A novel homozygous mutation in <Emphasis Type="Italic">SZT2</Emphasis> gene in Saudi family with developmental delay,macrocephaly and epilepsy

Epileptic encephalopathies are genetically heterogeneous disorders which leads to epilepsy and cause neurological disorders. Seizure threshold 2 (SZT2) gene located on chromosome 1p34.2 encodes protein mainly expressed predominantly in the parietal and frontal cortex and dorsal root ganglia in the brain. Previous studies in mice showed that mutation in this gene can confers low seizure threshold, enhance epileptogenesis and in human may leads to facial dysmorphism, intellectual disability, seizure and macrocephaly. Objective of this study was to find out novel gene or novel mutation related to the gene phenotype. We have identified a large consanguineous Saudi family segregating developmental delay, intellectual disability, epilepsy, high forehead and macrocephaly. Exome sequencing was performed in affected siblings of the family to study the novel mutation. Whole exome sequencing data analysis, confirmed by subsequent Sanger sequencing validation study. Our results showed a novel homozygous mutation (c.9368G>A) in a substitution of a conserved glycine residue into a glutamic acid in the exon 67 of SZT2 gene. The mutation was ruled out in 100 unrelated healthy controls. The missense variant has not yet been reported as pathogenic in literature or variant databases. In conclusion, the here detected homozygous SZT2 variant might be the causative mutation that further explain epilepsy and developmental delay in this Saudi family.     

Exome sequencing discloses <Emphasis Type="Italic">KALRN</Emphasis> homozygous variant as likely cause of intellectual disability and short stature in a consanguineous pedigree

Background

The recent availability of whole-exome sequencing has opened new possibilities for the evaluation of individuals with genetically undiagnosed intellectual disability.

Results

We report two affected siblings, offspring of first-cousin parents, with intellectual disability, hypotonia, short stature, growth hormone deficiency, and delayed bone age. All members of the nuclear family were genotyped, and exome sequencing was performed in one of the affected individuals. We used an in-house algorithm (CATCH v1.1) that combines homozygosity mapping with exome sequencing results and provides a list of candidate variants. One identified novel homozygous missense variant in KALRN (NM_003947.4:c.3644C>A: p.(Thr1215Lys)) was predicted to be pathogenic by all pathogenicity prediction software used (SIFT, PolyPhen, Mutation Taster). KALRN encodes the protein kalirin, which is a GTP-exchange factor protein with a reported role in cytoskeletal remodeling and dendritic spine formation in neurons. It is known that mice with ablation of Kalrn exhibit age-dependent functional deficits and behavioral phenotypes.

Conclusion

Exome sequencing provided initial evidence linking KALRN to monogenic intellectual disability in man, and we propose that KALRN is the causative gene for the autosomal recessive phenotype in this family.

     

Role of <Emphasis Type="Italic">PUF60</Emphasis> gene in Verheij syndrome: a case report of the first Chinese Han patient with a de novo pathogenic variant and review of the literature

Background

Verheij syndrome is a rare microdeletion syndrome of chromosome 8q24.3 that harbors PUF60, SCRIB, and NRBP2 genes. Subsequently, loss of function mutations in PUF60 have been found in children with clinical features significantly overlapping with Verheij.

Case presentation

Here we present the first Chinese Han patient with a de novo nonsense variant (c.1357C?>?T, p.Gln453*) in PUF60 by clinical whole exome sequencing. The 5-year-old boy presents with dysmorphic facial features, intellectual disability, and growth retardation but without apparent cardiac, renal, ocular, and spinal anomalies.

Conclusions

Our finding contributes to the understanding of the genotype and phenotype in PUF60 related disorder.

     

Transmission of double <Emphasis Type="Italic">FMR1</Emphasis> allelic premutations in a family

The fragile X mental retardation 1 (FMR1) gene is the only gene known responsible for fragile X related disorders, including fragile X syndrome (FXS), fragile X-associated primary ovarian insufficiency, and fragile X-associated tremor/ataxia. Although FMR1 premutation carriers are common, double mutations of the FMR1 gene is very rare. To our knowledge, only twelve such reports including twenty-three cases from fourteen families have been documented. We report here another family with a FXS family history in which the proband’s maternal grandmother had compound FMR1 gene premutations and we review twelve published papers associated with double allelic mutations. Our study and literature review indicated that compound premutations may have influences regarding the early onset of fragile X-associated primary ovarian insufficiency and severity of psychiatric issues, and less likely aggravate the cognitive deficits compared with one allele mutant patients. Further detailed studies of similar cases are needed to clarify the profile of double FMR1 premutaions.     

A prospective study of dietary and supplemental zinc intake and risk of type 2 diabetes depending on genetic variation in <Emphasis Type="Italic">SLC30A8</Emphasis>

Background

The solute carrier family 30 member 8 gene (SLC30A8) encodes a zinc transporter in the pancreatic beta cells and the major C-allele of a missense variant (rs13266634; C/T; R325W) in SLC30A8 is associated with an increased risk of type 2 diabetes (T2D). We hypothesized that the association between zinc intake and T2D may be modified by the SLC30A8 genotype.

Results

We carried out a prospective study among subjects with no history cardio-metabolic diseases in the Malmö Diet and Cancer Study cohort (N = 26,132, 38% men; 86% with genotype data). Zinc intake was assessed using a diet questionnaire and food record. During a median follow-up of 19 years, 3676 T2D cases occurred. A BMI-stratified Cox proportional hazards regression model with attained age as the time scale was used to model the association between total and dietary zinc intake, zinc supplement use, zinc to iron ratio, and risk of T2D adjusting for putative confounding factors.The median total zinc intake was 11.4 mg/day, and the median dietary zinc intake was 10.7 mg/day. Zinc supplement users (17%) had a median total zinc intake of 22.4 mg/day. Dietary zinc intake was associated with increased risk of T2D (P _trend < 0.0001). In contrast, we observed a lower risk of T2D among zinc supplement users (HR = 0.79, 95% CI 0.70–0.89). The SLC30A8 CC genotype was associated with a higher risk of T2D (HR = 1.16, 95% CI 1.07–1.24), and the effect was stronger among subjects with higher BMI (P _interaction = 0.007). We observed no significant modification of the zinc-T2D associations by SLC30A8 genotype. However, a three-way interaction between SLC30A8 genotype, BMI, and zinc to iron ratio was observed (P _interaction = 0.007). A high zinc to iron ratio conferred a protective associated effect on T2D risk among obese subjects, and the effect was significantly more pronounced among T-allele carriers.

Conclusions

Zinc supplementation and a high zinc to iron intake ratio may lower the risk of T2D, but these associations could be modified by obesity and the SLC30A8 genotype. The findings implicate that when considering zinc supplementation for T2D prevention, both obesity status and SLC30A8 genotype may need to be accounted for.

     

Estimation of association of <Emphasis Type="Italic">CNTN6</Emphasis> copy number variation with idiopathic intellectual disability

Analysis of the prevalence of copy number variations of the CNTN6 gene, recently selected as a new candidate gene for intellectual disorders, was performed. Real-time PCR did not detect any change in the number of CNTN6 gene copies in a group of 200 patients with impaired intellectual development. However, taking into account our data from the previous aCGH analysis and published data, the overall frequency of microdeletions and microduplications of CNTN6 was estimated as 1: 265 (0.4%). The common phenotypic features of 40 patients with microdeletions and microduplications of CNTN6 appeared to be the autism spectrum disorders, developmental delay, intellectual disability, seizures, cognitive impairment, cardiological defects, and behavioral problems.     

Homozygous <Emphasis Type="Italic">KCNMA1</Emphasis> mutation as a cause of cerebellar atrophy,developmental delay and seizures

Dominant gain-of-function mutations of the KCNMA1 gene, encoding the pore-forming subunit of the large conductance voltage- and Ca²⁺-activated K+ channel, have been described in a few patients with the syndrome of epilepsy, paroxysmal dyskinesias and developmental delay. In this report, we describe the loss-of-function phenotype of this newly described disease gene. In two siblings from a consanguineous family with epilepsy, developmental delay and severe cerebellar atrophy, combined exome/autozygome analysis identified a homozygous frameshift duplication in KCNMA1 (c.2026dupT; p. (Tyr676 Leufs^*7)) in both children. Our report defines a novel autosomal recessive KCNMA1-related epileptic phenotype that encompasses cerebellar atrophy without paroxysmal dyskinesia, and highlights the sensitivity of the developing brain to both increased and decreased activity of the KCNMA1-encoded channels.     

Expression pattern of <Emphasis Type="Italic">cdkl5</Emphasis> during zebrafish early development: implications for use as model for atypical Rett syndrome

Atypical Rett syndrome is a child neurodevelopmental disorder induced by mutations in CDKL5 gene and characterized by a progressive regression in development with loss of purposeful use of the hands, slowed brain and head growth, problems with walking, seizures, and intellectual disability. At the moment, there is no cure for this pathology and little information is available concerning animal models capable of mimicking its phenotypes, thus the development of additional animal models should be of interest to gain more knowledge about the disease. Zebrafish has been used successfully as model organism for many human genetic diseases; however, no information is available concerning the spatial and temporal expression of cdkl5 orthologous in this organism. In the present study, we identified the developmental expression patterns of cdkl5 in zebrafish by quantitative PCR and whole-mount in situ hybridization. cdkl5 is expressed maternally at low levels during the first 24 h of development. After that the expression of the gene increases significantly and it starts to be expressed mainly in the nervous system and in several brain structures, such as telencephalon, mesencephalon and diencephalon. The expression patterns of cdkl5 in zebrafish is in accordance with the tissues known to be affected in humans and associated to symptoms and deficits observed in Rett syndrome patients thus providing the first evidence that zebrafish could be an alternative model to study the molecular pathways of this disease as well as to test possible therapeutic approaches capable of rescuing the phenotype.     

A novel contiguous deletion involving $$\varvec{NDP},$$ MAOB and EFHC2 gene in a patient with familial Norrie disease: bilateral blindness and leucocoria without other deficits

Contiguous microdeletions of the Norrie disease pseudoglioma (NDP) region on chromosome Xp11.3 have been widely confirmed as contributing to the typical clinical features of Norrie disease (ND). However, the precise relation between genotype and phenotype could vary. The contiguous deletion of NDP and its neighbouring genes, MAOA/B and EFHC2, reportedly leads to syndromic clinical features such as microcephaly, intellectual disability, and epilepsy. Here we report a novel contiguous microdeletion of the NDP region containing the MAOB and EFHC2 genes, which causes eye defects but no cognitive disability. We detected a deletion of 494.6 kb at Xp11.3 in both the proband and carrier mother. This deletion was then used as the molecular marker in prenatal diagnosis for two subsequent pregnancies. The deletion was absent in one of the foetuses, who remain without any abnormalities at 2 years of age. The proband shows the typical ocular clinical features of ND including bilateral retinal detachment, microphthalmia, atrophic irides, corneal opacification, and cataracts, but no symptoms of microcephaly, intellectual disability, and epilepsy. This familial study demonstrates that a deficiency in one of two MAO genes may not lead to psychomotor delay, and deletion of EFHC2 may not cause epilepsy. Our observations provide new information on the genotype–phenotype relations of \({\textit{MAOA/B}}\) and EFHC2 genes involved in the contiguous deletions of ND.     

Manifestation and inheritance of <Emphasis Type="Italic">tpd1</Emphasis> phenotype in the tobacco insertion mutant with extended flowering period

The tpd1 (from tobacco pollen development 1) insertion mutant of tobacco (Nicotiana tabacum L., cv. Samsun) with extended flowering period was investigated in detail in the course of plant development, and the inheritance of the mutant phenotype was established. The wild-type and mutant plants did not differ in basic developmental indices until the floral transition; later they diverged in the characteristics of male reproductive organs, particularly in anther development and pollen maturation. The pollen of tpd1 plants was underdeveloped and sterile, resulting in a characteristic seedless phenotype with extended flowering period. When mutant flowers were pollinated with wild-type pollen, the tpd1 phenotype was maintained in at least two seed generations, indicating that this trait was heritable. The tpd1 phenotype was closely linked with kanamycin resistance; it follows that the developmental anomalies observed in our experiments immediately depended on the vector DNA insert. Our data presume that tpd1 is a rare dominant monogenic mutation with a narrowly directed physiological manifestation. A model is presented to describe the effect of TPD1. The tpd1 mutant would help identify and clone the new TPD1 gene crucial for viable pollen development.     

Genetic complementation analysis of rice sucrose transporter genes in Arabidopsis <Emphasis Type="Italic">SUC2</Emphasis> mutant <Emphasis Type="Italic">atsuc2</Emphasis>

Sucrose transporters (SUTs) play a critical role on the phloem plasma membrane in loading sucrose into the phloem of source leaves for long-distance transport to sink organs. Rice has a small gene family of five SUTs, Oryza sativa SUT1 (OsSUT1) to OsSUT5. To identify rice SUTs that function as phloem loaders, we adopted a growth restoration assay of the severe growth retardation phenotype of atsuc2, a mutant of the best-characterized Arabidopsis phloem loader AtSUC2, by introducing OsSUTs. The rice SUT genes were expressed by two different promoters, the native phloem-specific promoter of AtSUC2 (pAtSUC2) and the constitutive Cauliflower Mosaic Virus 35S (pCaMV35S) promoter. Of all the transgenic atsuc2 plants, only pAtSUC2: OsSUT1 complemented the atsuc2 mutant phenotype in a comparable manner to wild type (WT), and consistent levels of soluble sugars and starch were recovered compared to those of WT. This suggests that OsSUT1 is a functional ortholog of the Arabidopsis AtSUC2 and functions as an apoplastic phloem loader. In addition, ossut1 mutants were produced via anther culture and their primary carbohydrate levels and growth phenotypes were indistinguishable from those of WT. This suggests that the rice phloem loader OsSUT1 function may not be essential for rice vegetative growth under normal conditions.     

Genomewide analysis of <Emphasis Type="Italic">ABCB</Emphasis>s with a focus on <Emphasis Type="Italic">ABCB1</Emphasis> and <Emphasis Type="Italic">ABCB19</Emphasis> in <Emphasis Type="Italic">Malus domestica</Emphasis>

The B subfamily of ATP-binding cassette (ABC) proteins (ABCB) plays a vital role in auxin efflux. However, no systematic study has been done in apple. In this study, we performed genomewide identification and expression analyses of the ABCB family in Malus domestica for the first time. We identified a total of 25 apple ABCBs that were divided into three clusters based on the phylogenetic analysis. Most ABCBs within the same cluster demonstrated a similar exon–intron organization. Additionally, the digital expression profiles of ABCB genes shed light on their functional divergence. ABCB1 and ABCB19 are two well-studied auxin efflux carrier genes, and we found that their expression levels are higher in young shoots of M106 than in young shoots of M9. Since young shoots are the main source of auxin synthesis and auxin efflux involves in tree height control. This suggests that ABCB1 and ABCB19 may also take a part in the auxin efflux and tree height control in apple.     

Polymorphic Imprinting of <Emphasis Type="Italic">SLC38A4</Emphasis> Gene in Bovine Placenta

Imprinted genes are characterized by monoallelic expression that is dependent on parental origin. Comparative analysis of imprinted genes between species is a powerful tool for understanding the biological significance of genomic imprinting. The slc38a4 gene encodes a neutral amino acid transporter and is identified as imprinted in mice. In this study, the imprinting status of SLC38A4 was assessed in bovine adult tissues and placenta using a polymorphism-based approach. Results indicate that SLC38A4 is not imprinted in eight adult bovine tissues including heart, liver, spleen, lung, kidney, muscle, fat, and brain. It was interesting to note that SLC38A4 showed polymorphic status in five heterogeneous placentas, with three exhibiting paternal monoallelic expression and two exhibiting biallelic expression. Monoallelic expression of imprinted genes is generally associated with allele-specific differentially methylation regions (DMRs) of CpG islands (CGIs)-encompassed promoter; therefore, the DNA methylation statuses of three CGIs in the SLC38A4 promoter and exon 1 region were tested in three placentas (two exhibiting paternal monoallelic and one showing biallelic expression of SLC38A4) and their corresponding paternal sperms. Unexpectedly, extreme hypomethylation (<?3%) of the DNA was observed in all the three detected placentas and their corresponding paternal sperms. The absence of DMR in bovine SLC38A4 promoter region implied that DNA methylation of these three CGIs does not directly or indirectly affect the polymorphic imprinting of SLC38A4 in bovine placenta. This suggested other epigenetic features other than DNA methylation are needed in regulating the imprinting of bovine SLC38A4, which is different from that of mouse with respect to a DMR existence at the mouse’s slc38a4 promoter region. Although further work is needed, this first characterization of polymorphic imprinting status of SLC38A4 in cattle placenta provides valuable information on investigating the genomic imprinting phenomenon itself.     

Sudden death due to paralysis and synaptic and behavioral deficits when <Emphasis Type="Italic">Hip14/Zdhhc17</Emphasis> is deleted in adult mice

Background

Palmitoylation, the addition of palmitate to proteins by palmitoyl acyltransferases (PATs), is an important regulator of synaptic protein localization and function. Many palmitoylated proteins and PATs have been implicated in neuropsychiatric diseases, including Huntington disease, schizophrenia, amyotrophic lateral sclerosis, Alzheimer disease, and X-linked intellectual disability. HIP14/DHHC17 is the most conserved PAT that palmitoylates many synaptic proteins. Hip14 hypomorphic mice have behavioral and synaptic deficits. However, the phenotype is developmental; thus, a model of post-developmental loss of Hip14 was generated to examine the role of HIP14 in synaptic function in the adult.

Results

Ten weeks after Hip14 deletion (iHip14 ^Δ/Δ ), mice die suddenly from rapidly progressive paralysis. Prior to death the mice exhibit motor deficits, increased escape response during tests of anxiety, anhedonia, a symptom indicative of depressive-like behavior, and striatal synaptic deficits, including reduced probability of transmitter release and increased amplitude but decreased frequency of spontaneous post-synaptic currents. The mice also have increased brain weight due to microgliosis and astrogliosis in the cortex.

Conclusions

Behavioral changes and electrophysiological measures suggest striatal dysfunction in iHip14 ^Δ/Δ mice, and increased cortical volume due to astrogliosis and microgliosis suggests a novel role for HIP14 in glia. These data suggest that HIP14 is essential for maintenance of life and neuronal integrity in the adult mouse.

     

Case report of whole genome sequencing in the XY female: identification of a novel <Emphasis Type="Italic">SRY</Emphasis> mutation and revision of a misdiagnosis of androgen insensitivity syndrome

Background

The 46,XY female is characterised by a male karyotype and female phenotype arising due to any interruption in the sexual development pathways in utero. The cause is usually genetic and various genes are implicated.

Case presentation

Herein we describe a 46,XY woman who was first diagnosed with androgen insensitivity syndrome (testicular feminisation) at 18 years; however, this was later questioned due to the presence of intact Müllerian structures. The clinical phenotype suggested several susceptibility genes including SRY, DHH, NR5A1, NR0B1, AR, AMH, and AMHR2. To study candidate genes simultaneously, we performed whole genome sequencing. This revealed a novel and likely pathogenic missense variant (p.Arg130Pro, c.389G>C) in SRY, one of the major genes implicated in complete gonadal dysgenesis, hence securing this condition over androgen insensitivity syndrome as the cause of the patient’s disorder of sexual development.

Conclusion

This case highlights the emerging clinical utility of whole genome sequencing as a tool in differentiating disorders of sexual development.

     

X-chromosomale Intelligenzminderung

X-linked intellectual disability (XLID) is a heterogeneous disorder; more than 100 XLID genes have been identified so far. Fragile X syndrome with CGG repeat expansions in the 5’-UTR of FMR1, is the most frequent monogenic form of ID. Other XLID genes with a comparatively high prevalence of mutations are ATRX, RPS6KA3, GPC3, SLC16A2, SLC6A8, and ARX. The causes of XLID are distributed as follows: molecular genetically proven mutations in 90% and copy-number variations (CNVs) in approximately 10%. Common CNVs are duplications of Xq28 that include MECP2 and the Xp11.22 duplication syndrome, with overexpression of HUWE1. Using current investigative methods, mutations in X?chromosomal genes can be proven to be the underlying cause in approximately 10% of male patients with ID. Over the next few years, new discoveries are to be expected, primarily in the noncoding regions of the X?chromosome, where further causes of the preponderance in male patients, which has not yet been fully explained, are presumably to be sought.