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1.
Nature ; 606(7913): 382-388, 2022 06.
Article in English | MEDLINE | ID: mdl-35614220

ABSTRACT

Mitochondria are epicentres of eukaryotic metabolism and bioenergetics. Pioneering efforts in recent decades have established the core protein componentry of these organelles1 and have linked their dysfunction to more than 150 distinct disorders2,3. Still, hundreds of mitochondrial proteins lack clear functions4, and the underlying genetic basis for approximately 40% of mitochondrial disorders remains unresolved5. Here, to establish a more complete functional compendium of human mitochondrial proteins, we profiled more than 200 CRISPR-mediated HAP1 cell knockout lines using mass spectrometry-based multiomics analyses. This effort generated approximately 8.3 million distinct biomolecule measurements, providing a deep survey of the cellular responses to mitochondrial perturbations and laying a foundation for mechanistic investigations into protein function. Guided by these data, we discovered that PIGY upstream open reading frame (PYURF) is an S-adenosylmethionine-dependent methyltransferase chaperone that supports both complex I assembly and coenzyme Q biosynthesis and is disrupted in a previously unresolved multisystemic mitochondrial disorder. We further linked the putative zinc transporter SLC30A9 to mitochondrial ribosomes and OxPhos integrity and established RAB5IF as the second gene harbouring pathogenic variants that cause cerebrofaciothoracic dysplasia. Our data, which can be explored through the interactive online MITOMICS.app resource, suggest biological roles for many other orphan mitochondrial proteins that still lack robust functional characterization and define a rich cell signature of mitochondrial dysfunction that can support the genetic diagnosis of mitochondrial diseases.


Subject(s)
Mitochondria , Mitochondrial Proteins , Cation Transport Proteins , Cell Cycle Proteins , Energy Metabolism , Humans , Mass Spectrometry , Mitochondria/genetics , Mitochondria/metabolism , Mitochondrial Diseases/genetics , Mitochondrial Diseases/metabolism , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , Transcription Factors , rab5 GTP-Binding Proteins
2.
Am J Med Genet C Semin Med Genet ; 193(2): 193-197, 2023 06.
Article in English | MEDLINE | ID: mdl-37186482

ABSTRACT

Bone marrow failure type 3 (BMFS3) (MIM:617052) is a subtype of inherited bone marrow failure syndromes (IBMFS) caused by homozygous pathogenic variants in DNAJC21. It was first defined in 2016, and to date, 19 patients have been reported. Here we report the first adult patient; a 20-year-old female with a novel frameshift variant in DNAJC21 presents with thrombocytopenia, dysmorphic findings, and ovarian agenesis. Our patient expands the clinical spectrum to the milder end and suggests that DNAJC21-related disorders can have relatively mild presentations. Investigation of DNAJC21 variants in both childhood and adult patients with persistent, non-progressive thrombocytopenia will allow to broaden the gene-related phenotypic and genotypic spectrum and elucidate the pathophysiology. Therefore, we encourage revisiting undiagnosed patients to offer whole exome sequencing (WES) in adulthood.


Subject(s)
Thrombocytopenia , Humans , Female , Young Adult , Child , Adult , Genotype , Exome Sequencing , Thrombocytopenia/diagnosis , Thrombocytopenia/genetics , HSP40 Heat-Shock Proteins/genetics
3.
Am J Med Genet A ; 191(7): 1814-1825, 2023 07.
Article in English | MEDLINE | ID: mdl-37053206

ABSTRACT

Koolen-de Vries syndrome (KdVS) is a rare multisystemic disorder caused by a microdeletion on chromosome 17q21.31 including KANSL1 gene or intragenic pathogenic variants in KANSL1 gene. Here, we describe the clinical and genetic spectrum of eight Turkish children with KdVS due to a de novo 17q21.31 deletion, and report on several rare/new conditions. Eight patients from unrelated families aged between 17 months and 19 years enrolled in this study. All patients evaluated by a clinical geneticist, and the clinical diagnosis were confirmed by molecular karyotyping. KdVS patients had some common distinctive facial features. All patients had neuromotor retardation, and speech and language delay. Epilepsy, structural brain anomalies, ocular, ectodermal, and musculoskeletal findings, and friendly personality were remarkable in more than half of the patients. Hypertension, hypothyroidism, celiac disease, and postaxial polydactyly were among the rare/new conditions. Our study contributes to the clinical spectrum of patients with KdVS, while also provide a review by comparing them with previous cohort studies.


Subject(s)
Abnormalities, Multiple , Intellectual Disability , Humans , Abnormalities, Multiple/diagnosis , Abnormalities, Multiple/epidemiology , Abnormalities, Multiple/genetics , Intellectual Disability/diagnosis , Intellectual Disability/epidemiology , Intellectual Disability/genetics , Chromosome Deletion , Rare Diseases/genetics , Phenotype , Chromosomes, Human, Pair 17/genetics
4.
Genet Med ; 24(12): 2444-2452, 2022 12.
Article in English | MEDLINE | ID: mdl-36107167

ABSTRACT

PURPOSE: This study was undertaken to collect baseline growth parameters in children with achondroplasia who might enroll in interventional trials of vosoritide, and to establish a historical control. METHODS: In this prospective, observational study, participants (≤17 years) underwent a detailed medical history and physical examination and were followed every 3 months until they finished participating in the study by enrolling in an interventional trial or withdrawing. RESULTS: A total of 363 children were enrolled (28 centers, 8 countries). Mean (SD) follow up was 20.4 (15.0) months. In participants <1 year, mean annualized growth velocity (AGV) was 11.6 cm/year for girls and 14.6 cm/year for boys. By age 1 year, mean AGV decreased to 7.4 cm/year in girls and 7.1 cm/year in boys. By age 10 years, mean AGV decreased to 3.6 cm/year for both sexes. Mean height z-score in participants <1 year was -2.5 for girls and -3.2 for boys and decreased up to the age 5 years (-5.3 for girls; -4.6 for boys). Girls and boys had a disproportionate upper-to-lower body segment ratio. Mean ratio was highest in participants aged <1 year (2.9 for girls; 2.8 for boys) and decreased gradually to approximately 2 in both sexes from 4 years of age onward. CONCLUSION: This study represents one of the largest datasets of prospectively collected medical and longitudinal growth data in children with achondroplasia. It serves as a robust historical control to measure therapeutic interventions against and to further delineate the natural history of this condition.


Subject(s)
Achondroplasia , Child , Male , Female , Humans , Child, Preschool , Prospective Studies , Achondroplasia/epidemiology , Achondroplasia/genetics , Achondroplasia/diagnosis , Body Height
5.
Scand J Immunol ; 95(3): e13130, 2022 Mar.
Article in English | MEDLINE | ID: mdl-34951041

ABSTRACT

T cell receptor excision circles (TRECs) and kappa-deleting excision circles (KRECs) are DNA fragments potentially indicative of T and B cell development, respectively. Recent thymic emigrants (RTEs) are a subset of peripheral cells that may also represent thymic function. Here, we investigated TREC/KREC copy numbers by quantitative real-time PCR in the peripheral blood of patients with primary immunodeficiencies (PIDs, n = 145) and that of healthy controls (HCs, n = 86) and assessed the correlation between RTEs and TREC copy numbers. We found that TREC copy numbers were significantly lower in children and adults with PIDs (P < .0001 and P < .002, respectively) as compared with their respective age-matched HCs. A moderate correlation was observed between TREC copies and RTE numbers among children with PID (r = .5114, P < .01), whereas no significant correlation was detected between RTE values and TREC content in the HCs (r = .0205, P = .9208). Additionally, we determined TREC and KREC copy numbers in DNA isolated from the Guthrie cards of 200 newborns and showed that this method is applicable to DNA isolated from both peripheral blood samples and dried blood spots, with the two sample types showing comparable TREC and KREC values. We further showed that RTE values are not always reliable markers of T cell output. Although additional confirmatory studies with larger cohorts are needed, our results provide thresholds for TREC/KREC copy numbers for different age groups.


Subject(s)
B-Lymphocytes/immunology , Receptors, Antigen, T-Cell/immunology , Severe Combined Immunodeficiency/immunology , T-Lymphocytes/immunology , Adolescent , Adult , Child , Child, Preschool , DNA/genetics , DNA/immunology , Female , Hematopoiesis/genetics , Hematopoiesis/immunology , Humans , Infant , Infant, Newborn , Lymphocyte Activation/immunology , Male , Middle Aged , Neonatal Screening/methods , Real-Time Polymerase Chain Reaction/methods , Receptors, Antigen, T-Cell/genetics , Severe Combined Immunodeficiency/genetics , Young Adult
6.
Cleft Palate Craniofac J ; 59(9): 1114-1124, 2022 09.
Article in English | MEDLINE | ID: mdl-34410171

ABSTRACT

OBJECTIVE: Oculoauriculovertebral spectrum (OAVS) is a genetically and clinically heterogeneous disorder that occurs due to a developmental field defect of the first and second pharyngeal arches. Even though recent whole exome sequencing studies (WES) have led to identification of several genes associated with this spectrum in a subset of individuals, complete pathogenesis of OAVS remains unsolved. In this study, molecular genetic etiology of OAVS was systematically investigated. DESIGN/SETTING/PATIENTS: A cohort of 23 Turkish patients with OAVS, referred to Hacettepe University Hospital, Department of Pediatric Genetics from 2008 to 2018, was included in this study. Minimal diagnostic criteria for OAVS were considered as unilateral microtia or hemifacial microsomia with preauricular skin tag. The cohort was clinically reevaluated for craniofacial and extracranial findings. Molecular etiology was investigated using candidate gene sequencing following copy number variant (CNV) analysis. WES was also performed for 2 of the selected patients. RESULTS: Patients in the study cohort presented similar demographic and phenotypic characteristics to previously described patients in the literature except for a higher frequency of bilaterality, cardiac findings, and intellectual disability/developmental delay. CNV analysis revealed a possible genetic etiology for 3 patients (13%). Additional WES in 1 of the 2 patients uncovered a novel heterozygous nonsense variant in Elongation factor Tu GTP-binding domain-containing 2 (EFTUD2) causing mandibulofacial dysostosis with microcephaly (MFDM), which clinically overlaps with OAVS. CONCLUSION: Detailed clinical evaluation for any patient with OAVS is recommended due to a high rate of accompanying systemic findings. We further expand the existing genetic heterogeneity of OAVS by identifying several CNVs and a phenotypically overlapping disorder, MFDM.


Subject(s)
Goldenhar Syndrome , Mandibulofacial Dysostosis , Microcephaly , Child , Cohort Studies , Developmental Disabilities/genetics , Goldenhar Syndrome/genetics , Humans , Mandibulofacial Dysostosis/genetics , Microcephaly/genetics , Peptide Elongation Factors/genetics , Ribonucleoprotein, U5 Small Nuclear/genetics
7.
Lancet ; 396(10252): 684-692, 2020 09 05.
Article in English | MEDLINE | ID: mdl-32891212

ABSTRACT

BACKGROUND: There are no effective therapies for achondroplasia. An open-label study suggested that vosoritide administration might increase growth velocity in children with achondroplasia. This phase 3 trial was designed to further assess these preliminary findings. METHODS: This randomised, double-blind, phase 3, placebo-controlled, multicentre trial compared once-daily subcutaneous administration of vosoritide with placebo in children with achondroplasia. The trial was done in hospitals at 24 sites in seven countries (Australia, Germany, Japan, Spain, Turkey, the USA, and the UK). Eligible patients had a clinical diagnosis of achondroplasia, were ambulatory, had participated for 6 months in a baseline growth study and were aged 5 to less than 18 years at enrolment. Randomisation was done by means of a voice or web-response system, stratified according to sex and Tanner stage. Participants, investigators, and trial sponsor were masked to group assignment. Participants received either vosoritide 15·0 µg/kg or placebo, as allocated, for the duration of the 52-week treatment period administered by daily subcutaneous injections in their homes by trained caregivers. The primary endpoint was change from baseline in mean annualised growth velocity at 52 weeks in treated patients as compared with controls. All randomly assigned patients were included in the efficacy analyses (n=121). All patients who received one dose of vosoritide or placebo (n=121) were included in the safety analyses. The trial is complete and is registered, with EudraCT, number, 2015-003836-11. FINDINGS: All participants were recruited from Dec 12, 2016, to Nov 7, 2018, with 60 assigned to receive vosoritide and 61 to receive placebo. Of 124 patients screened for eligibility, 121 patients were randomly assigned, and 119 patients completed the 52-week trial. The adjusted mean difference in annualised growth velocity between patients in the vosoritide group and placebo group was 1·57 cm/year in favour of vosoritide (95% CI [1·22-1·93]; two-sided p<0·0001). A total of 119 patients had at least one adverse event; vosoritide group, 59 (98%), and placebo group, 60 (98%). None of the serious adverse events were considered to be treatment related and no deaths occurred. INTERPRETATION: Vosoritide is an effective treatment to increase growth in children with achondroplasia. It is not known whether final adult height will be increased, or what the harms of long-term therapy might be. FUNDING: BioMarin Pharmaceutical.


Subject(s)
Achondroplasia/drug therapy , Natriuretic Peptide, C-Type/analogs & derivatives , Osteogenesis , Absorptiometry, Photon , Achondroplasia/blood , Adolescent , Biomarkers/blood , Body Height , Bone Density , Child , Child, Preschool , Collagen Type X/blood , Double-Blind Method , Female , Humans , Injection Site Reaction , Injections, Subcutaneous , Male , Natriuretic Peptide, C-Type/therapeutic use
8.
Genet Med ; 23(12): 2443-2447, 2021 12.
Article in English | MEDLINE | ID: mdl-34341520

ABSTRACT

PURPOSE: Achondroplasia is caused by pathogenic variants in the fibroblast growth factor receptor 3 gene that lead to impaired endochondral ossification. Vosoritide, an analog of C-type natriuretic peptide, stimulates endochondral bone growth and is in development for the treatment of achondroplasia. This phase 3 extension study was conducted to document the efficacy and safety of continuous, daily vosoritide treatment in children with achondroplasia, and the two-year results are reported. METHODS: After completing at least six months of a baseline observational growth study, and 52 weeks in a double-blind, placebo-controlled study, participants were eligible to continue treatment in an open-label extension study, where all participants received vosoritide at a dose of 15.0 µg/kg/day. RESULTS: In children randomized to vosoritide, annualized growth velocity increased from 4.26 cm/year at baseline to 5.39 cm/year at 52 weeks and 5.52 cm/year at week 104. In children who crossed over from placebo to vosoritide in the extension study, annualized growth velocity increased from 3.81 cm/year at week 52 to 5.43 cm/year at week 104. No new adverse effects of vosoritide were detected. CONCLUSION: Vosoritide treatment has safe and persistent growth-promoting effects in children with achondroplasia treated daily for two years.


Subject(s)
Achondroplasia , Natriuretic Peptide, C-Type , Achondroplasia/drug therapy , Achondroplasia/genetics , Child , Double-Blind Method , Humans , Natriuretic Peptide, C-Type/analogs & derivatives , Natriuretic Peptide, C-Type/therapeutic use , Treatment Outcome
9.
J Hum Genet ; 66(6): 585-596, 2021 Jun.
Article in English | MEDLINE | ID: mdl-33288834

ABSTRACT

Acromesomelic dysplasia type Maroteaux (AMDM, OMIM #602875) is an autosomal recessive disorder characterized by severe short stature, shortened middle and distal segments of the limbs, redundant skin of fingers, radial head subluxation or dislocation, large great toes and cranium, and normal intelligence. Only the skeletal system appears to be consistently affected. AMDM is caused by biallelic loss-of-function variants in the natriuretic peptide receptor B (NPRB or NPR2, OMIM #108961) which is involved in endochondral ossification and longitudinal growth of limbs and vertebrae. In this study, we investigated 26 AMDM patients from 22 unrelated families and revealed their genetic etiology in 20 families, via Sanger sequencing or exome sequencing. A total of 22 distinct variants in NPR2 (14 missense, 5 nonsense, 2 intronic, and 1 one-amino acid deletion) were detected, among which 15 were novel. They were in homozygous states in 19 patients and in compound heterozygous states in four patients. Parents with heterozygous NPR2 variants were significantly shorter than the control. Extra-skeletal abnormalities, including global developmental delay/intellectual disability, nephrolithiasis, renal cyst, and oligodontia were noted in the patient cohort. The high parental consanguinity rate might have contributed to these findings, probably associated with other gene variants. This study represents the largest cohort of AMDM from Turkey and regional countries and further expands the molecular and clinical spectrum of AMDM.


Subject(s)
Dwarfism/genetics , Genetic Predisposition to Disease , Osteochondrodysplasias/epidemiology , Receptors, Atrial Natriuretic Factor/genetics , Child , Child, Preschool , Consanguinity , Dwarfism/diagnosis , Dwarfism/epidemiology , Dwarfism/physiopathology , Female , Heterozygote , Homozygote , Humans , Infant , Limb Deformities, Congenital/diagnosis , Limb Deformities, Congenital/epidemiology , Limb Deformities, Congenital/genetics , Limb Deformities, Congenital/physiopathology , Male , Mutation/genetics , Osteochondrodysplasias/diagnosis , Osteochondrodysplasias/genetics , Osteochondrodysplasias/physiopathology , Pedigree , Tertiary Healthcare , Turkey/epidemiology , Exome Sequencing
10.
Am J Med Genet A ; 185(10): 3104-3110, 2021 10.
Article in English | MEDLINE | ID: mdl-34089299

ABSTRACT

Spondyloepimetaphyseal dysplasia (SEMD) is a group of genetic skeletal disorders characterized by disproportionate short stature, and varying degrees of vertebral, epiphyseal, and metaphyseal involvement of the skeleton. According to the Nosology and classification of genetic skeletal disorders 2019 revision, more than 20 types of SEMD have been identified, and SEMD with immune deficiency, EXTL3 type is one of the newcomers. Affected individuals display variable skeletal abnormalities and neurodevelopmental findings. Liver and kidney cysts have also been reported frequently. Patients may exhibit varying degrees of immune deficiency as well. To date, only 14 patients from 9 unrelated families with SEMD with immune deficiency, EXTL3 type have been reported in the literature. We report a new patient who is currently 15 years old in whom cystic liver lesions were detected in the prenatal period. Disproportionate short stature, mild developmental delay and a T- NK+ B+ immunological profile were detected in the postnatal follow-up. Exome sequence analysis revealed a previously reported homozygous missense variant in exon 3 c.953C > T; p.(Pro318Leu) in EXTL3.


Subject(s)
Autoimmune Diseases/genetics , Genetic Predisposition to Disease , Immunologic Deficiency Syndromes/genetics , N-Acetylglucosaminyltransferases/genetics , Osteochondrodysplasias/genetics , Adolescent , Autoimmune Diseases/immunology , Autoimmune Diseases/pathology , Child , Child, Preschool , Dwarfism/genetics , Dwarfism/pathology , Female , Genetic Testing , Homozygote , Humans , Immunologic Deficiency Syndromes/immunology , Immunologic Deficiency Syndromes/pathology , Infant , Male , Mutation, Missense/genetics , N-Acetylglucosaminyltransferases/deficiency , Osteochondrodysplasias/immunology , Osteochondrodysplasias/pathology , Pedigree , Spine/pathology , Young Adult
11.
Am J Med Genet A ; 185(2): 517-527, 2021 02.
Article in English | MEDLINE | ID: mdl-33398909

ABSTRACT

Bone dysplasias (osteochondrodysplasias) are a large group of conditions associated with short stature, skeletal disproportion, and radiographic abnormalities of skeletal elements. Nearly all are genetic in origin. We report a series of seven children with similar findings of chondrodysplasia and growth failure following early hematopoietic stem cell transplantation (HSCT) for pediatric non-oncologic disease: hemophagocytic lymphohistiocytosis or HLH (five children, three with biallelic HLH-associated variants [in PRF1 and UNC13D] and one with HLH secondary to visceral Leishmaniasis), one child with severe combined immunodeficiency and one with Omenn syndrome (both children had biallelic RAG1 pathogenic variants). All children had normal growth and no sign of chondrodysplasia at birth and prior to their primary disease. After HSCT, all children developed growth failure, with standard deviation scores for height at or below -3. Radiographically, all children had changes in the spine, metaphyses and epiphyses, compatible with a spondyloepimetaphyseal dysplasia. Genomic sequencing failed to detect pathogenic variants in genes associated with osteochondrodysplasias. We propose that such chondrodysplasia with growth failure is a novel, rare, but clinically important complication following early HSCT for non-oncologic pediatric diseases. The pathogenesis is unknown but could possibly involve loss or perturbation of the cartilage-bone stem cell population.


Subject(s)
Hematopoietic Stem Cell Transplantation/adverse effects , Lymphohistiocytosis, Hemophagocytic/genetics , Osteochondrodysplasias/genetics , Child , Child, Preschool , Female , Humans , Lymphohistiocytosis, Hemophagocytic/complications , Lymphohistiocytosis, Hemophagocytic/diagnosis , Lymphohistiocytosis, Hemophagocytic/therapy , Male , Membrane Proteins/genetics , Osteochondrodysplasias/complications , Osteochondrodysplasias/diagnosis , Osteochondrodysplasias/therapy , Perforin/genetics , Treatment Outcome
12.
Am J Hum Genet ; 100(2): 216-227, 2017 02 02.
Article in English | MEDLINE | ID: mdl-28065471

ABSTRACT

Defects of the V-type proton (H+) ATPase (V-ATPase) impair acidification and intracellular trafficking of membrane-enclosed compartments, including secretory granules, endosomes, and lysosomes. Whole-exome sequencing in five families affected by mild to severe cutis laxa, dysmorphic facial features, and cardiopulmonary involvement identified biallelic missense mutations in ATP6V1E1 and ATP6V1A, which encode the E1 and A subunits, respectively, of the V1 domain of the heteromultimeric V-ATPase complex. Structural modeling indicated that all substitutions affect critical residues and inter- or intrasubunit interactions. Furthermore, complexome profiling, a method combining blue-native gel electrophoresis and liquid chromatography tandem mass spectrometry, showed that they disturb either the assembly or the stability of the V-ATPase complex. Protein glycosylation was variably affected. Abnormal vesicular trafficking was evidenced by delayed retrograde transport after brefeldin A treatment and abnormal swelling and fragmentation of the Golgi apparatus. In addition to showing reduced and fragmented elastic fibers, the histopathological hallmark of cutis laxa, transmission electron microscopy of the dermis also showed pronounced changes in the structure and organization of the collagen fibers. Our findings expand the clinical and molecular spectrum of metabolic cutis laxa syndromes and further link defective extracellular matrix assembly to faulty protein processing and cellular trafficking caused by genetic defects in the V-ATPase complex.


Subject(s)
Cutis Laxa/genetics , Mutation, Missense , Vacuolar Proton-Translocating ATPases/genetics , Adolescent , Alleles , Amino Acid Sequence , Case-Control Studies , Child , Female , Fibroblasts/metabolism , Gene Expression Regulation , Genome-Wide Association Study , Glycosylation , Golgi Apparatus/metabolism , Humans , Infant , Infant, Newborn , Male , Pedigree , Protein Conformation , Protein Transport , Tandem Mass Spectrometry
14.
Genet Med ; 21(6): 1295-1307, 2019 06.
Article in English | MEDLINE | ID: mdl-30349098

ABSTRACT

PURPOSE: Pathogenic variants in ARID1B are one of the most frequent causes of intellectual disability (ID) as determined by large-scale exome sequencing studies. Most studies published thus far describe clinically diagnosed Coffin-Siris patients (ARID1B-CSS) and it is unclear whether these data are representative for patients identified through sequencing of unbiased ID cohorts (ARID1B-ID). We therefore sought to determine genotypic and phenotypic differences between ARID1B-ID and ARID1B-CSS. In parallel, we investigated the effect of different methods of phenotype reporting. METHODS: Clinicians entered clinical data in an extensive web-based survey. RESULTS: 79 ARID1B-CSS and 64 ARID1B-ID patients were included. CSS-associated dysmorphic features, such as thick eyebrows, long eyelashes, thick alae nasi, long and/or broad philtrum, small nails and small or absent fifth distal phalanx and hypertrichosis, were observed significantly more often (p < 0.001) in ARID1B-CSS patients. No other significant differences were identified. CONCLUSION: There are only minor differences between ARID1B-ID and ARID1B-CSS patients. ARID1B-related disorders seem to consist of a spectrum, and patients should be managed similarly. We demonstrated that data collection methods without an explicit option to report the absence of a feature (such as most Human Phenotype Ontology-based methods) tended to underestimate gene-related features.


Subject(s)
DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Abnormalities, Multiple/genetics , Adolescent , Adult , Child , Child, Preschool , Chromosomal Proteins, Non-Histone/genetics , Exome , Face/abnormalities , Female , Genetic Association Studies/methods , Genetic Variation/genetics , Hand Deformities, Congenital/genetics , Humans , Infant , Infant, Newborn , Intellectual Disability/genetics , Male , Micrognathism/genetics , Middle Aged , Mutation , Neck/abnormalities , Penetrance
15.
BMC Med Genet ; 20(1): 15, 2019 01 14.
Article in English | MEDLINE | ID: mdl-30642273

ABSTRACT

BACKGROUND: Autosomal recessive nail dysplasia is characterized by thick and hard nails with a very slow growth on the hands and feet. Mutations in FZD6 gene were found to be associated with autosomal recessive nail dysplasia in 2011. Presently, only seven mutations have been reported in FZD6 gene; five mutations are clustered in the C-terminus, one is at the seventh transmembrane domain, and another is at the very beginning of third extracellular loop. METHODS: Whole exome sequencing (WES) was applied to the index case, her one affected sister and her healthy consanguineous parents. The mutation was verified via Sanger sequencing. Molecular dynamics simulations of the predicted structures of native and mutant proteins were compared to gain insight into the pathogenicity mechanism of the mutation. RESULTS: Here, we report a homozygous 8 bp deletion mutation, p.Gly559Aspfs*16; c.1676_1683delGAACCAGC, in FZD6 gene which causes a frameshift and creates a premature stop codon at position 16 of the new reading frame. Our molecular dynamics calculations predict that the pathogenicity of this frameshift mutation may be caused by the change in entropy of the protein with negative manner, disturbing the C-terminal domain structure, and hence interaction partners of FZD6. CONCLUSION: We identified a homozygous deletion mutation in FZD6 in a consanguineous Turkish family with nail dysplasia. We also provide a molecular mechanism about the effects of the deletion on the protein structure and its possible motions. This study provides a pathogenicity mechanism for this mutation in nail dysplasia for the first time.


Subject(s)
Frizzled Receptors/genetics , Genetic Predisposition to Disease , Mutation , Nails, Malformed/genetics , Adult , Amino Acid Sequence , Codon, Nonsense , Consanguinity , Female , Frameshift Mutation , Frizzled Receptors/chemistry , Genetic Association Studies , Homozygote , Humans , Models, Molecular , Pedigree , Protein Conformation , Sequence Analysis , Sequence Deletion , Turkey
16.
Am J Med Genet A ; 179(7): 1157-1172, 2019 07.
Article in English | MEDLINE | ID: mdl-30980518

ABSTRACT

3M syndrome is characterized by severe pre- and postnatal growth retardation, typical facial features, and normal intelligence. Homozygous or compound heterozygous mutations in either CUL7, OBSL1, or CCDC8 have been identified in the etiology so far. Clinical and molecular features of 24 patients (23 patients and a fetus) from 19 unrelated families with a clinical diagnosis of 3M syndrome were evaluated and genotype-phenotype correlations were investigated with the use of DNA sequencing, chromosomal microarray, and whole exome sequencing accordingly. A genetic etiology could be established in 20 patients (n = 20/24, 83%). Eleven distinct CUL7 or OBSL1 mutations, among which eight was novel, were identified in 18 patients (n = 18/24, 75%). Ten patients had CUL7 (n = 10/18, 56%) while eight had OBSL1 (n = 8/18, 44%) mutations. Birth weight and height standard deviation scores at admission were significantly (p < 0.05) lower in patients with CUL7 mutation compared to that of patients with OBSL1 mutation. Two patients with a similar phenotype had a de novo 20p13p deletion involving BMP2. No genetic etiology could be established in four patients (n = 4/28, 17%). This study yet represents the largest cohort of 3M syndrome patients from a single center in Turkey. Microdeletions involving BMP2 may cause a phenotype similar to 3M syndrome with some distinctive features. Larger cohort of patients are required to establish genotype-phenotype correlations in 3M syndrome.


Subject(s)
Bone Morphogenetic Protein 2/genetics , Cullin Proteins/genetics , Cytoskeletal Proteins/genetics , Dwarfism/genetics , Genetic Association Studies , Muscle Hypotonia/genetics , Mutation , Spine/abnormalities , Adolescent , Base Sequence , Bone Morphogenetic Protein 2/deficiency , Child , Child, Preschool , Chromosomes, Human, Pair 20 , Cohort Studies , Cullin Proteins/metabolism , Cytoskeletal Proteins/metabolism , Dwarfism/diagnosis , Dwarfism/metabolism , Dwarfism/pathology , Female , Fetus , Gene Expression , Genotype , Humans , Infant , Infant, Newborn , Male , Muscle Hypotonia/diagnosis , Muscle Hypotonia/metabolism , Muscle Hypotonia/pathology , Phenotype , Spine/metabolism , Spine/pathology , Exome Sequencing
17.
Am J Hum Genet ; 96(5): 841-9, 2015 May 07.
Article in English | MEDLINE | ID: mdl-25957469

ABSTRACT

Multiple pterygium syndrome (MPS) is a phenotypically and genetically heterogeneous group of rare Mendelian conditions characterized by multiple pterygia, scoliosis, and congenital contractures of the limbs. MPS typically segregates as an autosomal-recessive disorder, but rare instances of autosomal-dominant transmission have been reported. Whereas several mutations causing recessive MPS have been identified, the genetic basis of dominant MPS remains unknown. We identified four families affected by dominantly transmitted MPS characterized by pterygia, camptodactyly of the hands, vertebral fusions, and scoliosis. Exome sequencing identified predicted protein-altering mutations in embryonic myosin heavy chain (MYH3) in three families. MYH3 mutations underlie distal arthrogryposis types 1, 2A, and 2B, but all mutations reported to date occur in the head and neck domains. In contrast, two of the mutations found to cause MPS in this study occurred in the tail domain. The phenotypic overlap among persons with MPS, coupled with physical findings distinct from other conditions caused by mutations in MYH3, suggests that the developmental mechanism underlying MPS differs from that of other conditions and/or that certain functions of embryonic myosin might be perturbed by disruption of specific residues and/or domains. Moreover, the vertebral fusions in persons with MPS, coupled with evidence of MYH3 expression in bone, suggest that embryonic myosin plays a role in skeletal development.


Subject(s)
Arthrogryposis/genetics , Cytoskeletal Proteins/genetics , Myosins/biosynthesis , Arthrogryposis/physiopathology , Cytoskeletal Proteins/biosynthesis , Exome/genetics , Genetic Predisposition to Disease , High-Throughput Nucleotide Sequencing , Humans , Mutation , Myosins/genetics , Osteogenesis/genetics
19.
Am J Hum Genet ; 94(3): 405-14, 2014 Mar 06.
Article in English | MEDLINE | ID: mdl-24581741

ABSTRACT

Desbuquois dysplasia (DBQD) is a severe condition characterized by short stature, joint laxity, and advanced carpal ossification. Based on the presence of additional hand anomalies, we have previously distinguished DBQD type 1 and identified CANT1 (calcium activated nucleotidase 1) mutations as responsible for DBQD type 1. We report here the identification of five distinct homozygous xylosyltransferase 1 (XYLT1) mutations in seven DBQD type 2 subjects from six consanguineous families. Among the five mutations, four were expected to result in loss of function and a drastic reduction of XYLT1 cDNA level was demonstrated in two cultured individual fibroblasts. Because xylosyltransferase 1 (XT-I) catalyzes the very first step in proteoglycan (PG) biosynthesis, we further demonstrated in the two individual fibroblasts a significant reduction of cellular PG content. Our findings of XYLT1 mutations in DBQD type 2 further support a common physiological basis involving PG synthesis in the multiple dislocation group of disorders. This observation sheds light on the key role of the XT-I during the ossification process.


Subject(s)
Craniofacial Abnormalities/genetics , Dwarfism/genetics , Joint Instability/genetics , Mutation , Ossification, Heterotopic/genetics , Pentosyltransferases/genetics , Polydactyly/genetics , Adolescent , Adult , Bone and Bones/metabolism , Child , Consanguinity , DNA, Complementary/metabolism , Exome , Female , Fibroblasts/metabolism , Genetic Predisposition to Disease , Homozygote , Humans , Male , Microsatellite Repeats/genetics , Pentosyltransferases/metabolism , Proteoglycans/metabolism , Sequence Analysis, DNA , UDP Xylose-Protein Xylosyltransferase
20.
Genet Med ; 18(9): 882-91, 2016 09.
Article in English | MEDLINE | ID: mdl-26765342

ABSTRACT

PURPOSE: The Ehlers-Danlos syndrome (EDS), dermatosparaxis type, is a recessively inherited connective tissue disorder caused by deficient activity of ADAMTS-2, an enzyme that cleaves the aminoterminal propeptide domain of types I, II, and III procollagen. Only 10 EDS dermatosparaxis patients have been reported, all presenting a recognizable phenotype with characteristic facial gestalt, extreme skin fragility and laxity, excessive bruising, and sometimes major complications due to visceral and vascular fragility. METHODS: We report on five new EDS dermatosparaxis patients and provide a comprehensive overview of the current knowledge of the natural history of this condition. RESULTS: We identified three novel homozygous loss-of-function mutations (c.2927_2928delCT, p.(Pro976Argfs*42); c.669_670dupG, p.(Pro224Argfs*24); and c.2751-2A>T) and one compound heterozygous mutation (c.2T>C, p.? and c.884_887delTGAA, p.(Met295Thrfs26*)) in ADAMTS2 in five patients from four unrelated families. Three of these displayed a phenotype that was strikingly milder than that of previously reported patients. CONCLUSION: This study expands the clinical and molecular spectrum of the dermatosparaxis type of EDS to include a milder phenotypic variant and stresses the importance of good clinical criteria. To address this, we propose an updated set of criteria that accurately captures the multisystemic nature of the dermatosparaxis type of EDS.Genet Med 18 9, 882-891.


Subject(s)
ADAMTS Proteins/genetics , Ehlers-Danlos Syndrome/genetics , Adolescent , Adult , Child , Child, Preschool , Ehlers-Danlos Syndrome/complications , Ehlers-Danlos Syndrome/pathology , Female , Humans , Male , Mutation , Phenotype
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