A case of hypoparathyroidism, deafness, and renal dysplasia (HDR) syndrome with a novel frameshift variant in GATA3, p.W10Cfs40, lacks kidney malformation

Abstract Autosomal dominant hypoparathyroidism, deafness, and renal dysplasia (HDR) syndrome are typically diagnosed by manifestations of the three features with a positive family history. Our case carried a de novo variant in causative gene, GATA3, but presenting no renal dysplasia or family history. The phenotypic heterogeneity raises a caution for diagnosis.


| INTRODUCTION
We describe a patient diagnosed with hypoparathyroidism, deafness, and renal dysplasia (HDR) syndrome, but lacking one of the three features, renal disease. The detected germline variant in GATA3, p.W10Cfs, disrupting most of functional domains, could paradoxically cause the milder symptoms, compared to many other cases with a partial disruption.
HDR syndrome (OMIM #146255), also known as Barakat syndrome, is an autosomal dominant genetic disease caused by haplo-insufficiency of GATA3 located on chromosome of 10p14. 1,2 The clinical manifestation of the syndrome includes primary hypoparathyroidism, sensorineural hearing loss, renal dysplasia, cardiac malformation, and immune disorder. According to the ClinVar (https:// www.ncbi.nlm.nih.gov/clinv ar/), there are so far 14 pathogenic germline variants associated with HDR syndrome, including 3 missense variants, one nonsense variant, and 10 insertion-deletion variants. Although HDR syndrome stands for hypoparathyroidism, deafness, and renal dysplasia, variable phenotypes of GATA3 variants have been reported, 3 likely reflecting its wide tissue distribution, as well as the magnitude of alterations in GATA3. We recently experienced a case of HDR syndrome without renal dysplasia.

| CASE PRESENTATION
A 24-year-old man was referred to our department for investigation of hypocalcemia. He was born from nonconsanguineous Japanese parents as a low birth weight immature baby of 1114 g with ptosis and joint contracture, although no neonatal asphyxia, cerebral dysgenesis, or multiple abnormality were described. His moderate bilateral sensorineural hearing loss was pointed out at the age of 4, resulting in requirement for a hearing aid. He often experienced facial spasm, tetany,  (Table 1) demonstrated marked reduction of intact PTH to 15 pg/mL (reference interval: 18.5-88.0), but mild hypocalcemia with a serum calcium level of 8.3 mg/dL, and phosphorus within normal range at 4.9 mg/dL, due to the administrations of vitamin D and oral calcium supplement. Basal levels of other hormones were within the normal range. No evidence of renal dysfunction, proteinuria, hematuria, or urinary tract infection was obtained. Electrocardiography was negative for cardiac hypertrophy or ischemia. Neck ultrasound indicated no apparent nodule or abnormality in and around the thyroid glands. A brain CT showed multiple calcifications of basal nuclei ( Figure 1A), while abdominal CT demonstrated no morphological abnormality of kidneys ( Figure 1B).
Differential diagnosis of early-onset hypoparathyroidism includes several congenital diseases, DiGeorge syndrome, Kenny-Caffey syndrome, and a genetic abnormality in PTH or CaSR, although deafness is almost always observed in HDR syndrome and more rarely in DiGeorge syndrome. To distinguish between HDR syndrome and DiGeorge syndrome, we evaluated classification of leukocytes by flow cytometry (Table 2), resulting in a decreased ratio of Th2/CD4 + T cells to 0.3% (0.32-3.24), as well as an elevated ratio of Th1/Th2 to 76.2 (6.34-29.67). These indicated a reduced differentiation of naive CD4 + cells into Th2 lymphocytes, consistent with HDR syndrome. FISH analysis did not reveal any microdeletion in the 22q11. To perform genetic testing in his parents, several genetic counseling sessions were required for their acceptance. Disclosing the results, however, much improved their mood and reduced their anxiety, without apparently affecting their relationship.

| DISCUSSION
HDR syndrome is a rare autosomal dominant disease, caused by haplo-insufficiency of GATA3, typically leading to the three major symptoms: hypoparathyroidism, sensorineural hearing loss, and renal dysplasia. Differential diagnosis of early-onset hypoparathyroidism complicated with deafness includes HDR syndrome and DiGeorge syndrome. In the present case, low Th2 lymphocytes and absence of 22q11 abnormality, strongly suggested HDR syndrome. Genetic testing of GATA3 indicated  dysplasia is often associated with a worse prognosis. 5 GATA3 is abundantly expressed not only in the tissues associated with HDR syndrome, parathyroid, inner ear, and kidney, but also in lymphoid tissue, thyroid gland, pancreatic β-cells, and gonads. 6 Of those tissues, only three tissues, parathyroid, inner ear, and Th2 cells, were markedly affected in the present case. GATA3 haplo-insufficiency is thought to be a major pathogenic mechanism of HDR syndrome. Dominantnegative effects by a pathogenic variant, however, also play roles in some cases. 7 There are so far two types of dominant-negative variants in GATA3, with or without DNAbinding activity. A classical dominant-negative variant is KRR, which has an amino acid substitution between two zinc-finger motifs. 8 Such variants likely affect the function of unaffected GATA3 by occupying the GATA3 binding site. A following study has demonstrated that p.Cys321Ser exerts a dominant-negative effect even without DNA binding, likely due to competitive interactions with other GATA3-binding proteins. 7 GATA3 regulates differentiation of T lymphocytes as a transcription factor, interacting with another transcription factor, TBX21, through the N-terminal binding domain. 9 According to the ClinVar (Table 3), a large number of pathogenic variants reported in GATA3 are located in or around the DNA binding domain, downstream the TBX21 binding domain (1 to 257 a.a. according to the UniProt, https://www.unipr ot.org/unipr ot/P23771, see Figure 2B). Such variants will disrupt the DNA binding domain, but the TBX21 binding domain likely remains, leading to the dominant-negative effects on the functionality of GATA3 derived from the other unaffected allele. The frameshift variant detected in the present case, located just 30 to 49 bases downstream from the ATG start codon, likely disrupted both the DNA-binding domains and the TBX21 binding domain, so it would not retain the dominant-negative activity, but represent an effect of haplo-insufficiency. Lack of renal manifestation in the present case could be due to the disruption of TBX21 domain. Since a previous case with p.Met36fs was associated with kidney disease (Table 3), the N-terminal portion between 10 and 36 could be important for the differential phenotype.
In conclusion, the novel GATA3 frameshift variant, close to the start codon, represented relatively mild symptoms in HDR syndrome. The present case indicates the usefulness of genetic testing of GATA3 for clinical diagnosis in patients with hypoparathyroidism complicated with deafness, even without renal dysplasia or positive family histories.