İrEm Kalay

Background: In males, MECP2 loss of function was long thought to be lethal or uniformly severe, and affected boys remain under-recognised. Their clinical range is still poorly defined. Methods: We assembled a multicentre Turkish series of 22 hemizygous male probands ascertained through routine diagnostic testing rather than severe-phenotype registries. Variants were classified under the ClinGen Expert Panel specification for MECP2 (GN036, version 6.0.0) and its combining rules, with the Panel’s ClinVar classifications adopted where available. Phenotypic analysis was restricted to the 21 probands with pathogenic, likely pathogenic or uncertain variants. Results: The 22 probands carried 17 distinct variants (11 missense, 5 frameshift and one 3’ untranslated region deletion), of which 2 were classified as pathogenic, 1 likely pathogenic, 13 uncertain and 1 benign (3, 4, 14 and 1 probands, respectively). Where recorded, intellectual disability or developmental delay affected 7 of 7 probands with pathogenic or likely pathogenic variants and 8 of 10 with uncertain variants; seizures affected 2 of 3 and 8 of 10, respectively. Growth or head-circumference findings, recorded in 9 of 21 probands, included obesity or overgrowth (5), microcephaly (4, one borderline) and short stature (3). A maternal carrier was identified in 6 of 22 families (five laboratory-confirmed); the other 16 mothers were untested, so no de novo event was confirmed. Second-locus findings, reported by referring laboratories in 3 probands, could not be independently reclassified. Conclusions: In this diagnostically ascertained series, phenotypes observed among males carrying MECP2 variants were graded rather than uniformly severe. Fourteen of the 21 probands carry variants of uncertain significance, in whom causation is not established, so the range that may be attributed to MECP2 rests on seven individuals carrying variants classified as pathogenic or likely pathogenic under the stated criteria. In one of them, published functional data on the identical variant conflict with its pathogenic classification, so attribution of his phenotype to MECP2 remains uncertain. These provisional observations support a low threshold for MECP2 testing in males with unexplained neurodevelopmental presentations, attention to growth as well as head circumference, and consideration of additional loci.

Pathogenic variants in the OPHN1 gene are associated with X-linked intellectual developmental disorder, Billuart type (OMIM #300486), characterized by intellectual disability, distinctive facial features, cerebellar abnormalities, ventriculomegaly, epilepsy, and variable neuropsychiatric manifestations. In this study, four male individuals from four unrelated families presenting with intellectual disability and developmental delay were evaluated. Comprehensive clinical, neuroimaging, and molecular genetic data were collected. Genetic analyses were performed using whole-exome or clinical exome sequencing. Hemizygous OPHN1 variants were identified in all individuals. Two variants, a nonsense variant, c.226del (p.Leu76Ter), and a frameshift variant, c.226_227del (p.Leu76AspfsTer2), were predicted to introduce premature termination codons resulting in loss of protein function and were classified as pathogenic or likely pathogenic. Additionally, two intronic splice-site variants (c.1527–3 C > G and c.2158 + 5G > A) were classified as variants of uncertain significance; however, in silico analyses strongly supported their potential to disrupt normal splicing. The clinical features observed in the affected individuals, including developmental delay, intellectual disability of variable severity, characteristic facial features, and cerebellar and ventricular abnormalities, were consistent with previously reported OPHN1-associated phenotypes. Neuropsychiatric features, including autism spectrum disorder and hyperactivity, were also observed, highlighting phenotypic variability. This study reports the first OPHN1-related cases from Türkiye and expands the molecular and phenotypic spectrum of OPHN1-associated neurodevelopmental disorders by identifying three novel variants. Our findings support the pathogenic relevance of both loss-of-function and splice-site variants and contribute to improved genotype–phenotype correlation and diagnostic evaluation.

Xia–Gibbs syndrome (XGS) is a rare neurodevelopmental disorder caused by heterozygous variants in the AHDC1 gene. While the core phenotype includes developmental delay, hypotonia, and expressive language impairment, the syndrome displays considerable clinical and genetic heterogeneity. Data from non‐European populations remain scarce. We report the clinical and molecular findings of five unrelated Turkish patients with XGS diagnosed via whole‐exome sequencing (WES). This is a multicenter study, and clinical data were collected from participating centers using standardized forms. All patients carried heterozygous, de novo AHDC1 variants (three frameshift, two nonsense), all of which were classified as pathogenic or likely pathogenic. Three of these, p.(Ala1432Profs13), p.(Val900Glyfs2), and p.(Val704Profs*26), are novel and predicted to cause protein truncation. Nonsense mutations are p.(Arg108*) and p.(Trp638*), which were previously reported as disease‐causing. One patient had dual diagnoses with AHDC1 and CDK13 variants, explaining ocular and cardiac anomalies, leading to a particularly severe neurodevelopmental phenotype. This is the largest study reported to date in Turkey on XGS, a rare genetic disorder, further expanding the disease's genotypic and phenotypic spectrum. Recognition of dual diagnoses in a single patient underscores the value of WES in detecting complex genotypes and avoiding misattributed genotype–phenotype associations. As a recently described syndrome, careful evaluation of patients with XGS for atypical phenotypes may provide important contributions to the clinical presentation described in the literature.

Background/Objective: Prenatal cytogenetic testing is essential for pregnant women who are at high risk of having a child with a chromosomal abnormality. While conventional karyotyping detects large aneuploidies and structural rearrangements (>5–10 Mb), chromosomal microarray analysis (CMA) identifies smaller copy number variants (CNVs), increasing the diagnostic yield by approximately 5%. CMA is now recommended as the first-line test for evaluating fetal structural anomalies that are detected by ultrasound. Method: From March 2023 to September 2024, we analyzed 344 prenatal samples using conventional karyotyping and SNP-based CMA. Karyotyping was performed via flask culture, and CMA was conducted using the Infinium Global Screening Array Cyto (GSA-Cyto) on the Illumina iScan platform. We interpreted the CNVs using NxClinical v6.0 and curated databases including ClinVar, DECIPHER, OMIM, and ClinGen, among others. Our results aligned with the GRCh37/hg19 reference genome. Results: Chromosomal abnormalities were identified in 57/344 cases (16.5%). Of these, 39 cases were numerical chromosomal anomalies, and 18 cases were pathogenic or likely pathogenic CNVs. Notably, 11 CNVs (3.2%) were undetectable by conventional karyotyping, emphasizing the added value of CMA. Conclusions: CMA enhances the prenatal diagnostic accuracy by detecting submicroscopic CNVs that are not visible with conventional methods, supporting the routine use of this analysis in prenatal genetic evaluation.

Background/Objective: Prenatal cytogenetic testing is essential for pregnancies at high risk of chromosomal abnormalities. While conventional karyotyping detects large aneuploidies and structural rearrangements (>5–10 Mb), chromosomal microarray analysis (CMA) identifies smaller copy number variants (CNVs), increasing diagnostic yield by approximately 5%. CMA is now recommended as the first-tier test for evaluating fetal structural anomalies detected by ultrasound. Method: From March 2023 to September 2024, 344 prenatal samples were analyzed using conventional karyotyping and SNP-based CMA. Karyotyping was performed via flask culture, and CMA was conducted using the Infinium Global Screening Array Cyto (GSA-Cyto) on the Illumina iScan platform. CNVs were interpreted using NxClinical v6.0 and curated databases including ClinVar, DECIPHER, OMIM, ClinGen, and others. Results were aligned to the GRCh37/hg19 reference genome. Results: Chromosomal abnormalities were identified in 57/344 cases (16.5%). Of these, 39 were numerical chromosomal anomalies and 18 were pathogenic or likely pathogenic CNVs. Notably, 11 CNVs (3.2%) were undetectable by conventional karyotyping, emphasizing the added value of CMA. Conclusion: CMA enhances prenatal diagnostic accuracy by detecting submicroscopic CNVs that are not visible with conventional methods, supporting its routine use in prenatal genetic evaluation.

Background and Objectives: Checkpoint kinase 2 (CHEK2) is a tumor suppressor gene involved in DNA repair and cell cycle regulation. Pathogenic or likely pathogenic (P/LP) variants in CHEK2 are associated with increased cancer risk. Conversely, recent large cohort studies have identified certain variants that, despite being classified as P/LP by in silico analysis, are considered low risk. Thus, the genotype–phenotype correlations of CHEK2 require a better understanding. In this study, we aimed to characterize germline CHEK2 variants from a group of individuals who applied to cancer genetic clinics in the Marmara Region of Türkiye. We also aimed to assess the phenotypic impacts of these variants by using a new score of statistically significant in silico predictors (SSIPs). Methods: We analyzed 1707 individuals with high risk cancer predisposition, focusing on germline CHEK2 variants, using SSIP scores and population-specific data. Results:CHEK2 variants appeared in approximately 8% of cases. The SSIP scores indicated that the missense mutation, p.Arg117Gly, significantly impairs DNA repair. Almost half of the variants had higher allele frequencies than the variants listed in the Genome Aggregation Database (gnomAD), and three variants had significantly higher frequencies compared to the variants listed on the Turkish Variome database (p.Thr476Met, p.Arg137Gln, c.592+3A>T), emphasizing the importance of population-specific data. Conclusions: This comprehensive analysis of CHEK2 variants in the Turkish population provides crucial insights for cancer geneticists and oncologists. Our findings will help to enhance the evaluation and management of cancer predisposition associated with CHEK2 in Türkiye and other regions that have significant Turkish populations.

Classic galactosemia (OMIM#230400) is an autosomal recessive inborn error of carbohydrate metabolism caused by a deficiency of the galactose‐1‐phosphate‐uridyl‐transferase enzyme encoded by the GALT gene. Even though a galactose‐restricted diet efficiently resolves the acute complications, it is insufficient to prevent long‐term complications regarding speech defects, intellectual functioning, premature ovarian failure, cataract, hepatomegaly, dysarthria, ataxia, and tremor. Seventy‐seven patients who were genetically diagnosed with classic galactosemia were included in this cohort. Identified novel variants were classified based on their predicted effect on the GALT function. Further, potential genotype–phenotype correlations were investigated via statistical analysis. In total, 18 different sequence variants were identified, including four novels (c.200delG/p.(Arg67Profs^*19), c.533T>G/ p.(Met178Arg), c.708_709delGT/p.(Ser236Argfs^*30), c.467C>A/p.(Ser156^*)). Jaundice was the most common short‐term finding with 80% (61/77). Even with early diagnosis, intellectual disability is encountered with 36% (27/74) of the long‐term complications. Patients with biallelic missense variants have a significantly higher prevalence of cataracts (OR: 17.9). Longitudinal observations showed attenuation of cataracts and hepatomegaly. This study has shown the GALT variation spectrum of the Turkish population with a 30‐year retrospective cohort, submitting a significant contribution to the genotype/phenotype correlation in galactosemia. This study also highlights the cost‐effective importance of Sanger sequencing in the diagnosis of single‐gene metabolic diseases.