series, 17 of 20 patients also had features of incomplete renal tubular acidosis.[9] This was explained as a defect in the tubular transfer of ammonia, reduced hydrogen ion secretion in medullary collecting duct secondary to nephrocalcinosis, and reduced eGFR.[10]

FHHNC should be suspected in patients with nephrocalcinosis with or without nephrolithiasis, and hypercalciuria with impaired renal function, even if magnesium levels are normal. The presentation with an incomplete form of distal renal tubular acidosis may cause a clinical dilemma. Genetic confirmation of FHHNC has implications for the diagnosis and management, including therapy with magnesium supplements, genetic counseling, and establishing the risk of progression to kidney failure.

Declaration of patient consent

The authors certify that they have obtained all appropriate patient consent forms. In the form the patient(s) has/have given his/her/their consent for his/her/their images and other clinical information to be reported in the journal. The patients understand that their names and initials will not be published and due efforts will be made to conceal their identity, but anonymity cannot be guaranteed.

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Conflicts of interest

There are no conflicts of interest.

  References Top

Konrad M, Hou J, Weber S, Dötsch J, Kari JA, Seeman T, et al. CLDN16 genotype predicts renal decline in familial hypomagnesemia with hypercalciuria and nephrocalcinosis. J Am Soc Nephrol 2008;19:171-81.  Back to cited text no. 1
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 2015;17:405-24.  Back to cited text no. 2
Piontek J, Winkler L, Wolburg H, Müller SL, Zuleger N, Piehl C, et al. Formation of tight junction: Determinants of homophilic interaction between classic claudins. FASEB J 2008;22:146-58.  Back to cited text no. 3
Piehl C, Piontek J, Cording J, Wolburg H, Blasig IE. Participation of the second extracellular loop of claudin-5 in paracellular tightening against ions, small and large molecules. Cell Mol Life Sci 2010;67:2131-40.  Back to cited text no. 4
Benigno V, Canonica CS, Bettinelli A, von Vigier RO, Truttmann AC, Bianchetti MG. Hypomagnesaemia-hyperc alciuria-nephrocalcinosis: A report of nine cases and a review. Nephrol Dial Transplant 2000;15:605-10.  Back to cited text no. 5
Seeley HH, Loomba-Albrecht LA, Nagel M, Butani L, Bremer AA. Familial hypomagnesemia with hypercalciuria and nephrocalcinosis in three siblings having the same genetic lesion but different clinical presentations. World J Pediatr 2012;8:177-80.  Back to cited text no. 6
Sikora P, Zaniew M, Haisch L, Pulcer B, Szczepańska M, Moczulska A, et al. Retrospective cohort study of familial hypomagnesaemia with hypercalciuria and nephrocalcinosis due to CLDN16 mutations. Nephrol Dial Transplant 2015;30:636-44.  Back to cited text no. 7
Hanssen O, Castermans E, Bovy C, Weekers L, Erpicum P, Dubois B, et al. Two novel mutations of the CLDN16 gene cause familial hypomagnesaemia with hypercalciuria and nephrocalcinosis. Clin Kidney J 2014;7:282-5.  Back to cited text no. 8
Weber S, Schneider L, Peters M, Misselwitz J, Rönnefarth G, Böswald M, et al. Novel paracellin-1 mutations in 25 families with familial hypomagnesemia with hypercalciuria and nephrocalcinosis. J Am Soc Nephrol 2001;12:1872-81.  Back to cited text no. 9
Rodríguez-Soriano J, Vallo A. Pathophysiology of the renal acidification defect present in the syndrome of familial hypomagnesaemia-hypercalciuria. Pediatr Nephrol 1994;8:431-5.  Back to cited text no. 10


  [Figure 1], [Figure 2]

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