Digenetic inheritance of SLC12A3 and CLCNKB genes in a Chinese girl with Gitelman syndrome

The first compound heterozygous mutations in SLC12A3 and PDX1 genes: a unique presentation of Gitelman syndrome with distinct insulin resistance and familial diabetes insights

Background

Gitelman Syndrome (GS) patients frequently exhibit disrupted glucose metabolism, attributed to hypokalemia, hypomagnesemia and heightened aldosterone. This study delved into the genetic underpinnings linked to insulin resistance and diabetes in a GS patient, contextualized within his family history.

Methods

The hydrochlorothiazide and furosemide loading test were performed to ascertain the presence of GS. Oral glucose tolerance test (OGTT) evaluated glucose metabolism and insulin sensitivity. Whole-exome sequencing, validated by Sanger sequencing, was employed to confirm gene mutations, which were then tracked among the patient's relatives.

Results

Symptoms and laboratory examination confirmed the clinical diagnosis of GS. Comprehensive whole-exome sequencing, augmented by Sanger sequencing validation, revealed a compound heterozygous mutation within the SLC12A3 gene (c.1108G>C in exon 9, c.676G>A in exon 5 and c.2398G>A in exon 20) in the patient. The OGTT affirmed diabetes and heightened insulin resistance, distinct from previous patients with GS we evaluated. Further genetic analysis identified a missense heterozygous mutation (c.97C>G in exon 1) within the PDX1 gene, inherited from the patient's diabetic mother without GS. Furthermore, the patient's brother, with impaired glucose tolerance but regular potassium levels, also bore this mutation, hinting at additional impacts of the PDX1 gene mutation on glucose metabolism regulation beyond the known impacts of GS.

Conclusion

This study unveils unprecedented compound heterozygous mutations in the SLC12A3 and PDX1 genes in a GS patient. These findings illuminate the potential complex genetic factors influencing glucose metabolism disruptions in GS.

Take-home message

This research uncovers a novel combination of SLC12A3 and PDX1 gene mutations in a Gitelman Syndrome patient, revealing intricate genetic factors that potentially disrupt glucose metabolism and shedding light on familial diabetes links.

Gitelman syndrome combined with diabetes mellitus: A case report and literature review

RATIONALE

Gitelman syndrome (GS) is an uncommon autosomal recessive tubulopathy resulting from a functional deletion mutation in the SLC12A3 gene. Its onset is typically insidious and challenging to discern, and it is characterized by hypokalemia, metabolic alkalosis, and reduced urinary calcium excretion. There is limited literature on the diagnosis and management of GS in individuals with concomitant diabetes.

PATIENT CONCERNS

A 36-year-old male patient with a longstanding history of diabetes exhibited suboptimal glycemic control. Additionally, he presented with concurrent findings of hypokalemia, hypomagnesemia, hypocalciuria, and metabolic alkalosis.

DIAGNOSIS

Building upon the patient's clinical manifestations and extensive laboratory evaluations, we conducted thorough genetic testing, leading to the identification of a compound heterozygous mutation within the SLC12A3 gene. This definitive finding confirmed the diagnosis of GS.

INTERVENTIONS

We have formulated a detailed medication regimen for patients, encompassing personalized selection of hypoglycemic medications and targeted electrolyte supplementation.

OUTCOMES

Following 1 week of comprehensive therapeutic intervention, the patient's serum potassium level effectively normalized to 3.79 mmol/L, blood glucose parameters stabilized, and there was significant alleviation of clinical symptoms.

LESSONS

GS has a hidden onset and requires early diagnosis and intervention based on patient related symptoms and laboratory indicators in clinical practice, and personalized medication plans need to be provided according to the specific situation of the patient.

Spectrum of variants in a large Chinese Gitelman syndrome cohort

Gitelman syndrome (GS) is caused by SLC12A3 biallelic variants. A previous study showed that large rearrangements (LRGs) of SLC12A3 accounted for the low sensitivity of genetic testing. However, a systematic screening for LRGs in Chinese GS patients is lacking. Massively parallel sequencing (MPS) and multiplex ligation-dependent probe amplification (MLPA) were performed to sequence the genomic DNA of patients with clinically diagnosed GS. Of 165 index cases, MPS identified 151 cases with two or more affected alleles and 14 cases with one variant allele. LRGs were detected by MLPA in 20 out of 27 cases, including 15 cases with suspected LRGs by MPS. Among these 20 cases with LRGs, the results of MPS and MLPA were identical in only 8 cases. Additional LRGs in 6 cases were detected by MLPA alone. In 6 cases, E4_E6del was identified by MPS, while E4_E5del and Intron6del were identified by MLPA. Among the 102 distinct variants, 30 are novel. LRGs were found in 20 cases (12.1%). LRGs were found in 12.1% of our Chinese GS patients cohort. We show that MPS and MLPA are two complementary techniques with the ability to improve the diagnostic yield of GS.

Case report: Gitelman syndrome with diabetes: Confirmed by both hydrochlorothiazide test and genetic testing

RATIONALE

Gitelman syndrome (GS) is an autosomal recessive tubulopathy caused by mutations of the SLC12A3 gene. It is characterized by hypokalemic metabolic alkalosis, hypomagnesemia and hypocalciuria. Hypokalemia, hypomagnesemia, and increased renin-angiotensin-aldosterone system (RAAS) activity can cause glucose metabolism dysfunction. The diagnosis of GS includes clinical diagnosis, genetic diagnosis and functional diagnosis. The gene diagnosis is the golden criterion while as functional diagnosis is of great value in differential diagnosis. The hydrochlorothiazide (HCT) test is helpful to distinguish GS from batter syndrome, but few cases have been reported to have HCT testing.

PATIENT CONCERNS

A 51-year-old Chinese woman presented to emergency department because of intermittent fatigue for more than 10 years.

DIAGNOSES

Laboratory test results showed hypokalemia, hypomagnesemia, hypocalciuria and metabolic alkalosis. The HCT test showed no response. Using next-generation and Sanger sequencing, we identified 2 heterozygous missense variants (c.533C > T:p.S178L and c.2582G > A:p.R861H) in the SLC12A3 gene. In addition, the patient was diagnosed with type 2 diabetes mellitus 7 years ago. Based on these findings, the patient was diagnosed with GS with type 2 diabetic mellitus (T2DM).

INTERVENTIONS

She was given potassium and magnesium supplements, and dapagliflozin was used to control her blood glucose.

OUTCOMES

After treatments, her fatigue symptoms were reduced, blood potassium and magnesium levels were increased, and blood glucose levels were well controlled.

LESSONS

When GS is considered in patients with unexplained hypokalemia, the HCT test can be used for differential diagnosis, and genetic testing can be continued to confirm the diagnosis when conditions are available. GS patients often have abnormal glucose metabolism, which is mainly caused by hypokalemia, hypomagnesemia, and secondary activation of RAAS. When a patient is diagnosed with GS and type 2 diabetes, sodium-glucose cotransporter 2 inhibitors (SGLT2i) can be used to control the blood glucose level and assist in raising blood magnesium.

Novel compound heterozygous variants of SLC12A3 gene in a Chinese patient with Gitelman syndrome: a case report

Background: The Gitelman syndrome (GS) is an autosomal recessive disorder of renal tubular salt handling. Gitelman syndrome is characterized by hypokalemia, metabolic alkalosis, hypomagnesemia, hypocalciuria, and renin-angiotensin-aldosterone system (RAAS) activation, and is caused by variants in the SLC12A3 gene. Gitelman syndrome has a heterogeneous phenotype, which may or may not include a range of clinical signs, posing certain difficulties for clinical diagnosis. Case presentation: A 49-year-old man was admitted to our hospital due to muscular weakness. The patient's history revealed previous recurrent muscular weakness events associated with hypokalemia, featured by a minimum serum potassium value of 2.3 mmol/L. The reported male patient had persistent hypokalemia, hypocalciuria and normal blood pressure, without presenting obvious metabolic alkalosis, growth retardation, hypomagnesemia, hypochloremia or RAAS activation. We performed whole-exome sequencing and identified a novel compound heterozygous variant in the SLC12A3 gene, c.965-1_976delGCGGACATTTTTGinsACCGAAAATTTT in exon8 and c.1112T>C in exon9 in the proband. Conclusion: This is a study to report a heterogeneous phenotype Gitelman syndrome with a novel pathogenic compound heterozygous variant in the SLC12A3 gene. This genetic study expands the variants spectrum, and improve the diagnostic accuracy of Gitelman syndrome. Meanwhile, further functional studies are required to investigate the pathophysiological mechanisms of Gitelman syndrome.

The genetic spectrum of Gitelman(-like) syndromes

PURPOSE OF REVIEW

Gitelman syndrome is a recessive salt-wasting disorder characterized by hypomagnesemia, hypokalemia, metabolic alkalosis and hypocalciuria. The majority of patients are explained by mutations and deletions in the SLC12A3 gene, encoding the Na+-Cl--co-transporter (NCC). Recently, additional genetic causes of Gitelman-like syndromes have been identified that should be considered in genetic screening. This review aims to provide a comprehensive overview of the clinical, genetic and mechanistic aspects of Gitelman(-like) syndromes.

RECENT FINDINGS

Disturbed Na+ reabsorption in the distal convoluted tubule (DCT) is associated with hypomagnesemia and hypokalemic alkalosis. In Gitelman syndrome, loss-of-function mutations in SLC12A3 cause impaired NCC-mediated Na+ reabsorption. In addition, patients with mutations in CLCKNB, KCNJ10, FXYD2 or HNF1B may present with a similar phenotype, as these mutations indirectly reduce NCC activity. Furthermore, genetic investigations of patients with Na+-wasting tubulopathy have resulted in the identification of pathogenic variants in MT-TI, MT-TF, KCNJ16 and ATP1A1. These novel findings highlight the importance of cell metabolism and basolateral membrane potential for Na+ reabsorption in the DCT.

SUMMARY

Altogether, these findings extend the genetic spectrum of Gitelman-like electrolyte alterations. Genetic testing of patients with hypomagnesemia and hypokalemia should cover a panel of genes involved in Gitelman-like syndromes, including the mitochondrial genome.

Novel mutations of the SLC12A3 gene in patients with Gitelman syndrome

Mutations in the SLC12A3 gene have been reported to cause Gitelman syndrome (GS). This study aimed to investigate the genetic mutations and clinical features of patients with GS. Four pedigrees (4 GS patients and 14 family members) were enrolled. The symptoms, laboratory results, management, and genotypes were analyzed. Genomic DNA was screened for gene variations using Sanger sequencing. DNA sequences were compared with reference sequences. The effects of the mutations were predicted using prediction tools (Mutation Taster, PolyPhen-2, SIFT, and PROVEAN). Genetic analysis revealed six genetic variants of SLC12A3, including three novel heterozygous mutations (c.2T > C, c.1609C > T, c.3055G > A) and three previously characterized mutations (c.1456G > A, c.2542G > A, c.1077C > G). These mutations were predicted to exert a damaging effect based on predictive in silico tools. GS patients had low blood pressure and low levels of serum K⁺, serum Mg²⁺, and 24-h urinary Ca²⁺ but high levels of 24-h urinary K⁺. These clinical manifestations and genotypes were consistent with the diagnostic criteria of GS. The study described the phenotypes and genotypes of 4 pedigrees involving GS patients, demonstrating the importance of SLC12A3 gene screening for GS.

Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network

Rare diseases affect millions of people worldwide, and discovering their genetic causes is challenging. More than half of the individuals analyzed by the Undiagnosed Diseases Network (UDN) remain undiagnosed. The central hypothesis of this work is that many of these rare genetic disorders are caused by multiple variants in more than one gene. However, given the large number of variants in each individual genome, experimentally evaluating combinations of variants for potential to cause disease is currently infeasible. To address this challenge, we developed the digenic predictor (DiGePred), a random forest classifier for identifying candidate digenic disease gene pairs by features derived from biological networks, genomics, evolutionary history, and functional annotations. We trained the DiGePred classifier by using DIDA, the largest available database of known digenic-disease-causing gene pairs, and several sets of non-digenic gene pairs, including variant pairs derived from unaffected relatives of UDN individuals. DiGePred achieved high precision and recall in cross-validation and on a held-out test set (PR area under the curve > 77%), and we further demonstrate its utility by using digenic pairs from the recent literature. In contrast to other approaches, DiGePred also appropriately controls the number of false positives when applied in realistic clinical settings. Finally, to enable the rapid screening of variant gene pairs for digenic disease potential, we freely provide the predictions of DiGePred on all human gene pairs. Our work enables the discovery of genetic causes for rare non-monogenic diseases by providing a means to rapidly evaluate variant gene pairs for the potential to cause digenic disease.

Improving Molecular Therapy in the Kidney

Mutations in approximately 80 genes have been implicated as the cause of various genetic kidney diseases. However, gene delivery to kidney cells from the blood is inefficient because of the natural filtering functions of the glomerulus, and research into and development of gene therapy directed toward kidney disease has lagged behind as compared with hepatic, neuromuscular, and ocular gene therapy. This lack of progress is in spite of numerous genetic mouse models of human disease available to the research community and many vectors in existence that can theoretically deliver genes to kidney cells with high efficiency. In the past decade, several groups have begun to develop novel injection techniques in mice, such as retrograde ureter, renal vein, and direct subcapsular injections to help resolve the issue of gene delivery to the kidney through the blood. In addition, the ability to retarget vectors specifically toward kidney cells has been underutilized but shows promise. This review discusses how recent advances in gene delivery to the kidney and the field of gene therapy can leverage the wealth of knowledge of kidney genetics to work toward developing gene therapy products for patients with kidney disease.

Simultaneous Homozygous Mutations in SLC12A3 and CLCNKB in an Inbred Chinese Pedigree

Gitelman syndrome (GS) and Bartter syndrome (BS) type III are both rare, recessively inherited salt-losing tubulopathies caused by SLC12A3 and CLCNKB mutations, respectively. We described a 48-year-old male patient with fatigue, carpopedal spasm, arthralgia, hypokalemic alkalosis, mild renal dysfunction, hypomagnesemia, hypocalciuria, hyperuricemia, normotension, hyperreninemia and chondrocalcinosis in knees and Achilles tendons. His parents are first cousin. Genetic analysis revealed simultaneous homozygous mutations in SLC12A3 gene with c.248G>A, p.Arg83Gln and CLCNKB gene with c.1171T>C, p.Trp391Arg. The second younger brother of the proband harbored the same simultaneous mutations in SLC12A3 and CLCNKB and exhibited similar clinical features except normomagnesemia and bilateral kidney stones. The first younger brother of the proband harbored the same homozygous mutations in CLCNKB and exhibited clinical features of hypokalemia, normomagnesemia, hypercalciuria and hyperuricemia. Potassium chloride, spironolactone and potassium magnesium aspartate were prescribed to the proband to correct electrolytic disturbances. Benzbromarone and febuxostat were prescribed to correct hyperuricemia. The dose of potassium magnesium aspartate was subsequently increased to alleviate arthralgia resulting from calcium pyrophosphate deposition disease (CPPD). To the best of our knowledge, we are the first to report an exceptionally rare case in an inbred Chinese pedigree with simultaneous homozygous mutations in SLC12A3 and CLCNKB. GS and BS type III have significant intrafamilial phenotype heterogeneity. When arthralgia is developed in patients with GS and BS, gout and CPPD should both be considered.

A novel homozygous mutation (p.N958K) of SLC12A3 in Gitelman syndrome is associated with endoplasmic reticulum stress

PURPOSE

Gitelman syndrome (GS) is an autosomal recessive renal tubular disease that arises as a consequence of mutations in the SLC12A3 gene, which codes for an Na-Cl cotransporter (NCC) in distal renal tubules. This study was designed to explore the mutations associated with GS in an effort to more fully understand the molecular mechanisms governing GS.

METHODS

We analyzed SLC12A3 mutations in a pedigree including a 42-year-old male with GS as well as four related family members over three generations using Sanger and next generation sequencing approaches. We additionally explored the functional ramifications of identified mutations using both Xenopus oocytes and the HEK293T cell line.

RESULTS

We found that the subject with GS exhibited characteristic symptoms including sporadic thirst, fatigue, excess urination, and substantial hypokalemia and hypocalciuria, although magnesium levels were normal. Other analyzed subjects in this pedigree had normal laboratory findings and did not exhibit clear signs of GS. Sequencing analyses revealed that the GS subject exhibited a homozygous missense mutation (c.2874C > G, p.N958K) in exon 24 of SLC12A3. Both parents of this GS subject, as well as his older brother and daughter all exhibited heterozygous mutations at this same site. Functional analyses in Xenopus oocytes indicated that this mutated SLC12A3 gene encodes a protein which fails to mediate normal sodium transport, and when this mutant gene was expressed in HEK293T cells, we observed significant increases in endoplasmic reticulum (ER)-stress pathway activation.

CONCLUSION

The p.N958K mutation in exon 24 of SLC12A3 can trigger GS at least in part via enhancing ER stress responses.

Digenic Heterozygous Mutations in SLC34A3 and SLC34A1 Cause Dominant Hypophosphatemic Rickets with Hypercalciuria

CONTEXT

Hypophosphatemia and metabolic bone disease are associated with hereditary hypophosphatemic rickets with hypercalciuria (HHRH) due to biallelic mutations of SLC34A3 encoding the NPT2C sodium-phosphate cotransporter and nephrolithiasis/osteoporosis, hypophosphatemic 1 (NPHLOP1) due to monoallelic mutations in SLC34A1 encoding the NPT2A sodium-phosphate cotransporter.

OBJECTIVE

To identify a genetic cause of apparent dominant transmission of HHRH.

DESIGN AND SETTING

Retrospective and prospective analysis of clinical and molecular characteristics of patients studied in 2 academic medical centers.

METHODS

We recruited 4 affected and 3 unaffected members of a 4-generation family in which the proband presented with apparent HHRH. We performed clinical examinations, biochemical and radiological analyses, and molecular studies of genomic DNA.

RESULTS

The proband and her affected sister and mother carried pathogenic heterozygous mutations in 2 related genes, SLC34A1 (exon 13, c.1535G>A; p.R512H) and SLC34A3 (exon 13, c.1561dupC; L521Pfs*72). The proband and her affected sister inherited both gene mutations from their mother, while their clinically less affected brother, father, and paternal grandmother carried only the SLC34A3 mutation. Renal phosphate-wasting exhibited both a gene dosage-effect and an age-dependent attenuation of severity.

CONCLUSIONS

We describe a kindred with autosomal dominant hypophosphatemic rickets in which whole exome analysis identified digenic heterozygous mutations in SLC34A1 and SLC34A3. Subjects with both mutations were more severely affected than subjects carrying only one mutation. These findings highlight the challenges of assigning causality to plausible genetic variants in the next generation sequencing era.

Atypical features and de novo heterozygous mutations in two siblings with Cockayne syndrome

BACKGROUND

Cockayne syndrome (CS) is a rare autosomal recessive disorder which displays multiorgan dysfunction, especially within the nervous system including psychomotor retardation, cerebral atrophy, microcephaly, cognitive dysfunction, mental retardation, and seizures. Many genetic variations reported were related to this syndrome, but splicing mutations with cardiac anomalies have not been found in previous studies.

METHODS

Herein, we described a pair of brothers and sisters who present essential manifestations of CS including premature feature, developmental delay, growth failure, microcephaly, and characteristic facial features, such as sunken eyes and a beaked nose. Interestingly, the brother also presented with atypical features which included cardiac anomalies such as left atrioventricular enlargement and cardiac dysfunction such as dilated cardiomyopathy. In addition, whole exome sequencing and RNA sequencing were employed to analyze their genetic landscape.

RESULTS

WES analysis showed that these two cases carried double unreported heterozygous spliced mutations in the excision repair cross-complementing group 8 (ERCC8, also known as CSA, NM_000082) gene, which were c.78-2 (IVS1) A>T and c.1042-1 (IVS10) G>A, respectively. Moreover, transcript sequencing analysis validated these mutation sites. In this study, Gene Ontology enrichment and KEGG pathway analyses from RNA sequencing demonstrated similarities but some differences when compared with previous studies.

CONCLUSION

For patients with Cockayne syndrome, cardiac changes need to be monitored carefully, especially for cases with splicing mutations of the ERCC8 gene.

Inherited Renal Tubulopathies-Challenges and Controversies

Electrolyte homeostasis is maintained by the kidney through a complex transport function mostly performed by specialized proteins distributed along the renal tubules. Pathogenic variants in the genes encoding these proteins impair this function and have consequences on the whole organism. Establishing a genetic diagnosis in patients with renal tubular dysfunction is a challenging task given the genetic and phenotypic heterogeneity, functional characteristics of the genes involved and the number of yet unknown causes. Part of these difficulties can be overcome by gathering large patient cohorts and applying high-throughput sequencing techniques combined with experimental work to prove functional impact. This approach has led to the identification of a number of genes but also generated controversies about proper interpretation of variants. In this article, we will highlight these challenges and controversies.

A novel compound heterozygous mutation of SLC12A3 gene in a Chinese pedigree with Gitelman syndrome

PURPOSE

Gitelman syndrome (GS) is an autosomal recessive renal tubular disorder characterized by salt wasting and hypokalemia resulting from loss-of-function mutations in the solute carrier family 12A3 (SLC12A3) gene encoding the thiazide-sensitive NaCl cotransporter (NCC). Here, we investigated the clinical manifestations and genetic features of a Chinese pedigree with GS.

METHODS

Next-generation sequencing and Sanger sequencing analysis were performed to define and confirm the SLC12A3 gene mutations of the patient (proband II:1) and this pedigree. Clinical manifestations and biochemical parameters were collected and analyzed.

RESULTS

Genetic analysis of the SLC12A3 gene identified two novel mutations in the proband, heterozygous (c.2842delT) and heterozygous (c.1569_1586del) mutation, respectively. Additionally, heterozygous (c.2842delT) mutation in SLC12A3 gene was found in his father and younger brother. The other heterozygous (c.1569_1586del) mutation in SLC12A3 gene was carried by his mother.

CONCLUSIONS

Two novel mutations may be related to the occurrence of the GS in the pedigree. However, additional studies are particularly required to explore the underlying molecular mechanisms.

Genetic Analysis of SLC12A3 Gene in Chinese Patients with Gitelman Syndrome

Background

The incidence of Gitelman syndrome (GS) has been increasing in our hospital. The aim of this study was to explore the diagnostic accuracy and features of SLC12A3 gene in Chinese patients with GS.

Material/Methods

We searched the literature about Chinese patients with GS in the PubMed database up to July 2018 and also included 8 GS Chinese patients from our hospital in our analysis that explored the features of SLC12A3 gene. We divided all the patients into 3 groups according to diagnostic consensus. Complete compliance was defined to mean containing 2 allelic mutations, partial compliance to mean one allelic mutation, and clinical compliance to mean no mutations.

Results

Totally, 137 patients were enrolled in this study and 90 mutations were counted. Missense mutations accounted for over 72% in Chinese GS patients and the most common one was Thr60Met. According to the consensus, there were 102 patients (74.5%) in the complete compliance group, 31 patients (22.6%) in the partial compliance group, and only 4 patients (2.9%) in the clinical compliance group.

Conclusions

The SLC12A3 gene analysis in Chinese GS patients revealed that the most common mutation was Thr60Met, one of the missense mutations. Most of the patients were in the complete compliance group (i.e., 2 allelic mutations); the other cases might be explained by gene rearrangement.