Clinical Genetics

Intellectual disability (ID) is defined as a severe impairment in reasoning, learning, and problem‐solving abilities along with adaptive behavior that occurs before the age of 18 years. The present study aimed to present the clinical and genetic data of a cohort of Turkish pediatric patients diagnosed with the ultrarare (which only up to 20 cases having been reported in the relevant literature thus far) ID phenotype. A total of 29 patients from 26 different families, who were diagnosed with ultrarare ID upon whole exome sequencing (WES) analysis, were included in the study. Of the patients included in the study, 18 (62%) were male and 11 (38%) were female. There was consanguinity between parents in 16 families (55%). With respect to the ID phenotype, three families had cases with a similar phenotype, while 23 families (88%) had sporadic cases. Upon molecular analysis, 28 different variations in 23 different genes were noted. Of the variations detected, 15 were missense, 6 nonsense, 4 frameshift, 2 splice‐site, and 1 gross exonic deletion. Nine (32%) variations were novel among the detected variations. This study summarized the clinical and genetic features of 23 different ultrarare ID phenotypes by means of WES study, including copy number variations (CNVs) analysis. Novel clinical and genetic findings in the present study contribute to a better understanding of the genotypic and phenotypic spectrum. The effects of some rare variations on protein structure were revealed by means of in silico modeling. Newly described cases with ultrarare phenotypes help achieve a clearer description of the clinical and genetic manifestations of the syndromes and gain a better understanding of the molecular mechanisms.

SOFT syndrome (SOFTS) is an autosomal recessive disorder caused by biallelic POC1A variants, characterized by short stature, distinctive facial features, onychodysplasia, and hypotrichosis. To date, 21 pathogenic POC1A variants have been reported in 26 families. This study aims to broaden the phenotypic and genotypic spectrum of SOFTS with emphasis on the long‐term effects of growth hormone (GH) therapy. We report four unrelated patients with three homozygous POC1A variants and demonstrate the transcriptional effects of two canonical splicing variants. All four patients had severe growth retardation, sparse hair/eyebrows, high/prominent forehead, long/triangular face, prominent nose, short middle/distal phalanges, puffy/tapering fingers, and prominent heels. Endocrine abnormalities included insulin resistance and impaired glucose tolerance, dyslipidemia, GH deficiency, central hypothyroidism, and precocious puberty. Two patients treated long‐term with recombinant human GH showed insufficient responses. We also provide an extensive review of 43 cases including those we report, contributing to a better understanding of the full clinical and endocrinological spectrum of SOFTS.

Screening for Lynch syndrome (LS) is essential in colorectal carcinoma (CRC) diagnosis. The hallmark of CRC in LS is mismatch repair (MMR) deficiency, a vital biomarkers assessed by microsatellite instability (MSI) analysis and/or immunohistochemistry (IHC) staining of the MMR proteins in the tumor, that also predict response to immune checkpoint inhibitors. We report two LS patients who developed MMR proficient CRCs. Patient A, with a pathogenic MSH6 germline variant, presented with two MMR discordant CRCs: a rectal MMRd/MSI adenocarcinoma, and a sigmoid MMR proficient (MMRp) and microsatellite stable (MSS) adenocarcinoma, leading to metastasis. While the MMRd/MSI carcinoma was recognized early and showed complete pathologic response after pembrolizumab treatment, the MMRp/MSS adenocarcinoma was underrecognized and poorly responsive to treatment. A second patient, with a pathogenic PMS2 variant, also developed a MMRp CRC. These cases highlight the complex biological pathways in CRC development and the impact of molecular classification on treatment.

Variants in the SYNGAP1 gene leading to decreased SynGAP protein expression are critical for the pathogenesis of mental retardation type 5 (MRD5). This study aims to explore the relationship between SYNGAP1 genotype and clinical phenotype through an expanded sample size, thereby enhancing the understanding of the specific mechanisms underlying MRD5. Data from previously published cases of patients with SYNGAP1 mutations were collected, and the relationship between genotype and clinical phenotype was analyzed. A total of 246 MRD5 patients were included in the analysis. Among them, 98.7% (224/227) were diagnosed with intellectual disability (ID), 91.6% (208/227) with epilepsy, and 57.3% (137/239) with autism spectrum disorder (ASD). The clinical phenotypes of MRD5 patients were found to be associated with their genotypes. Variants located in exons 1 to 6 may correlate with milder ID and reduced risk of ASD, yet they are more likely to present as refractory epilepsy.

Microphthalmia, anophthalmia and coloboma (MAC) comprise a highly heterogeneous spectrum of congenital ocular malformations with an estimated incidence of 1 in 5000 to 1 in 30 000 live births. Although there is likely to be a genetic component in the majority of cases, many remain without a molecular diagnosis. Netrin‐1 was previously identified as a mediator of optic fissure closure from transcriptome analyses of chick and zebrafish and was shown to cause ocular coloboma when knocked out in both mouse and zebrafish. Here, we report the first patient with chorioretinal coloboma and microphthalmia harbouring a novel heterozygous likely pathogenic NTN1 missense variant, c.1483T>A p.(Tyr495Asn), validating a conserved gene function in ocular development. In addition, the patient displayed bilateral sensorineural hearing loss which was investigated by examining the sensory hair cells of ntn1a morphant zebrafish, suggesting a role for netrin‐1 in hair cell development.

Split hand‐foot malformation (SHFM) is a congenital limb malformation affecting primarily the central rays of the hands and/or feet, with variable expressivity, incomplete penetrance and syndromic forms. It is genetically heterogeneous, including point mutations and structural variants in different loci. Five individuals with SHFM were clinically evaluated in a Tertiary Center in Brazil: four of them presented additional, nonskeletal findings, including one individual with split foot, hand syndactyly, and ectodermal findings. Structural variants and point mutations in genes associated with SHFM were identified in all individuals. Our results highlight genetic heterogeneity observed in this group of skeletal disorders, alongside incomplete penetrance, a challenging task imposed on genetic counseling. Of note, an individual harboring a recurrent heterozygous variant in MAP3K20 presented a phenotype reminiscent of TP63‐related disorders, contrary to the one recently reported in the literature with prominent facial dysmorphisms, expanding the phenotypic spectrum of this newly recognized syndromic form of SHFM.

Leucine ‐ rich repeat containing 45 protein (LRRC45) protein localizes at the proximal end of centrioles and forms a component of the proteinaceous linker between them, with an important role in centrosome cohesion. In addition, a pool of it localizes at the distal appendages of the modified parent centriole that forms the primary cilium and it has essential functions in the establishment of the transition zone and axonemal extension during early ciliogenesis. Here, we describe three individuals from two unrelated families with severe central nervous system anomalies. Exome sequencing identified biallelic variants in LRRC45 in the affected individuals: P1: c.1402‐2A>G; P2 and P3: c.1262G>C (p.Arg421Thr). Investigation of the variant c.1402‐2A>G in patient‐derived skin fibroblasts revealed that it triggers aberrant splicing, leading to an abnormal LRRC45 transcript that lacks exon 14. Consistent with this the mRNA and protein levels of LRRC45 were drastically reduced in P1‐derived fibroblast cells compared to the controls. P1 fibroblasts showed a significant reduction of primary cilia frequency and length. In silico modeling of the missense variant in P2/P3 suggested a destabilizing effect on LRRC45. Given these findings, we propose that the pathogenic loss‐of‐function variants in LRRC45 are associated with a novel spectrum of neurological ciliopathy phenotypes.

Limb abnormalities are the second most frequent birth defects seen in infants, after congenital heart disease. Over the past 150 years, more than 50 classifications for limb malformations based on morphology and osseous anatomy have been presented. The goal of the current study is to investigate the genetic basis of congenital limb abnormalities in the Pakistani population. Eight families, presenting different forms of limb anomalies, including syndactyly, polydactyly, synpolydactyly, and ectrodactyly in an autosomal dominant manner, were genetically and clinically investigated. Whole exome sequencing followed by Sanger sequencing was used to search for the disease‐causing variants. Sequence analysis revealed five novel variants in LMBR1, GJA1, HOXD13, and TP63 and three previously reported variants in GJA1 and HOXD13. This study expanded the mutation spectrum in the identified genes and will also help in improved diagnosis of the limb anomalies in the local population.

Pathogenic variants in the receptor tyrosine kinase TIE2, encoded by TEK, are known to cause vascular malformations (VMs). In this study, we retrospectively reviewed the deidentified data generated through clinical NGS testing in our laboratory and found 88 VM cases with a total of 107 clinically significant TEK variants. Among those, 23 unique variants at the amino acid level were identified, including five novel (p.Cys1040Arg, p.Arg1099PhefsTer12, p.Glu1109Ter, p.Phe1111LeufsTer7, p.Phe1111ValfsTer7) and 18 previously published variants. Missense variants were identified more often in the tyrosine kinase domain, while all nonsense/frameshift variants were clustered in the C‐terminal tail (CTT). In addition, most variants occurred as solitary alterations, whereas certain variants always co‐occurred with a second TEK variant. Five patterns of TEK variants (P1–P5) were identified: (P1) Arg849 + another variant; (P2) Tyr897 + another variant; (P3) Leu914 single variants; (P4) Arg915/918 single variants; and (P5) CTT single /co‐occurring variants. This study provides the most comprehensive view of pathogenic TEK variants in VMs to date.

Osteogenesis imperfecta (OI) is a heterogeneous group of rare, inherited connective tissue disorders. It includes over 20 defined subtypes, each of which is associated with distinct causative genes that are listed in the Online Mendelian Inheritance in Man (OMIM) database. Type XXII OI (OI 22) is caused by a homozygous variant in the coiled‐coil domain containing 134 (CCDC134) gene, which is located on chromosome 22q13. OI, which is associated with CCDC134, is extremely rare with only five cases reported worldwide. All known cases involve the c.2 T > C (p. Met1Thr) homozygous missense variant in the CCDC134 gene. We present the case of a 13‐year‐old Chinese girl with non‐union fracture, short stature and specific radiographic findings, which include scoliosis, pelvic tilt, thin clavicles, ribs, and limbs. Whole exome sequencing revealed a novel, homozygous c.492G > C (p. Leu164=) variation in the CCDC134 gene. RNA sequencing (RNA‐seq) analysis identified this variant as an abnormal splicing variant that causes the deletion of Exon 5, which result in the observed disease phenotype. This case demonstrates the clinical phenotype of OI 22 associated with the c.492G > C (p. Leu164=) novel synonymous variation in the coding region of the CCDC134 gene in a female patient. This is the first reported case of OI 22 in the Chinese population, the sixth reported worldwide and the fourth reported genotype for diseases associated with a CCDC134 variant. It also enriches the global clinical phenotype spectrum of OI 22 patients.

WDFY3 (MIM#617485) defects may manifest neurodevelopmental disorders (NDDs) and opposite effects on brain size based on allelic effect. This case highlights a heterozygous WDFY3 nonsense variant linked to mild‐to‐moderate NDDs, macrocephaly, and unique facial features. Findings emphasize the importance of exome sequencing in NDDs for accurate diagnosis and clinical management. image

To investigate the clinical features and mutational spectrum underlying hypertrophic cardiomyopathy (HCM) in São Miguel Island (Azores, Portugal), we analyzed 37 adult patients (12 sporadic, 25 familial) with positive genetic tests. Seven disease‐causing variants were identified, being two novels, in three sarcomeric genes (MYH7, TNNT2, and MYBPC3) and one non‐sarcomeric gene (ALPK3). The novel variants, classified as likely pathogenic (LP), involved large multi‐exon deletions in MYBPC3 (exons 26–32 and 28–33). These deletions were found in heterozygosity in two young males who remained clinically stable, though early onset may predict a more severe prognosis. Segregation analysis in a consanguineous family revealed two new genotypes: a digenic heterozygous for MYH7:c.1750G>C (p.Gly584Arg; P) and TNNT2:c.842A>T (p.Asn281Ile; LP) variants, and a homozygous for the TNNT2 variant. The 70‐year‐old homozygous patient remained stable and without arrhythmic events, challenging the belief that homozygous variants have a worse prognosis. This study is the first molecular and clinical analysis of HCM in the Azores.

Shprintzen‐Goldberg‐syndrome (SGS) is caused by pathogenic exon 1 variants of SKI. Symptoms include dysmorphic features, skeletal and cardiovascular comorbidities, and cognitive and developmental impairments. We delineated the neurodevelopmental and behavioral features of SGS, as they are not well‐documented. We collected physician‐reported data of people with molecularly confirmed SGS through an international collaboration. We identified and deep‐phenotyped the neurodevelopmental and behavioral features in four patients. Within our cohort, all exhibited developmental delays in motor skills and/or speech, with the average age of first words at 2 years and 6 months and independent walking at 3 years and 5 months. All four had learning disabilities and difficulties regulating emotions and behavior. Intellectual disability, ranging from borderline to moderate, was present in all four participants. Moreover, we reviewed the literature and identified 52 additional people with SGS, and summarized the features across both datasets. Mean age was 23 years (9–48 years). When combining our cohort and reported cases, we found that 80% (45/56) had developmental and/or cognitive impairment, with the remainder having normal intelligence. Our study elucidates the developmental, cognitive, and behavioral features in participants with SGS and contributes to a better understanding of this rare condition.

Rubinstein–Taybi syndrome (RSTS) is a rare autosomal dominant neurodevelopmental disorder linked to haploinsufficiency of CREBBP (RSTS1) and EP300 (RSTS2) genes. Characteristic features often include distinctive facial traits, broad thumbs and toes, short stature, and various degrees of intellectual disability. The clinical presentation of RSTS is notably variable, making it challenging to establish a clear genotype–phenotype correlation, except for specific variants which cause the allelic Menke–Hennekam syndrome. Trio exome analysis, data collection via networking and GeneMatcher platforms, transcript processing analysis, and DNA methylation profiling were performed. We identified two unrelated patients with de novo variants in EP300 (NM_001429.4: c.3671+5G>C; c.3671+5_3671+8delGTAA) predicted to cause in‐frame exon 20 skipping, confirmed in one patient. In silico 3D protein modeling suggested that exon 20 deletion (comprising 27 amino acids) likely alters the structural conformation between the RING_CBP‐p300 and HAT‐KAT11 domains. Clinically, both patients displayed severe RSTS2‐like clinical features, including autism spectrum disorder, speech delay, hearing loss, microcephaly, developmental delay, and intellectual disability, alongside ocular, respiratory, and cardiovascular abnormalities. Additionally, one patient developed early‐onset colorectal cancer. DNA methylation profiling in Subject #1 confirmed RSTS but did not align with the specific episignatures for RSTS1 or RSTS2. We propose that skipping of exon 20 in EP300 is associated with a distinct form of Rubinstein–Taybi syndrome featuring clinical characteristics not fully aligning with RSTS1 or RSTS2. Our findings increase the understanding of RSTS genetic and molecular basis and stress the need for further research to establish definitive genotype–phenotype correlations.

Finite clinical genetics services combined with expanding genomic testing have driven development of mainstreaming models‐of‐care for genomic testing: specifically genetic counselor embedded (GEM) and upskilled‐clinician (UPC) models. To determine feasibility, acceptability, and health economic impact in cancer mainstreaming settings we conducted a scoping review of the literature. A comprehensive PubMed search identified relevant manuscripts, published in English between 2013 and 2023. Of 156 identified articles, 37 proceeded to full review, encompassing five cancer types. In both models‐of‐care, testing uptake was > 90% and referral/testing rates increased 1.2–6.7‐fold. Time from diagnosis to result disclosure decreased 1.5–6‐fold and pathogenic variant detection rates were ≥ 10%. GEM model studies evaluated neither cost‐effectiveness nor physician/patient outcomes. UPC models were economically viable, primarily through reducing genetics‐related appointments. Physicians found the UPC model workload acceptable and reported improvements in knowledge and confidence. Patient distress in the UPC model was low overall and comparable to standard‐of‐care. Patients' acceptance and satisfaction/decisional satisfaction were high, and continuity‐of‐care was appreciated. Mainstreaming cancer genomic testing is feasible and beneficial to patients, physicians, and healthcare systems. More studies are needed to capture GEM model impacts and to compare GEM with UPC models. Further detail of allied health and nursing support for the UPC model is also required.

Loss‐of‐function ABCC8 variants are the commonest cause of congenital hyperinsulinism. On a systematic search of our databases, the p.(Gly111Arg) ABCC8 variant was identified in 26 individuals, of which 23 were from the Indian Agarwal community. Haplotype analysis subsequently confirmed that p.(Gly111Arg) is a founder variant in the Agarwal population. image

Biallelic mutations in BRAT1 result in lethal neonatal rigidity and multifocal seizure syndrome and a milder neurodevelopmental disorder of cerebellar atrophy with or without seizures (NEDCAS, MIM 618056). Combining linkage analysis and whole‐genome sequencing (WGS), we identified a novel deep intronic BRAT1 variant, NC_000007.14 (NM_152743.4):c.128‐1585 T > G, in 3 siblings of a consanguineous Bedouin family exhibiting NEDCAS. In silico analyses followed by molecular studies demonstrated this variant's impact on splice regulatory elements, forming a cryptic exon, resulting in a deleterious frameshift and aberrant transcript. Previously reported pathogenic BRAT1 splice‐site mutations were adjacent to exons, affecting canonical consensus splice sites, and identifiable by whole‐exome sequencing. The deep intronic BRAT1 disease‐causing variant is thus unique and underscores the potential of intronic splice regulatory elements in BRAT1 disease pathogenesis, demonstrating the utility of WGS in identifying noncoding variants in unresolved cases. The affected individuals (deep into their twenties) are among the longest‐surviving patients described to date—delineating the NEDCAS phenotype at these ages. Although sharing homozygosity of the same variant, they show varying penetrance of nystagmus and extreme variability in the extent of ataxia and age of onset of developmental delay. Notably, we summarize all documented BRAT1 splice variants reported to date and their phenotypic associations.

Mobile elements (ME) can transpose by copy‐and‐paste mechanisms. A heterozygous insertion in APOB exon 3 coding sequence was suspected in a patient with hypobetalipoproteinemia (HBL), by gel electrophoresis of the PCR products. An insertion of a 85 bp fragment flanked by a polyA stretch and a target replication site duplication was identified as a ME insertion (MEI) from the AluYa5 subfamily, NM_000384.3(APOB):c.135_136ins(160). Then, the DNA was reanalyzed using our NGS custom panel. Routine analysis did not reveal any causative variant, but manual inspection of the alignments and MELT enabled us to detect this MEI from NGS data. A functional study revealed that this MEI introduces a stop codon p.(Phe46Alafs*2) and additionally leads to p.(Lys41Serfs*2) due to an exon skipping. This is the first report of a MEI into APOB, as a cause of HBL. Furthermore, our study highlights the value of including MEI‐callers in routine pipelines to improve primary dyslipidemia diagnosis.

Silver‐Russell syndrome (SRS) is an imprinting disorder mainly characterized by pre‐ and postnatal growth restriction. Most SRS cases are due to 11p15.5 loss of methylation (11p15.5 LOM) or maternal uniparental disomy of chromosome 7 [UPD(7)mat], but several patients remain molecularly undiagnosed. This study describes the molecular investigation of children with a clinical diagnosis or suspicion of SRS at a tertiary center specialized in growth disorders. Thirty‐nine patients were evaluated with multiplex ligation‐dependent probe amplification, chromosomal microarray and/or massively parallel sequencing. The most common result was 11p15.5 LOM (n = 17; 43.5%), followed by UPD(7)mat (n = 2; 5.1%). Additionally, we found maternal duplications of the imprinting centers in 11p15.5 (n = 2; 5.1%), and genetic defects in SRS‐causing genes (IGF2 and HMGA2) (n = 3; 7.7%; two mutations and one deletion). Alternative molecular diagnoses included UPD(14)mat (n = 1; 2,6%), UPD(20)mat (n = 1;2,6%), copy number variants (n = 2; 5.1%), and mutations in genes associated with other growth disorders (n = 4; 10.3%), leading to diagnoses of Temple syndrome, Mulchandani‐Bhoj‐Conlin syndrome, IGF‐1 resistance (IGF1R), Bloom syndrome (BLM), Gabriele‐De Vries syndrome (YY1), Intellectual developmental disorder autosomal dominant 50 with behavioral abnormalities (NAA15), and Intellectual developmental disorder 64 (ZNF292). These findings underscore the importance of establishing the molecular diagnosis of SRS and its differential diagnoses to guide appropriate management and genetic counseling.

Mulibrey nanism (MUL) is a monogenic growth disorder caused by mutations in TRIM37, with pre‐and postnatal growth failure, typical craniofacial features, perimyocardial heart disease, infertility and predisposition to tumors. Clinically, patients are gracile with relative macrocephaly, thin extremities, and narrow shoulders, but the full spectrum of skeletal features remains unknown. We conducted a cross‐sectional study in order to further clarify the skeletal phenotype. We assessed radiographs of the long bones and spine in 33 MUL patients, aged 4.5–48 years (14 females and 19 males, median age 16.7 years) for skeletal features. Hospital records were reviewed for clinical characteristics and fractures. Results confirmed significant skeletal abnormalities related to MUL. Skeletal changes were present in all patients; long bones were slender and bowed with broad metaphyses and narrow diaphysis, the cortices were thick, and medullary cavities were narrow. The vertebral bodies were tall. Fibrous dysplasia was found in 19/33 patients (58%); changes were monostotic in 58% and polyostotic in 42%. Altogether 17/33 patients (52%) had a history of fractures. This study confirms that in addition to short stature, patients with MUL have a specific skeletal dysplasia. Our findings suggest an important role for TRIM37 in cellular functions governing skeletal modelling and remodelling.

Moyamoya angiopathy is a cerebral vasculopathy causing progressive stenosis of the internal carotid arteries and the compensatory development of collateral blood vessels, leading to brain ischemia and an increased risk of cerebral haemorrhage. Although multiple non‐genetic causes have been associated with moyamoya syndrome, it can also be associated with rare genetic syndromes. Moyamoya Disease 4, characterised by a short stature, hypergonadotropic hypogonadism and facial dysmorphism (MYMY4, OMIM #300845), also referred to as BRCC3‐associated moyamoya syndrome, has so far been described in 11 individuals. Here, we describe a 23‐year‐old male presenting with moyamoya syndrome, global developmental delay and intellectual disability, epilepsy, short stature and dysmorphic features, who after > 17 years of uninformative diagnostics was diagnosed with BRCC3‐associated moyamoya syndrome after clinical RNA‐seq. Transcriptome analysis showed reduced expression of the likely disease‐causing gene BRCC3 in patient‐derived fibroblasts, which was subsequently found to be caused by a ~ 26 kb Xq28 deletion. We furthermore review all reported cases of BRCC3‐associated moyamoya syndrome, further delineating this clinical entity.

This study aims to investigate the clinical, biochemical, and genetic characteristics of Fanconi‐Bickel syndrome (FBS) in a cohort of 20 individuals from Palestine and to identify novel pathogenic variants. A retrospective analysis was conducted on medical records from Al‐Makassed Hospital's pediatric department spanning 2015 to 2023. Individuals diagnosed with FBS via molecular genetic testing were included in the study. Among the 20 genetically confirmed FBS patients, hepatomegaly was prevalent in 95%, whereas 70% exhibited both developmental delay and hypophosphatemic rickets, and 68.4% experienced growth retardation. Hypertriglyceridemia (HTG) was universal. Elevated liver enzymes and alkaline phosphatase were common, along with hypophosphatemia (95%) and urinary abnormalities. Genetic analysis revealed five distinct SLC2A2 pathogenic variants, including three previously unreported variants: p.Gln23Arg (c.68A > G), p.Thr353Arg (c.1058_1059delinsGG), and an exon 7 deletion. This study presents the largest single‐center cohort of FBS patients, expanding our understanding of the disorder's phenotypic and genotypic spectrum. Despite FBS generally carrying a favorable prognosis, timely diagnosis remains crucial to prevent severe complications.

We identified an AMOTL1 variant in a patient that adds evidence supporting the clinical and molecular overlap between AMOTL1‐related disorders and other syndromes affecting craniofacial, cardiac, and hepatic development. As more cases are identified, we propose naming this entity as AMOTL1‐associated multiple congenital anomalies or craniofaciocardiohepatic syndrome (CFCHS). image

A novel compound heterozygous genotype of the WDR73 gene associated with a psychomotor retardation syndrome without cerebellar atrophy and other CNS structural abnormalities. image

Identification of the first pathogenic branch point variant in the SMS gene in a large French non‐consanguineous family with a phenotype retrospectively consistent with Snyder–Robinson syndrome. RT‐PCR analysis followed by RNA‐sequencing demonstrated that this variant, lead to the synthesis of a predominant aberrant transcript with complete intron 6 retention. image