A Homozygous Missense Variant in HSD17B4 Identified in Two Different Families.

Background: Perrault syndrome is an inherited disorder with clinical findings that differ according to sex. It is characterized by a variable age of onset and sensorineural hearing loss in both sexes, as well as ovarian dysfunction in females with a 46,XX karyotype. Although it is a rare autosomal recessive syndrome, with approximately 100 affected individuals reported in the literature, it shows both genotypic and phenotypic variations. Mutations in the HSD17B4 gene have been identified as one of the genetic causes of Perrault syndrome. Case Presentation: A female case and a male case from two different unrelated families with a new variant in the HSD17B4 gene, which were not previously described in the literature and were accompanied by hearing loss, skeletal anomalies, and neurological symptoms, were presented. Conclusion: We defined Perrault syndrome cases in Turkey caused by a novel mutation in HSD17B4. Whole-exome sequencing is a useful diagnostic technique with varying clinical results due to genetic and phenotypic heterogeneity.

GRM7-related disorder: five additional patients from three independent families and review of the literature.

Developmental and epileptic encephalopathies (DEEs) refer to a group of severe epileptic syndromes characterized by seizures as well as a developmental delay which can be a consequence of the underlying etiology and/or the epileptic encephalopathy. The genes responsible for DEEs are numerous and their number is increasing since the availability of Next-Generation Sequencing. Pathogenic variants in GRM7, encoding the metabotropic glutamate receptor 7, were recently shown as a cause of a severe DEE with autosomal recessive inheritance. To date, only ten patients have been reported in the literature, generally with severe phenotypes including early-onset epilepsy, microcephaly, brain anomalies, and spasticity. We report here 5 patients from 3 independent families with biallelic variants in the GRM7 gene. We review the literature and provide further elements for the understanding of the genotype-phenotype correlation of this rare syndrome.

3D modelling of surface spreading and underground dam groundwater recharge: Egri Creek Subbasin, Turkey.

This study investigated surface spreading and underground dam recharge methods to replenish groundwater in Turkey's Egri Creek Sub-basin of the Kucuk Menderes River Basin. A three-dimensional numerical model was employed for this purpose. Field and lab data are provided to the model for realistic simulations. Pumping test results were used to determine the aquifer parameters. The laboratory works involved sieve analysis, permeability tests, and porosity and water content prediction. The numerical model's boundary conditions were determined from the geological and hydrogeological characteristics of the study area. Initial conditions were expressed regarding water content and pressure head in the vadose zone. The numerical model was satisfactorily validated by simulating water levels in three different pumping wells in the study area. Seven different scenarios, each having a different pool size, were investigated for the surface spreading recharge method. The results showed that a pool size of 30 × 30 m with a 6-m depth basin was the most optimal choice, raising the groundwater level to about 29.3 m. On the other hand, it was found that an underground dam could raise the levels by an average of 9.5 m, which might not be significant to warrant the construction.

Eighth case of Li-Campeau syndrome in a Turkish patient caused by a novel pathogenic variant in UBR7 and expanding the phenotype.

Li-Campeau syndrome (LICAS) is an autosomal recessive disorder characterized by developmental delay, intellectual disability, genital anomalies, congenital heart defects, and dysmorphic features. LICAS is caused by biallelic pathogenic variants in the UBR7 gene, acting as an E3 ubiquitin-protein ligase. Using exome sequencing (ES), we identified a homozygous novel pathogenic splice site variation c.1185+1G>C in UBR7 in a 32-month-old male from a nonconsanguineous Turkish family with clinical features of LICAS. Sanger sequencing revealed the heterozygous state of parents for this variant and confirmed the co-segregation study. The variant may lead to the loss of function of UBR7 and is in a highly conserved residue. Bioinformatic prediction analysis using in silico algorithms supports the pathogenic effect of the splice site variant in the UBR7.

Seroreactivity against retinal proteins in a case of POC1B gene associated cone dystrophy with normal funduscopic appearance: a systematic approach to diagnosis.

PURPOSE: To report a case of cone dystrophy, associated with autosomal recessive homozygote POC1B gene variant, mimicking autoimmune retinopathy. CASE: A 45-year-old female presented with a complaint of decreased vision in both eyes. Her best corrected visual acuity was 20/32 in the right eye and 20/50 in the left eye. Anterior segment and dilated fundus examinations were unremarkable. Spectral domain optical coherence tomography showed a subfoveal blurred dome-shaped ellipsoid zone and an extinguished interdigitation zone affecting the entire macula. Full field electroretinography revealed reduced cone responses. The differential diagnosis included inflammatory chorioretinopathies, autoimmune retinopathies (paraneoplastic or nonparaneoplastic), and hereditary retinal dystrophies. No remarkable finding was observed on combined fluorescein and indocyanine green angiographies. Paraneoplastic autoimmune antibody panel revealed nothing; however, aldolase, enolase, pyruvate kinase M2, and glyceraldehyde-3-phosphate dehydrogenase antibodies were positive on autoimmune retinopathy panel. To exclude hereditary retinal dystrophies, whole-exome sequencing (WES) was applied. WES identified an autosomal recessive homozygote POC1B gene variant (c.680A>G, p.His227Arg). Cone dystrophy diagnosis was given. CONCLUSION: Cone dystrophy associated with POC1B gene variant may present without visible fundus abnormalities. It should be kept in mind that retinal autoantibodies may be positive in such a hereditary dystrophy case due to long-term exposure of the immune system to self-antigens. Therefore, autoimmune retinopathy is a diagnosis of exclusion and should not be diagnosed until all other causes, including hereditary dystrophies, have been ruled out.

Multiple Genomic Alterations, Including a Novel AFF4::IRF1 Fusion Gene, in a Treatment-Refractory Blastic Plasmacytoid Dendritic-Cell Neoplasm: A Case Report and Literature Review.

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare hematologic malignancy with an aggressive clinical course and poor prognosis. The genetic abnormalities in BPDCN are heterogeneous; therefore, its molecular pathogenesis and the prognostic importance of genomic alterations associated with the disease are not well defined. Here we report a case of BPDCN with a novel AFF4::IRF1 fusion predicted to lead to a loss-of-function of the IRF1 tumor suppressor, somatic mutations of ASXL1, TET2, and MYD88, as well as multiple intrachromosomal deletions. The patient showed resistance to Tagraxofusp and Venetoclax, and he died about 16 months after diagnosis. Considering the predicted effect of the AFF4::IRF1 fusion on IRF1's antitumor effects and immune regulation, and the possibility of its relevance to the aggressive course observed in this case, we propose further evaluation of the clinical significance of this fusion in BPDCN in future cooperative group studies and the consideration of therapeutic strategies aimed at restoring IRF1-dependent antineoplastic effects in such cases.

Novel homozygous AP3B2 mutations in four individuals with developmental and epileptic encephalopathy: A rare clinical entity.

OBJECTIVES: Developmental and epileptic encephalopathies (DEEs) are heterogeneous severe neurodevelopmental disorders characterized by recurrent clinical seizures that begin in the neonatal period and early childhood and regression or delay in cognitive, sensory and motor skills in the context of accompanying epileptiform abnormalities. Adaptor-related protein complex 3 beta-2 subunit (AP3B2) gene variants are thought to cause disruption of neuron-specific neurotransmitter release. METHODS: In this case report, whole exome sequencing (WES) was performed on two of the four pediatric patients who came from two unrelated families and were affected by DEE. As a result of WES, previously unreported variants, that is, p.Ala149Serfs* 34 and p.Pro993Argfs* 5, were detected in the AP3B2 gene. These variants were studied using Sanger sequencing in the siblings affected by DEE of the said pediatric patients and in their healthy parents. RESULTS: Autosomal recessive variants of the AP3B2 are associated with the development of DEE. To date, only 14 cases of AP3B2 mutations have been reported in the literature. Consequentially, DEE phenotype involving severe global developmental delay emerged, which is characterized by early-onset infantile epileptic encephalopathy, severe hypotonia, postnatal microcephaly, poor eye contact, speech retardation, abnormal involuntary movements, stereotypical hand movements, progressive intellectual disability, and behavioral and neuropsychiatric findings. CONCLUSION: Given the limited number of patients reported in the literature, detailed studies of the specific clinical and molecular features of AP3B2 gene variants, will shed light on the genotype-phenotype correlation.

A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease.

PURPOSE: The mediator (MED) multisubunit-complex modulates the activity of the transcriptional machinery, and genetic defects in different MED subunits (17, 20, 27) have been implicated in neurologic diseases. In this study, we identified a recurrent homozygous variant in MED11 (c.325C>T; p.Arg109Ter) in 7 affected individuals from 5 unrelated families. METHODS: To investigate the genetic cause of the disease, exome or genome sequencing were performed in 5 unrelated families identified via different research networks and Matchmaker Exchange. Deep clinical and brain imaging evaluations were performed by clinical pediatric neurologists and neuroradiologists. The functional effect of the candidate variant on both MED11 RNA and protein was assessed using reverse transcriptase polymerase chain reaction and western blotting using fibroblast cell lines derived from 1 affected individual and controls and through computational approaches. Knockouts in zebrafish were generated using clustered regularly interspaced short palindromic repeats/Cas9. RESULTS: The disease was characterized by microcephaly, profound neurodevelopmental impairment, exaggerated startle response, myoclonic seizures, progressive widespread neurodegeneration, and premature death. Functional studies on patient-derived fibroblasts did not show a loss of protein function but rather disruption of the C-terminal of MED11, likely impairing binding to other MED subunits. A zebrafish knockout model recapitulates key clinical phenotypes. CONCLUSION: Loss of the C-terminal of MED subunit 11 may affect its binding efficiency to other MED subunits, thus implicating the MED-complex stability in brain development and neurodegeneration.

Developmental genomics of limb malformations: Allelic series in association with gene dosage effects contribute to the clinical variability.

Genetic heterogeneity, reduced penetrance, and variable expressivity, the latter including asymmetric body axis plane presentations, have all been described in families with congenital limb malformations (CLMs). Interfamilial and intrafamilial heterogeneity highlight the complexity of the underlying genetic pathogenesis of these developmental anomalies. Family-based genomics by exome sequencing (ES) and rare variant analyses combined with whole-genome array-based comparative genomic hybridization were implemented to investigate 18 families with limb birth defects. Eleven of 18 (61%) families revealed explanatory variants, including 7 single-nucleotide variant alleles and 3 copy number variants (CNVs), at previously reported "disease trait associated loci": BHLHA9, GLI3, HOXD cluster, HOXD13, NPR2, and WNT10B. Breakpoint junction analyses for all three CNV alleles revealed mutational signatures consistent with microhomology-mediated break-induced replication, a mechanism facilitated by Alu/Alu-mediated rearrangement. Homozygous duplication of BHLHA9 was observed in one Turkish kindred and represents a novel contributory genetic mechanism to Gollop-Wolfgang Complex (MIM: 228250), where triplication of the locus has been reported in one family from Japan (i.e., 4n = 2n + 2n versus 4n = 3n + 1n allelic configurations). Genes acting on limb patterning are sensitive to a gene dosage effect and are often associated with an allelic series. We extend an allele-specific gene dosage model to potentially assist, in an adjuvant way, interpretations of interconnections among an allelic series, clinical severity, and reduced penetrance of the BHLHA9-related CLM spectrum.

A case with congenital disorder of glycosylation with defective fucosylation 2 and new mutation in FUK gene.

INTRODUCTION: Congenital disorders of glycosylation (CDG) is a group of rare, hereditary, multisystem disorders, predominantly affecting nervous system. There are N- and O- types of glycosylation. Fucosylation, a form of N-glycosylation, involves many enzymes. Until today, type 1 and type 2 fucosylation defects were identified, having pathogenic variants in genes encoding α-1,6-fucosyltransferase and fucokinase enzymes, respectively. In this article, a patient with type 2 fucosylation defect will be presented, with hypotonia, developmental delay and blindness and a pathogenic variant that was previously described in two patients. METHOD: Whole exome sequencing (WES) was performed, since the patient had no time to implement diagnostic algorithm for hypotonia etiology. RESULTS: WES revealed a new pathogenic variant of homozygous c.993_1011del (p.Glu335Hisfs*55) frameshift variant of the FUK gene NM_145059 transcript. She had milder clinical manifestation than reported two patients. CONCLUSION: Congenital Defect of Glycosylation should be considered when the clinical findings cannot be explained by other known diseases, particularly in patients with multisystemic, predominantly neurological involvement.

Whole exome sequencing identifies a novel variant in ABCA3 in an individual with fatal congenital surfactant protein deficiency.

BACKGROUND: Adenosine triphosphate-binding cassette subfamily A member 3 (ABCA3) gene variants, which cause severe respiratory distress syndrome (RDS) in term newborns, can cause death, especially due to the lack of congenital surfactant protein. The relationship between the types, pathophysiology and effects of ABCA3 gene variants on surfactant metabolism and the clinical phenotype have not yet been fully clarified, but the ABCA3 genotype is known to affect clinical severity. CASE: In our study, in a term newborn with a diagnosis of RDS resulting in death, we detected the c.3677 T > C (p.Leu1226Pro) variant homozygous variant in the ABCA3 gene according to the NM_001089.3 transcript, which, to our knowledge, was identified for the first time in the literature. CONCLUSIONS: We consider that this case report contributes to the literature on RDS by showing the presence of c.3677 T > C (p.Leu1226Pro), a new homozygous variant of ABCA3 in our patient.

MED27 Variants Cause Developmental Delay, Dystonia, and Cerebellar Hypoplasia.

The Mediator multiprotein complex functions as a regulator of RNA polymerase II-catalyzed gene transcription. In this study, exome sequencing detected biallelic putative disease-causing variants in MED27, encoding Mediator complex subunit 27, in 16 patients from 11 families with a novel neurodevelopmental syndrome. Patient phenotypes are highly homogeneous, including global developmental delay, intellectual disability, axial hypotonia with distal spasticity, dystonic movements, and cerebellar hypoplasia. Seizures and cataracts were noted in severely affected individuals. Identification of multiple patients with biallelic MED27 variants supports the critical role of MED27 in normal human neural development, particularly for the cerebellum. ANN NEUROL 2021;89:828-833.

Functional biology of the Steel syndrome founder allele and evidence for clan genomics derivation of COL27A1 pathogenic alleles worldwide.

Previously we reported the identification of a homozygous COL27A1 (c.2089G>C; p.Gly697Arg) missense variant and proposed it as a founder allele in Puerto Rico segregating with Steel syndrome (STLS, MIM #615155); a rare osteochondrodysplasia characterized by short stature, congenital bilateral hip dysplasia, carpal coalitions, and scoliosis. We now report segregation of this variant in five probands from the initial clinical report defining the syndrome and an additional family of Puerto Rican descent with multiple affected adult individuals. We modeled the orthologous variant in murine Col27a1 and found it recapitulates some of the major Steel syndrome associated skeletal features including reduced body length, scoliosis, and a more rounded skull shape. Characterization of the in vivo murine model shows abnormal collagen deposition in the extracellular matrix and disorganization of the proliferative zone of the growth plate. We report additional COL27A1 pathogenic variant alleles identified in unrelated consanguineous Turkish kindreds suggesting Clan Genomics and identity-by-descent homozygosity contributing to disease in this population. The hypothesis that carrier states for this autosomal recessive osteochondrodysplasia may contribute to common complex traits is further explored in a large clinical population cohort. Our findings augment our understanding of COL27A1 biology and its role in skeletal development; and expand the functional allelic architecture in this gene underlying both rare and common disease phenotypes.

A hereditary angioedema screening in two villages, based on an index case, and identification of a novel mutation, "1033G>T", at the SERPING1 gene.

INTRODUCTION: Hereditary angioedema (HAE) may be fatal and diagnosis can be delayed up to 10 years. We aimed to screen HAE in two villages based on an index case of HAE and to investigate for the mutation of the C1 esterase inhibitor (C1-INH) gene. MATERIAL AND METHODS: A total of 124 people were screened in two villages. The frequency and severity of symptoms were scored. C4, C1-INH levels and C1-INH activity were measured. We investigated for mutations of the C1-INH gene. RESULTS: Thirty-five cases of type I HAE and 7 cases of type II HAE were determined. Thirty-one (73.8%) patients diagnosed with HAE were 18 years old or younger. There was a positive correlation between C4 levels, C1-INH levels (p < 0.0001, r = 0.81), and C1-INH activity levels (p < 0.0001, r = 0.631) and between the age at diagnosis and severity score (p < 0.0001, r = 0.651). A positive correlation was found between the age at first symptom onset and C4 levels (p = 0.002, r = 0.774), and C1-INH levels (p = 0.006, r = 0.714). A marginally significant negative correlation was found between C1-INH activity levels and severity scores (p = 0.1, r = -0.515). We identified a novel heterozygous 1033G>T missense variant of the C1-INH gene, SERPING1, in patients with type I HAE. CONCLUSIONS: There are long delay periods in the diagnosis of HAE and when the index case is present, family screening may be very important and even life-saving, in particular, in paediatric patients without symptoms. Furthermore, the present study provides evidence to link a novel mutation, c.1033G>T, to the development of HAE in a large HAE family from Turkey.

Histologic Evaluation of Regenerated Tissues in the Pulp Spaces of Teeth with Mature Roots at the Time of the Regenerative Endodontic Procedures.

INTRODUCTION: Recently, regenerative endodontic procedures (REPs) have been used to treat mature permanent teeth with apical periodontitis. Although animal studies with regard to histopathological findings after REPs exist, there is a paucity of studies on mature human teeth. As yet, the nature of tissues formed in the root canal of such teeth has not been established. This report presents histologic findings with regard to regenerative tissues in the pulp spaces exposed after dental trauma in human mature maxillary incisor teeth successfully treated with REPs. METHODS: A 20-year-old girl was referred to our clinic for the treatment of her central incisors (#8 and #9). The incisors had apical periodontitis. REPs were performed on both maxillary central incisors. Three years 5 months after the initial treatment, the teeth had a horizontal crown fracture and needed a fiber post as well as root canal treatment. Mineral trioxide aggregate was carefully removed, and the tissue that had formed in the canal space was processed for routine histologic and immunohistochemical examination. RESULTS: Histologic findings of the present case showed that the vital tissue formed in the canal space was fibrous connective tissue that contains bonelike tissue, vascular structures, and inflammation. These histologic findings obtained from mature teeth were similar to the findings of previous reports relating to immature teeth. CONCLUSIONS: Based on the present case, the vital tissue formed in the canal space is fibrous connective tissue that contains bonelike tissue, vascular structures, and inflammation. These histologic findings with regard to mature teeth were similar to the findings of previous reports relating to immature teeth.

The Genomics of Arthrogryposis, a Complex Trait: Candidate Genes and Further Evidence for Oligogenic Inheritance.

Arthrogryposis is a clinical finding that is present either as a feature of a neuromuscular condition or as part of a systemic disease in over 400 Mendelian conditions. The underlying molecular etiology remains largely unknown because of genetic and phenotypic heterogeneity. We applied exome sequencing (ES) in a cohort of 89 families with the clinical sign of arthrogryposis. Additional molecular techniques including array comparative genomic hybridization (aCGH) and Droplet Digital PCR (ddPCR) were performed on individuals who were found to have pathogenic copy number variants (CNVs) and mosaicism, respectively. A molecular diagnosis was established in 65.2% (58/89) of families. Eleven out of 58 families (19.0%) showed evidence for potential involvement of pathogenic variation at more than one locus, probably driven by absence of heterozygosity (AOH) burden due to identity-by-descent (IBD). RYR3, MYOM2, ERGIC1, SPTBN4, and ABCA7 represent genes, identified in two or more families, for which mutations are probably causative for arthrogryposis. We also provide evidence for the involvement of CNVs in the etiology of arthrogryposis and for the idea that both mono-allelic and bi-allelic variants in the same gene cause either similar or distinct syndromes. We were able to identify the molecular etiology in nine out of 20 families who underwent reanalysis. In summary, our data from family-based ES further delineate the molecular etiology of arthrogryposis, yielded several candidate disease-associated genes, and provide evidence for mutational burden in a biological pathway or network. Our study also highlights the importance of reanalysis of individuals with unsolved diagnoses in conjunction with sequencing extended family members.

Regenerative Endodontic Procedures in Necrotic Mature Teeth with Periapical Radiolucencies: A Preliminary Randomized Clinical Study.

INTRODUCTION: This preliminary study compared clinical and radiographic outcomes of regenerative endodontic procedures (REPs) with that of conventional root canal treatment (CRCT) in necrotic mature teeth with periapical radiolucencies. METHODS: Fifty-six mature necrotic teeth with large periapical radiolucencies were distributed into 2 groups: group 1, REPs and group 2, CRCT (n = 28/group). Clinical and radiographic follow-up assessments were undertaken up to 12 months. Statistical analysis was performed using the independent samples t test and the chi-square test, and the level of significance was set at P = .05. RESULTS: With a follow-up rate of about 73.4% of the total patients for 12 months, favorable clinical and radiographic outcomes were found in 92.3% and 80% in REPs and CRCT groups, respectively, and the difference was not statistically significant (P > .05). Half of the teeth treated with REPs responded to the electric pulp test. CONCLUSIONS: Regenerative endodontic procedures have the potential to be used as a treatment option for mature teeth with large periapical radiolucencies.

A hereditary angioedema screening on an index case: Turkey.

BACKGROUND: Hereditary angioedema (HAE) is characterised by recurrent episodes of angioedema and can be fatal. OBJECTIVE: The present study aimed to screen HAE. METHODS: A total of 60 individuals were screened. The frequency and severity of symptoms were scored from 0 to 8. Measurements were taken of C4 and C1 esterase inhibitor protein (C1-INH) levels. Mutation in the C1 inhibitor gene was examined in 9 patients with HAE. RESULTS: A positive correlation between the C1 esterase inhibitor protein levels and C4 level was detected in the group as a whole (p < 0.001, r = 0.725, n = 60). Anegative correlation between the C1 esterase inhibitor protein level and severity score was observed in the whole group (p < 0.001, r = -0.486, n = 60). A negative correlation was also detected in the entire group between the C4 level and severity score (p = 0.002, r = -0.389, n = 60). In the patients with HAE, a positive correlation between the C1 esterase inhibitor protein level and C4 levels was detected (p = 0.034, r = 0.705, n = 9). A heterozygous c. 601A > T nonsense variant was identified at the C1 esterase inhibitor gene-SERPING1-in patients with Type 1 HAE. CONCLUSION: It is well known that there is a prolonged delay in the diagnosis of HAE. The present study demonstrates that it is very important and even life-saving to screen for HAE on the basis of an index case.