Identification of a novel homozygous NR5A1 variant in a patient with a 46,XY disorders of sex development.

OBJECTIVES: Nuclear receptor subfamily 5 group A member 1 (NR5A1) is a transcription factor critical for the development of various organs. Pathogenic variants in NR5A1 are associated with a spectrum of disorders of sex development (DSD). CASE REPORT: A 15-month-old baby, raised as a girl, was referred for genital swelling and ambiguous genitalia. Born to healthy consanguineous parents, the baby had a phallus, perineal hypospadias, labial fusion, and a hypoplastic scrotum. Hormonal evaluation showed normal levels, and ultrasonography revealed small gonads and absence of Müllerian derivatives. Post-human chorionic gonadotropin (hCG) testing indicated an adequate testosterone response. The karyotype was 46,XY, and in it was found a homozygous NR5A1 variant (c.307 C>T, p.Arg103Trp) in a custom 46 XY DSD gene panel. Notably, the patient exhibited complete sex reversal, hyposplenia, and no adrenal insufficiency. CONCLUSIONS: Previously, NR5A1 pathogenic variants were considered to be dominantly inherited, and homozygous cases were thought to be associated with adrenal insufficiency. Despite the homozygous pathogenic variant, our patient showed hyposplenism with normal adrenal function; this highlights the complexity of NR5A1 genotype-phenotype correlations. These patients should be monitored for adrenal insufficiency and DSD as well as splenic function.

Genetic diagnosis of congenital hypopituitarism in Turkish patients by a target gene panel: novel pathogenic variants in GHRHR, GLI2, LHX4 and POU1F1 genes

ABSTRACT Objective: Congenital hypopituitarism (CH) is a rare disease characterized by one or more hormone deficiencies of the pituitary gland. To date, many genes have been associated with CH. In this study, we identified the allelic variant spectrum of 11 causative genes in Turkish patients with CH. Materials and methods: This study included 47 patients [21 girls (44.6%) and 26 boys (55.4%)] from 45 families. To identify the genetic etiology, we screened 11 candidate genes associated with CH using next-generation sequencing. To confirm and detect the status of the specific familial variant in relatives, Sanger sequencing was also performed. Results: We identified 12 possible pathogenic variants in GHRHR, GH1, GLI2, PROP-1, POU1F1, and LHX4 in 11 patients (23.4%), of which six were novel variants: two in GHRHR, two in POU1F1, one in GLI2, and one in LHX4. In all patients, these variants were most frequently found in GLI2, followed by PROP-1 and GHRHR. Conclusion: Genetic causes were determined in only 23.4% of all patients with CH and 63% of molecularly diagnosed patients (7/11) from consanguineous families. Despite advances in genetics, we were unable to identify the genetic etiology of most patients with CH, suggesting the effect of unknown genes or environmental factors. More genetic studies are necessary to understand the etiology of CH.

Genetic diagnosis of congenital hypopituitarism in Turkish patients by a target gene panel: novel pathogenic variants in GHRHR, GLI2, LHX4 and POU1F1 genes.

Objective: Congenital hypopituitarism (CH) is a rare disease characterized by one or more hormone deficiencies of the pituitary gland. To date, many genes have been associated with CH. In this study, we identified the allelic variant spectrum of 11 causative genes in Turkish patients with CH. Materials and methods: This study included 47 patients [21 girls (44.6%) and 26 boys (55.4%)] from 45 families. To identify the genetic etiology, we screened 11 candidate genes associated with CH using next-generation sequencing. To confirm and detect the status of the specific familial variant in relatives, Sanger sequencing was also performed. Results: We identified 12 possible pathogenic variants in GHRHR, GH1, GLI2, PROP-1, POU1F1, and LHX4 in 11 patients (23.4%), of which six were novel variants: two in GHRHR, two in POU1F1, one in GLI2, and one in LHX4. In all patients, these variants were most frequently found in GLI2, followed by PROP-1 and GHRHR. Conclusion: Genetic causes were determined in only 23.4% of all patients with CH and 63% of molecularly diagnosed patients (7/11) from consanguineous families. Despite advances in genetics, we were unable to identify the genetic etiology of most patients with CH, suggesting the effect of unknown genes or environmental factors. More genetic studies are necessary to understand the etiology of CH.

A rare cause of intellectual disability: Novel mutations of NFIX gene in two patients with clinical features of Marshall-Smith syndrome and Malan syndrome.

Marshall-Smith syndrome (MSS) and Malan syndrome (MS) are both allelic disorders caused by mutations in the NFIX gene. MS is characterized by overgrowth, intellectual disability, distinctive facial features, and accelerated skeletal maturation. On the other hand, clinical features of MSS consist of advanced bone age, dysmorphic features, intellectual disability, and failure to thrive at birth. In this study, we presented the clinical and molecular findings of two different patients with MS and MSS as a rare cause of intellectual disability and reported two novel variants in the NFIX gene. NFIX gene sequencing revealed a novel heterozygous c.1287delC (p.G430Vfs*34) mutation in patient 1 whose clinical diagnosis was compatible with Marshall-Smith syndrome, and in the second patient, physical features consistent with Malan syndrome, was detected a heterozygous one nucleotide duplication, c.303dupC (pCys102LeufsTer17).

Novel RPS6KA3 mutations cause Coffin-Lowry syndrome in two patients and concurrent compulsive eyebrow-pulling behavior in one of them.

Coffin-Lowry syndrome (CLS) is a rare X-linked disorder that, usually affects males, presenting with intellectual disability, short stature, growth retardation, short hands, hyperextensible fingers and progressive kyphoscoliosis. Due to skewed X chromosome inactivation, the clinical presentations of the affected females vary greatly and clinical manifestations could range from mild intellectual disability to typical features of CLS in males. Here, we reported two different novel RPS6KA3 gene mutations in two unrelated CLS patients and also described concomitant compulsive eyebrow-pulling behavior in one of these cases for the first time in the literature.

Clinical and Genetic Characteristics of Patients with Common and Rare Types of Congenital Adrenal Hyperplasia: Novel Variants in STAR and CYP17A1.

Objectives: Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive diseases characterized by salt wasting or virilization. 21 hydroxylase deficiency (21-OHD) accounts for 90-95% of all cases of CAH and caused by the genetic defects of CYP21A2. Other forms include 3-ß-hydroxysteroid dehydrogenase deficiency, 11-ß-hydroxylase deficiency (11ß-OHD) (%5-8), 17-α-hydroxylase deficiency (17α-OHD), and steroidogenic acute regulatory protein (STAR) defects (congenital lipoid adrenal hyperplasia) with mutations in HSD3B2, CYP11B1, CYP17A1, and STAR, respectively. Objectives: Herein, we aimed to present the clinical and genetic features of 64 patients with various types of CAH. Methods: Sixty-four patients with CAH, monitored in the Izmir Dr. Behcet Uz Children Hospital Division of Pediatric Endocrinology, were retrospectively analyzed for the clinical, laboratory, and genetic data. Results: Fifty-six patients (87.5%) had 21-OHD and four patients (6.3%) had 17α-OHD, three patients (4.7%) had 11ß-OHD, and one patient (1.5%) had STAR defect. The most common presenting features in 21-OHD were ambiguous genitalia. Patients with 21-OHD were diagnosed earlier than the rare groups. Disease-causing variants of CYP21A2 were identified in 46 patients. The most common mutations were IVS2, Q318X, I172N, and large deletions. Three patients with 11ß-OHD were presented with enlargement of penis and early pubic hair at the median presenting age of 26 months. 17α-OHD deficiency was detected in 4 cases. Genetic analysis revealed two different homozygous CYP17A1 variants. The patient with STAR defect was presented with dehydration and cholestasis in 44 days of the life. Genetic analysis of patient with STAR deficiency revealed a novel homozygous variant. Conclusion: The current study reported a genotype-phenotype correlation consistent with literature data in CAH cases with 21-OHD. This study also reported novel homozygous variants in STAR and CYP17A1 genes that lead to rare types of CAH.

A Null Mutation of TNFRSF11A Causes Dysosteosclerosis, Not Osteopetrosis.

Dysosteosclerosis (DOS) is a rare sclerosing bone dysplasia characterized by unique osteosclerosis of the long tubular bones and platyspondyly. DOS is inherited in an autosomal recessive manner and is genetically and clinically heterogeneous. To date, four individuals with DOS who have five different TNFRSF11A mutations have been reported. Based on their data, it is hypothesized that mutations producing aberrant mutant RANK proteins (missense or truncated or elongated) cause DOS, while null mutations lead to osteopetrosis, autosomal recessive 7 (OPTB7). Herein, we present the fifth case of TNFRSF11A-associated DOS with a novel homozygous frame-shift mutation (c.19_31del; p.[Arg7CysfsTer172]). The mutation is predicted to cause nonsense mutation-mediated mRNA decay (NMD) in all RANK isoform transcripts, resulting in totally null allele. Our findings suggest genotype-phenotype relationship in TNFRSF11A-associated OPTB7 and DOS remains unclear, and that the deficiency of TNFRSF11A functions might cause DOS, rather than osteopetrosis. More data are necessary to understand the phenotypic spectrum caused by TNFRSF11A mutations.

Screening of non-syndromic early-onset child and adolescent obese patients in terms of LEP, LEPR, MC4R and POMC gene variants by next-generation sequencing.

OBJECTIVES: Non-syndromic monogenic obesity is a rare cause of early-onset severe obesity in the childhood period. The aim of this study was to screen four obesity related genes (LEP, LEPR, MC4R and POMC) in children and adolescents who had severe, non-syndromic early onset obesity. METHODS: Next-generation sequencing of all exons in LEP, LEPR, MC4R and POMC was performed in 154 children and adolescents with early onset severe obesity obesity. RESULTS: Fifteen different variants in nineteen patients were identified with a variant detection rate of 12.3%. While six different heterozygous variants were observed in MC4R gene (10/154 patients; 6.5%), five different variants in POMC gene (four of them were heterozygous and one of them was homozygous) (6/154 patients; 3.9%) and four different homozygous variants in LEPR gene (3/154 patients; 1.9%) were described. However, no variants were detected in the LEP gene. The most common pathogenic variant was c.496G>A in MC4R gene, which was detected in four unrelated patients. Six novel variants (6/15 variants; 40%) were described in seven patients. Four of them including c.233C>A and c.752T>C in MC4R gene and c.761dup and c.1221dup in LEPR gene were evaluated as pathogenic or likely pathogenic. CONCLUSIONS: In conclusion, MC4R variants are the most common genetic cause of monogenic early-onset obesity, consistent with the literature. The c.496G>A variant in MC4R gene is highly prevalent in early-onset obese patients.

A Neonatal Case of Infantile Malignant Osteopetrosis Presenting with Thrombocytopenia and Hypotonicity: A Novel Mutation in Chloride Voltage-Gated Channel 7 Gene.

Autosomal recessive osteopetrosis is also known as infantile malignant osteopetrosis (IMO). The clinical course is often serious and if left untreated, it is fatal in the 1st year of life. Diagnosis is challenging and often delayed or misdiagnosed. Herein, we present an infant girl who was diagnosed with IMO during evaluations for her hypotonicity and thrombocytopenia. A novel mutation of the chloride voltage-gated channel 7 (CLCN7) gene was also reported. A 10-day-old female patient was referred to our hospital for evaluation of hypotonicity. Her physical examination was normal, other than hypotonicity. Laboratory analysis revealed thrombocytopenia and hypocalcemia. In the progress, while she was followed in outpatient clinic, hepatosplenomegaly was detected at the age of 3 months. IMO was suspected with the findings of hepatosplenomegaly, cytopenia, hypocalcemia, difficulty of obtaining bone marrow, peripheral smear findings, and hearing loss. The X-ray of the bones was consistent with IMO. A novel pathogenic homozygous c.1504>T (p.Arg502Trp) mutation in CLCN7 gene was revealed. IMO is a rare disorder and it is important to differentiate this entity for better clinical outcome. The presence of neurological and hematological findings, organomegaly, hearing loss, and vision disorders must attract attention to IMO.

Evaluation of Sporadic and Familial Cases with Craniofrontonasal Syndrome: A Wide Clinical Spectrum and Identification of a Novel EFNB1 Gene Mutation.

Craniofrontonasal syndrome (CFNS) is a rare X-linked genetic disorder which is characterized by coronal synostosis, widely spaced eyes, a central nasal groove, and various skeletal anomalies. Mutations in the EFNB1 gene in Xq13.1 are responsible for familial and sporadic cases. In the present study, we aimed to evaluate the clinical characteristics and molecular results of 4 patients with CFNS. Genomic DNA was extracted from the peripheral blood lymphocytes of all patients and their parents, and Sanger sequencing of the EFNB1 gene was performed. A novel EFNB1 gene mutation (c.65delG; p.Cys22SerfsTer24) was detected in a newborn who had only dysmorphic facial features and bicornuate uterus. The other 3 patients (2 familial cases and 1 sporadic case) shared the same mutation (c.196C>T; p.R66X). However, the clinical features of these patients were highly variable. Additionally, central (meso-axial) polydactyly and deep palmar creases were detected, which have not been previously reported. CFNS has a wide clinical spectrum, but there is no clear genotype-phenotype correlation. However, central (meso-axial) polydactyly and deep palmar creases may be part of the clinical spectrum seen in CFNS. In addition, our findings expand the mutational spectrum in patients with CFNS.

Identification of two AMH gene variants in two unrelated patients with persistent Müllerian duct syndrome: one novel variant.

INTRODUCTION: Persistent müllerian duct syndrome (PMDS) is a rare form of 46, XY disorder of sex development characterized by the persistence of the müllerian structures (uterus, fallopian tubes, the upper part of the vagina) in phenotypically and genotypically normal males. This disease occurs as a result of impairment in the synthesis, release or effect of anti-Müllerian hormone (AMH) during the embryonic period. Approximately 85-88% of PMDS cases have been reported to have AMH or AMHRII mutation. CASE: Herein, we report two PMDS cases from unrelated two families who presented with bilateral undescended testes, persistence of müllerian remnants, and low/undetectable serum AMH levels. Molecular genetic analysis revealed two homozygous variants in AMH. The first one is a novel missense variant (c.1315C > T), the latter is a frameshift variant caused by a deletion (c.343_344delCT), which is less frequently reported type in AMH. CONCLUSION: The diagnosis of PMDS should be kept in mind in patients with externally normal males, bilateral cryptorchidism, and signs of müllerian remnants on laparoscopy.

Evaluation of clinical findings and neurofibromatosis type 1 bright objects on brain magnetic resonance images of 60 Turkish patients with NF1 gene variants.

Neurofibromatosis type 1 (NF1) is caused by mutations in the NF1 gene. This retrospective study aims to evaluate the clinical manifestations and brain magnetic resonance images (MRI) analysis in 60 genetically confirmed NF1 patients. The results of next-generation sequencing (NGS), Sanger sequencing, and MLPA of NF1 gene were evaluated. A total of 54 different variants were identified. Fourteen out of them were novel variants (25.9%). Patients who complied with NIH criteria had most frequently frameshift variants (11/32 patients), and those with only CALMs had missense variants (9/28 patients). Neurofibromatosis type 1 bright objects (NBOs) on T2-weighted MRI were detected in 42 patients (42/56; 75%). These brain lesions were detected mostly in basal ganglia and in cerebellar vermis. NBOs were detected more in the patients who complied with NIH criteria (80.6%) compared to those who were only CALMs (68%). While frameshift variants (33.3%) were the most common type variants in the patients who had NBOs, the most common variants were splicing (35.7%) and missense (35.7%) variants in the patients whose MRIs were normal. Frameshift variants (11/28 patients; 39.3%) were the most common in the patients with more than one brain locus involvement. Therefore, we consider that frameshift variants may be associated with increased incidence of NBOs and involvement of more than one brain locus. In addition, NBOs may occur less frequently in the patients with splicing variants. To our knowledge, this is the first study evaluated the relationship between NF1 gene variants and NBOs. Future studies may help us understand the etiology of NBOs.

Orodental, Facial and Clinical Features of Mutation-Positive Noonan Syndrome: A Monocentric Study.

OBJECTIVE: To evaluate orodental, facial, clinical and molecular characteristics of the patients with Noonan Syndrome (NS). STUDY DESIGN: The orodental, clinical and molecular characteristics of 29 mutation-positive patients with NS were recorded. Orodental examination was performed in 17 patients. All exons and exonintron boundries of PTPN11 and SOS1 genes were analyzed by Sanger sequencing. RESULTS: A total of 29 patients with NS from 27 unrelated families were included in the study. Seventeen patients were examined by a specialist in oral medicine. The most common orodental findings were high-arched palate (n=13), gingivitis (n=6) and severe caries (n=6). Anterior open bite, posterior cross bite, Class II malocclusion, hypodontia, prognathism (maxillary or mandibular), macroglossia and gingival hyperplasia were also detected. Thirteen different mutations were observed in PTPN11 gene and exon 3 was the hotspot region. Hypodontia was detected in two patients who had the same mutation in PTPN11 gene, c.181G>A, p.D61N. CONCLUSION: This study indicated a high prevalance of orodental problems including high-arched palate, severe dental caries and gingivitis in patients with mutation-positive NS. The mutation in PTPN11 gene, c.181G>A, p.D61N, may be associated with hypodontia in patients with NS.

Do microdeletions lead to immune deficiency?

INTRODUCTION: Microdeletion syndromes may be accompanied by immunological disorders. This study aimed to evaluate the clinical and laboratory data as well as the immune functions of patients diagnosed with a microdeletion syndrome. MATERIAL AND METHODS: 39 patients diagnosed with microdeletion syndrome who were monitored at the Pediatric Genetics and Immunology clinics at Dr. Behcet Uz Children's Hospital were included in this study. All data for this research were obtained from patient records and by individual consultation with their parents. RESULTS: Of the 39 patients, 15 were monitored for a diagnosis of Williams syndrome, 12 for DiGeorge syndrome, 4 for Prader-Willi syndrome, 2 for Wolf-Hirschhorn syndrome, 1 for a 1p36 deletion, 1 for Smith-Magenis syndrome, 2 for Trichorhinophalangeal syndrome type 2 (TRPS2), and 2 for Cri-du-chat syndrome. Of these 39 patients, 10 (25.6%) had a medical history of frequent upper respiratory tract infections. One of the cases with TRPS2 and another with Smith-Magenis syndrome had previously received intravenous antibiotic therapy for infectious disease. Five of the 12 patients with DiGeorge syndrome had low T lymphocytes. Two of the patients with DiGeorge syndrome with a history of frequent infections, with hypogammaglobinemia, and low lymphocytes were receiving regular intravenous immunoglobulin (IVIG) replacement. CONCLUSIONS: It must be taken into account that patients with microdeletion syndromes, especially those with DiGeorge syndrome, may also have immunodeficiencies; therefore, these patients should be closely monitored to prevent development of any complications.

Detection of SHOX Gene Variations in Patients with Skeletal Abnormalities with or without Short Stature

Objective: SHOX gene mutations constitute one of the genetic causes of short stature. The clinical phenotype includes variable degrees of growth impairment, such as Langer mesomelic dysplasia (LMD), Léri-Weill dyschondrosteosis (LWD) or idiopathic short stature (ISS). The aim of this study was to describe the clinical features and molecular results of SHOX deficiency in a group of Turkish patients who had skeletal findings with and without short stature. Methods: Forty-six patients with ISS, disproportionate short stature or skeletal findings without short stature from 35 different families were included. SHOX gene analysis was performed using Sanger sequencing and multiplex ligation-dependent probe amplification analysis. Results: Three different point mutations (two nonsense, one frameshift) and one whole SHOX gene deletion were detected in 15 patients from four different families. While 4/15 patients had LMD, the remaining patients had clinical features compatible with LWD. Madelung's deformity, cubitus valgus, muscular hypertrophy and short forearm were the most common phenotypic features, as well as short stature. Additionally, hearing loss was detected in two patients with LMD. Conclusion: This study has presented the clinical spectrum and molecular findings of 15 patients with SHOX gene mutations or deletions. SHOX deficiency should be especially considered in patients who have disproportionate short stature or forearm anomalies with or without short stature. Although most of the patients had partial or whole gene deletions, SHOX gene sequencing should be performed in suspected cases. Furthermore, conductive hearing loss may rarely accompany these clinical manifestations.

Novel Ocular and Inner Ear Anomalies in a Patient with Myhre Syndrome.

Myhre syndrome is a rare autosomal dominant multisystemic disorder. Typical features of this disorder include distinctive facial appearance, deafness, intellectual disability, cardiovascular abnormalities, short stature, brachydactyly, and skeletal anomalies. Gain-of-function mutations in the SMAD4 gene are responsible for this syndrome. Herein, we present a 9.6-year-old Turkish girl with molecularly confirmed Myhre syndrome who had novel findings including bilateral Axenfield Rieger anomaly with secondary glaucoma and bilateral enlarged vestibular aqueducts.

Three Siblings with Idiopathic Hypogonadotropic Hypogonadism in a Nonconsanguineous Family: A Novel KISS1R/GPR54 Loss-of-Function Mutation

Idiopathic hypogonadotropic hypogonadism (IHH) is a rare disease caused by defects in the secretion of gonadotropin releasing hormone (GnRH) or the action of GnRH on the pituitary gonadotrophes. KISS1R is one of the genes which, when mutated, cause IHH and mutations of this gene are responsible for about 2-5% of patients with normosmic IHH (NIHH). In this report, we present three siblings with NIHH due to a compound heterozygous KISS1R mutation. Genetic studies were carried out in the 14 year old index case with IHH and three siblings, two of whom were prepubertal. Genomic DNA was extracted from peripheral leukocytes and KISS1R gene was sequenced by using standard polymerase chain reaction amplification procedures. In molecular analysis of the index case, a compound heterozygous mutation was determined in KISS1R gene c.969C>A (p.Y323X) (known pathogenic) and c.170T>C (p.L57P) (novel). Mutation c.170T>C (p.L57P) was inherited from the mother while c.969C>A (p.Y323X) was inherited from the father. The same genotype was also found in two of the three siblings. A compound heterozygous mutation of the KISS1 gene, including one novel mutation, was found to cause NIHH and also incomplete puberty in a non-consanguineous family.

The clinical and molecular features of three Turkish patients with a rare genetic disorder: 2q37 deletion syndrome.

Gürsoy S, Kutbay YB, Özdemir TR, Hazan F. The clinical and molecular features of three Turkish patients with a rare genetic disorder: 2q37 deletion syndrome. Turk J Pediatr 2019; 61: 589-593. Chromosome 2q37 deletion syndrome is a rare chromosomal disorder which is characterized by mild-moderate intellectual disability, brachymetaphalangy of digits 3-5, short stature, obesity, hypotonia and characteristic facial appearance. Here, we report three Turkish patients who have 2q37 deletion in aCGH analysis with various sizes (9.08 Mb, 2.3 Mb and 2.021 Mb, respectively). HDAC4 gene, which is a class II histone deacetylase, has been considered to be associated with most of the features including brachymetaphalangy and intellectual disability. The deletion region included HDAC4 gene in the two patients. However, all of the patients had intellectual disability, especially with a cheerful mood. Some autistic features were detected in one of our patients. Although two patients had some skeletal findings, the deletion region did not contain HDAC4 gene in one of the patients. We suggest that our findings support understanding and updating knowledge on the phenotype-genotype correlation in patients with 2q37 deletion syndrome.

Phenotypic spectrum of CHARGE syndrome based on clinical characteristics

Background/aim: CHARGE syndrome is a rare autosomal dominant disease with multiple congenital anomalies and cognitive impairment, which is caused by mutations in the CHD7 gene. This study aimed to disclose the mild end of the phenotypic spectrum of CHARGE syndrome, which has a highly variable expressivity. Materials and methods: Twenty-one patients who had at least one of the major symptoms of CHARGE syndrome (coloboma, choanal atresia, characteristic ear anomalies, semicircular canal hypoplasia, and cranial nerve anomalies) were included in the study. All patients were tested for karyotype analysis and CHD7 gene mutation/deletion. Results: In the study population, 6 different mutations were detected in 5 patients, and 2 different polymorphisms were detected in the CHD7 gene in 3 patients. MLPA analysis of all coding exons of the CHD7 gene revealed no pathogenic deletion/duplication. Conclusion: CHARGE syndrome should be considered as a differential diagnosis to detect the mild end of the spectrum, even if the patient does not fit the criteria.