Heterozygous loss of SRRM1 may be associated with neurodevelopmental phenotypes and anomalies in cell growth and neurite morphology.

Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing

Whole-exome sequencing (WES) represents a significant breakthrough in clinical genetics, and identifies a genetic etiology in up to 30% of cases of intellectual disability (ID). Using WES, we identified seven unrelated patients with a similar clinical phenotype of severe intellectual disability or neurodevelopmental delay who were all heterozygous for de novo truncating variants in the AT-hook DNA-binding motif–containing protein 1 (AHDC1). The patients were all minimally verbal or nonverbal and had variable neurological problems including spastic quadriplegia, ataxia, nystagmus, seizures, autism, and self-injurious behaviors. Additional common clinical features include dysmorphic facial features and feeding difficulties associated with failure to thrive and short stature. The AHDC1 gene has only one coding exon, and the protein contains conserved regions including AT-hook motifs and a PDZ binding domain. We postulate that all seven variants detected in these patients result in a truncated protein missing critical functional domains, disrupting interactions with other proteins important for brain development. Our study demonstrates that truncating variants in AHDC1 are associated with ID and are primarily associated with a neurodevelopmental phenotype.

Introduction: Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2 is a very rare genetic disorder caused by biallelic pathogenic variants in the SCUBE3 gene and has been reported in approximately 20 patients to date. SCUBE3 protein exhibits significant expression in various tissues, including primary osteoblasts, long bones, and the cartilage of the axial skeleton throughout development, while also playing a regulatory role in the FGF, Hedgehog, and TGF-β signaling pathways. Case Presentation: We report a 13-year-old female patient from a consanguineous Turkish family with a novel homozygous missense variant, c.908G>C (p.Cys303Ser) in the SCUBE3 gene identified, through exome sequencing. The patient exhibited prenatal growth retardation, short stature, microcephaly, distinctive facial traits, such as long face, high arched eyebrows, epicanthus, blepharoptosis, hypotelorism, high nasal bridge, micrognathia, and large ears, dental anomalies, and skeletal abnormalities, including scoliosis, eleven pairs of ribs, mild radial bowing, irregular endplates in the lower thoracic vertabrae, and narrow iliac wings. Conclusion: Protein modeling using AlphaFold3 revealed disruption of a critical disulfide bridge within the seventh epidermal growth factor-like repeat, likely affecting protein stability. In this study, we aimed to further characterize the clinical, radiological, and molecular features of this disorder with protein modeling.

Although copy number changes of 5q31 have been rarely reported, deletions have been associated with some common characteristics, such as short stature, failure to thrive, developmental delay (DD)/intellectual disability (ID), club feet, dislocated hips, and dysmorphic features. We report on three individuals with deletions and two individuals with duplications at 5q31, ranging from 3.6 Mb to 8.1 Mb and 830 kb to 3.4 Mb in size, respectively. All five copy number changes are apparently de novo and involve several genes that are important in developmental pathways, including PITX1, SMAD5, and WNT8A. The individuals with deletions have characteristic features including DD, short stature, club feet, cleft or high palate, dysmorphic features, and skeletal anomalies. Haploinsufficiency of PITX1, a transcription factor important for limb development, is likely the cause for the club feet, skeletal anomalies, and cleft/high palate, while additional genes, including SMAD5 and WNT8A, may also contribute to additional phenotypic features. Two patients with deletions also presented with corneal anomalies. To identify a causative gene for the corneal anomalies, we sequenced candidate genes in a family with apparent autosomal dominant keratoconus with suggestive linkage to 5q31, but no mutations in candidate genes were found. The duplications are smaller than the deletions, and the patients with duplications have nonspecific features. Although development is likely affected by increased dosage of the genes in the region, the developmental disruption appears less severe than that seen with deletion.

ObjectiveMutations in the KMT2B gene have been identified in patients previously diagnosed with idiopathic dystonia. Literature on KMT2B-related dystonia is sparse in the Indian and Asian populations.MethodsWe report seven patients with KMT2B-related dystonia studied prospectively from May 2021 to September 2022. Patients underwent deep clinical phenotyping and genetic testing by whole-exome sequencing (WES). A systematic literature search was performed to identify the spectrum of previously published KMT2B-related disorders in the Asian subcontinent.ResultsThe seven identified patients with KMT2B-related dystonia had a median age at onset of four years. The majority experienced onset in the lower limbs (n = 5, 71.4%), with generalization at a median duration of 2 years. All patients except one had complex phenotypes manifesting as facial dysmorphism (n = 4), microcephaly (n = 3), developmental delay (n = 3), and short stature (n = 1). Magnetic resonance imaging (MRI) abnormalities were present in four cases. WES revealed novel mutations in the KMT2B gene in all patients except one. Compared to the largest cohort of patients with KMT2B-related disorders, the Asian cohort, comprising 42 patients, had a lower prevalence of female patients, facial dysmorphism, microcephaly, intellectual disability, and MRI abnormalities. Protein-truncating variants were more prevalent than missense variants. While microcephaly and short stature were more common in patients with missense mutations, facial dysmorphism was more common in patients with truncating variants. Deep brain stimulation, performed in 17 patients, had satisfactory outcomes.ConclusionThis is the largest series of patients with KMT2B-related disorders from India, further expanding the clinico-genotypic spectrum. The extended Asian cohort emphasizes the unique attributes of this part of the world.

Genetic Complementation Studies Reveal That Many Disease-Associated DDX41 Variants Do Not Cause Loss of Protein Function

We report a 23 year old female with biallelic truncating variants in the ITCH (Itchy E3 Ubiquitin protein ligase, mouse homolog of; OMIM60649) gene associated with marked short stature, severe early onset chronic lung disease resembling asthma, dysmorphic facial features, and symmetrical camptodactyly of the fingers but normal intellect. The condition has only been reported once previously (Lohr et al., American Journal of Human Genetics, 2010, 86, 447-453) in 10 children from an Old Order Amish family found to have a homozygous frameshift truncating variant in association with failure to thrive, chronic lung disease, motor and cognitive delay, and variable autoimmune diseases including autoimmune hepatitis, enteropathy, hypothyroidism, and diabetes. The condition is listed in OMIM as Autoimmune disease, Multisystem with Facial Dysmorphism (OMIM613385). The clinical course as well as the dysmorphic facial and limb features overlap closely with our patient. We believe the triad of marked syndromic short stature, chronic lung disease, and dysmorphism (with or without cognitive impairment and wider autoimmune involvement) is distinctive.

De Novo and Inherited Pathogenic Variants in KDM3B Cause Intellectual Disability, Short Stature, and Facial Dysmorphism

Application of Multicolor Banding for Identification of Complex Chromosome 18 Rearrangements

Monoallelic BMP2 Variants Predicted to Result in Haploinsufficiency Cause Craniofacial, Skeletal, and Cardiac Features Overlapping Those of 20p12 Deletions

Background: Coffin–Lowry syndrome (CLS) [OMIM#303600] is a rare X-linked dominant syndrome. CLS is caused by highly heterogeneous loss-of-function mutations in the RPS6KA3 gene (OMIM*300,075). CLS is characterized by intellectual disability (ID), short stature, tapered fingers, characteristic facial features, and progressive skeletal changes. Distal 22q11.2 microdeletion syndrome (OMIM#611867) is an autosomal dominant and recurrent genomic disorder. It mainly includes three types [distal type I (D–E/F), type II (E–F), and type III (F–G)] and exhibits variable clinical phenotypes (mild, moderate, or even normal): preterm birth, pre- and/or postnatal growth restriction, development delay, ID, behavioral problems, cardiovascular defects, skeletal anomalies, and dysmorphic facial features. We investigated the genetic etiology of a Chinese pedigree with ID, short stature, digit abnormalities, facial dysmorphism, and menstrual disorder. A heterozygous RPS6KA3 gene variant c.898C>T (p.R300X) was identified in this familial case. Two female CLS patients with distal 22q11.2 microdeletion presented with more severe clinical phenotypes. We provided clinical characteristics of these Chinese female CLS patients. Case presentation: We described a Chinese family with three affected females (the mother, the elder sister, and the proband). The mother and the elder sister had more severe clinical phenotypes (moderate facial dysmorphism, more severe cognitive impairment, and shorter stature). The common characteristic phenotypes are ID, short stature, facial dysmorphism, irregular menstruation, and cardiovascular disorders. Peripheral blood samples were collected from the pedigree. Whole-exome sequencing (WES) identified a heterozygous nonsense RPS6KA3 gene variant c.898C>T (p.R300X). It was verified by Sanger sequencing. Copy number variation sequencing (CNV-seq) showed that both the mother and the elder sister carried a CNVseq [hg19] del (22) (q11.22-q11.23) (22997582–23637176)×0.5. RNA from peripheral blood samples was used for measuring the relative quantification of mRNA (expressed by exon 14 of RPS6KA3). The levels of mRNA relative expressions were significantly lower in the mother’s and the elder sister’s blood samples. The levels of mRNA relative expressions were significantly higher in the proband’s blood sample. X-chromosome inactivation (XCI) studies demonstrated that the proband showed extremely skewed XCI, and the XCI pattern of the elder sister was random. Conclusion: Herein, we reported three Chinese female patients with a heterozygous nonsense RPS6KA3 gene variant c.898C>T. Further genetic studies were performed. To our knowledge, Chinese patients with this variant have not been previously reported in the literature. The three female patients presented with variable degrees of severity. The clinical characteristics of these Chinese female CLS patients could expand the phenotypic spectrum of CLS. We helped physicians to understand the genotype–phenotype correlation further.

LEOPARD syndrome is a complex disorder characterized by multiple dysmorphogenetic features. Both syndromes LEOPARD and Noonan are caused by different mutations in the same gene (PTPN11). Authors emphasize diagnosis peculiarities in two related cases with facial dysmorphism. Index case is represented by a 10 year-old boy admitted for evaluation because of cephalofacial dysmorphism associated with mental disabilities. Family history: non-consanguineous parents; the father’s case and his sister with face dysmorphism. Clinical exam: short stature, impaired nutritional status, axillary freckles, widespread café-au-lait spots, face dysmorphism, webbed neck, skeletal anomalies and mental retardation. Blood investigations and cardiac ultrasonography: no anomalies. Differential diagnosis includes Noonan syndrome, Greig syndrome, type 1 neurofibromatosis, Albright syndrome. Regarding patient genetic evaluation: normal karyotype; DNA sequencing revealed mutation in PTPN11 gene suggestive for LEOPARD syndrome. Authors also found same mutation for probant’s father. Conclusions. Authors described two cases with dysmorphic skull, skeletal anomalies, skin pigmentation, mental disabilities and short stature, justifying further genetic evaluation that revealed a very rare disorder.

BackgroundPathogenic germline variants in subunits of succinate dehydrogenase (SDHB, SDHC and SDHD) are broadly associated with disease subtypes of phaeochromocytoma–paraganglioma (PPGL) syndrome. Our objective was to investigate the role of...

Analysis of Genomic Predispositions to Sporadic Myeloid Neoplasms Mediated By DDX41 in Japan

BACKGROUND AND OBJECTIVE:Data on stature in Saudi children and adolescents are limited. The objective of this report was to establish the national prevalence of short stature in Saudi children and adolescents.DESIGN AND SETTING:Community-based, cross-sectional study conducted over 2 years (2004, 2005)PATIENTS AND METHODS:The national data set of the Saudi reference was used to calculate the stature for age for children and adolescents 5 to 18 years of age. Using the 2007 World Health Organization (WHO) reference, the prevalence of moderate and severe short stature was defined as the proportion of children whose standard deviation score for stature for age was less than -2 and -3, respectively. In addition, the 2000 Center for Disease Control (CDC) and the older 1978 National Center for Health Statistics (NCHS)/WHO references were used for comparison.RESULTS:Using the 2007 WHO reference, sample size in the Saudi reference was 19 372 healthy children and adolescents 5 to 17 years of age, with 50.8% being boys. The overall prevalence of moderate and severe short stature in boys was 11.3% and 1.8%, respectively; and in girls, 10.5% and 1.2%, respectively. The prevalence of moderate short stature was 12.1%, 11% and 11.3% in boys and 10.9%, 11.3% and 10.5% in girls when the 1978 WHO, the 2000 CDC and the 2007 WHO references were used, respectively.CONCLUSIONS:The national prevalence of short stature in Saudi children and adolescents is intermediate compared with the international level. Improvement in the socioeconomic and health status of children and adolescents should lead to a reduction in the prevalence of short stature.