Rett syndrome (RTT) is a severe neurodevelopmental disorder, with MECP2 mutations accounting for 90–95% of classic and 50–70% of atypical cases. However, many clinically diagnosed RTT patients remain without molecular diagnoses. While point mutations and large rearrangements in MECP2 are well studied, the role of small-intermediate structural variants (SVs) remains mostly elusive. Using standard short-read whole genome sequencing, we identified novel de novo SVs in three out of three previously unresolved RTT cases: a complex SV with two deletions ( ~ 5Kbp and ~60Kbp) and a ~105Kbp inversion; a ~200Kbp translocation; and a ~3Kbp deletion. These findings suggest that such elusive SVs might be a common cause for “MECP2-negative” RTT. Incorporating SV detection into routine genetic testing through bioinformatic analysis of short-read sequencing or manual review using IGV could improve diagnostic rates and expand our understanding of RTT and similar disorders.

Genomic sequences residing within introns of few genes have been shown to act as enhancers affecting expression of neighboring genes. We studied an autosomal recessive phenotypic continuum of microphthalmia, anophthalmia and ocular coloboma, with no apparent coding-region disease-causing mutation. Homozygosity mapping of several affected Jewish Iranian families, combined with whole genome sequence analysis, identified a 0.5 Mb disease-associated chromosome 2q35 locus (maximal LOD score 6.8) harboring an intronic founder variant in NHEJ1, not predicted to affect NHEJ1. The human NHEJ1 intronic variant lies within a known specifically limb-development enhancer of a neighboring gene, Indian hedgehog (Ihh), known to be involved in eye development in mice and chickens. Through mouse and chicken molecular development studies, we demonstrated that this variant is within an Ihh enhancer that drives gene expression in the developing eye and that the identified variant affects this eye-specific enhancer activity. We thus delineate an Ihh enhancer active in mammalian eye development whose variant causes human microphthalmia, anophthalmia and ocular coloboma. The findings highlight disease causation by an intronic variant affecting the expression of a neighboring gene, delineating molecular pathways of eye development.

Carbonic anhydrase VA (CA5A) deficiency (OMIM 615751) is an ultra-rare inborn error of metabolism, presenting in newborns, infants, and young children with a pentad of encephalopathy, hyperammonemia, lactic acidosis, ketonuria, and hypoglycemia. We present two cases: a case of a healthy Bedouin infant admitted with hyperammonemic encephalopathy that required urgent hemodialysis, and her younger sibling, who presented with a milder episode. Molecular analysis confirmed the diagnosis of CA5A deficiency due to a homozygous missense variant in the CA5A gene. Both patients had a favorable outcome with continued normal development. These were the first identified cases of CA5A deficiency in the Bedouin population, emphasizing the importance of a high index of suspicion, early genetic consultation and diagnosis, and prompt treatment at the earliest possible stage of a hyperammonemic crisis.

Intestinal malrotation (IM) is a relatively common congenital anomaly of the gastrointestinal tract resulting from abnormal rotation during embryonic development. While some cases of IM are part of syndromic manifestations, most are isolated, with their genetic basis remaining largely unknown. We present a familial case of apparently autosomal recessive isolated IM in a consanguineous kindred of Arab-Bedouin descent. Nine individuals from two nuclear families were recruited. Homozygosity mapping and logarithm of odds (LOD) score calculations were performed using single nucleotide polymorphism (SNP) array data. Whole-exome and whole-genome sequencing data were analyzed to identify candidate variants. Various analysis and interpretation tools were applied to evaluate and describe potential disease-associated variants. Homozygosity mapping identified a 2 Mb candidate locus on chromosome 21q22.3. Multipoint linkage analysis identified an overlapping locus on chromosome 21 (maximal LOD score: 3.168). A missense variant in PCNT (Gln1951Pro), along with several other segregating candidates, was evaluated. Our findings demonstrate a novel candidate locus at chromosome 21q22.3 associated with isolated IM, with PCNT emerging as a potential candidate gene. Further studies involving additional affected families and functional validation are required to establish the contribution of this locus and the identified variant to the pathogenesis of isolated IM.

Background/Objectives: Contiguous Xq26.2 deletions involving FRMD7 and IGSF1 are rare and incompletely characterized. FRMD7 loss causes X-linked idiopathic infantile nystagmus (IIN), whereas IGSF1 loss causes central hypothyroidism and other pituitary-related abnormalities. We aimed to define the clinical and molecular spectrum of an Xq26.2 contiguous gene deletion in a large Bedouin kindred with infantile nystagmus. Methods: We clinically evaluated ten family members (3 males and 7 females); genomic analyses included chromosomal microarrays, whole-exome and whole-genome sequencing, breakpoint PCR, and Sanger sequencing. Results: We identified a novel 1.44-Mb Xq26.1-q26.2 deletion, NC_000023.11:g.130756102_132199443del (GRCh38), encompassing complete loss of FRMD7, IGSF1, ARHGAP36, OR13H1, and STK26 and partial deletion of the 5′ end of ENOX2. The deletion was molecularly confirmed in six family members. The kindred exhibited a broad phenotypic spectrum, from an asymptomatic confirmed female carrier to isolated nystagmus and combined ocular–endocrine manifestations. Nystagmus was highly penetrant, whereas endocrine abnormalities were less frequent and variable. Hypoprolactinemia occurred in one confirmed female carrier, and a confirmed hemizygous boy had low-normal free T4 without overt central hypothyroidism. The only relative with overt central hypothyroidism was not genotyped; therefore, co-segregation could not be established. Conclusions: These findings further delineate the clinical spectrum of Xq26.2 deletions, highlight marked intrafamilial variability, and support structural variant analysis in unexplained IIN and/or endocrine abnormalities. Longitudinal endocrine assessment of individuals with Xq26.2 deletions and at-risk relatives in affected families may enable early detection and treatment of hypothyroidism.