Anju Shukla

A homozygous nonsense variant in IFT52 is associated with a human skeletal ciliopathy

Intraflagellar transport (IFT) is vital for the functioning of primary cilia. Defects in several components of IFT complexes cause a spectrum of ciliopathies with variable involvement of skeleton, brain, eyes, ectoderm and kidneys. We examined a child from a consanguineous family who had short stature, narrow thorax, short hands and feet, postaxial polydactyly of hands, pigmentary retinopathy, small teeth and skeletal dysplasia. The clinical phenotype of the child shows significant overlap with cranioectodermal dysplasia type I (Sensenbrenner syndrome). Whole‐exome sequencing revealed a homozygous nonsense variant p.R142* in IFT52 encoding an IFT‐B core complex protein as the probable cause of her condition. This is the first report of a human disease associated with IFT52.

Progressive Pseudorheumatoid Dysplasia

Abstract. A rare case of progressive pseudorheumatoid dysplasia (PPD) in a 9-year-old girl is presented. Clinically, chronic painless swollen joints, accompanied by progressive motion restriction and progressive walking difficulties, were found. Radiologically, there was enlargement of the epimetaphyseal portions of the large joints, metacarpal heads, and phalanges, and generalized platyspondyly with irregular delineation of the endplates of the vertebral bodies. The radioclinical features at the peripheral joints were originally misdiagnosed as juvenile rheumatoid arthritis (JRA), and the structural spinal abnormalities were neglected and interpreted as Scheuermanns disease. However, the absence of active inflammatory parameters argues against JRA, whereas the low age of onset of the irregularities at the vertebral endplates is an argument against the diagnosis of Scheuermanns disease. The combination of the dysplastic abnormalities of the spine, with platyspondyly and Scheuermann-like lesions at an unusually low age of onset, and radiological features mimicking JRA of the peripheral joints, is the clue to the diagnosis of this rare autosomal-recessive disease. This case is the first to document the MRI features of PPD of the spine.

Mutations in patients with osteogenesis imperfecta from consanguineous Indian families

Osteogenesis imperfecta (OI) is a spectrum of genetic disorders with decreased bone density and bone fragility. Most of the cases of OI are inherited in autosomal dominant fashion with mutations in COL1A1 or COL1A2 genes. Over last few years, twelve genes for autosomal recessive OI have been identified. In this study we have evaluated seven patients with OI from consanguineous Indian families. Homozygosity mapping using SNP microarray was done and selected candidate genes were sequenced. Candidate genes were identified in four out of seven patients studied. Four mutations, namely; a homozygous non-sense (p.Q178*) and a deletion (p.F277del) mutations in SERPINF1 gene, a missense mutation (p.M101K) in PPIB gene and a nonsense mutation (p.E45*) in CRTAP gene were identified. In three patients for whom the regions of homozygosity did not reveal any known autosomal recessive OI genes, exome sequencing was performed and we identified a known missense mutation (p.G1012S) in COL1A2 gene in one of the patients. As WNT1 gene was not properly covered in exome sequencing in one patient, the gene was sequenced and a homozygous in-frame deletion of four amino acids (p.Phe176_Leu179del) was identified. In one of the three cases the exome sequencing did not reveal a mutation in any known OI genes, suggesting the possibility of mutations in an unidentified gene. The phenotypes of all the cases are described. This work proves the power of homozygosity mapping followed by candidate gene sequencing approach for clinical application in consanguineous families.

Homozygous p.(Glu87Lys) variant in ISCA1 is associated with a multiple mitochondrial dysfunctions syndrome

The iron–sulfur (Fe–S) cluster (ISC) biogenesis pathway is indispensable for many fundamental biological processes and pathogenic variations in genes encoding several components of the Fe–S biogenesis machinery, such as NFU1, BOLA3, IBA57 and ISCA2 are already implicated in causing four types of multiple mitochondrial dysfunctions syndromes (MMDS). We report on two unrelated families, with two affected children each with early onset neurological deterioration, seizures, extensive white matter abnormalities, cortical migrational abnormalities, lactic acidosis and early demise. Exome sequencing of two affected individuals, one from each family, revealed a homozygous c.259G>A [p.(Glu87Lys)] variant in ISCA1 and Mendelian segregation was confirmed in both families. The ISCA1 variant lies in the only shared region of homozygosity between the two families suggesting the possibility of a founder effect. In silico functional analyses and structural modeling of the protein predict the identified ISCA1 variant to be detrimental to protein stability and function. Notably the phenotype observed in all affected subjects with the ISCA1 pathogenic variant is similar to that previously described in all four types of MMDS. Our findings suggest association of a pathogenic variant in ISCA1 with another MMDS.

Status of 25-hydroxyvitamin D deficiency and effect of vitamin D receptor gene polymorphisms on bone mineral density in thalassemia patients of North India

Abstract Background Bone disease comprising of low bone mineral density (BMD), bone pain, and fractures is a characteristic feature of thalassemia. Vitamin D receptors (VDRs – FokI, TaqI, and Bsml) polymorphisms are closely related to low BMD at the lumbar spine and hips which can be used as a useful genetic marker in predicting bone disease in these patients. Aim To find out the status of VDRs gene polymorphisms and its effect on osteoporosis in thalassemia patients of North Indian origin. Material and methods BMD was measured in 40 beta-thalassemia major patients by dual-energy X-ray densitometry (DXA). Serum vitamin D levels were estimated by enzyme linked immunosorbant assay. VDR gene polymorphisms (FokI, TaqI, and BsmI) were analyzed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) method. Results About 80.6% cases were found to be vitamin D deficient. Z score of BMD of lumbar spine and hips were −2.31 ± 1.18 and −2.09 ± 0.89. Osteoporotic lumbar spine was observed in 42.5% cases of thalassemia. A positive correlation of vitamin D level was found with Z score of BMD of lumbar spine (r = 0.398, P value = 0.027). Polymorphisms of FokI and BsmI were found significantly correlated with BMD of lumbar spine. However, no association of BMD was observed with TaqI polymorphism. Conclusion The present study showed a high prevalence of low BMD in thalassemia, suggesting that they should be targeted for DXA screening and osteoporosis prevention before permanent end organ bone damage occurs. The VDR genotyping can be used as additional test in individuals who are susceptible to osteoporosis so that early preventive measurements can be taken.

Cytokine gene polymorphisms in northern Indian women with recurrent miscarriages

OBJECTIVE To determine association of cytokine gene polymorphism with risk for recurrent miscarriages (RM). DESIGN Retrospective case-control study on northern Indian RM cases versus control subjects. SETTING Medical facility. PATIENT(S) A total of 200 women with at least three unexplained spontaneous abortions before 20 weeks of gestation. INTERVENTION(S) Subjects were genotyped by polymerase chain reaction amplification followed by restriction digestion and allele-specific oligonucleotides. MAIN OUTCOME MEASURE(S) Detection of pro- and antiinflammatory gene polymorphism genotypes and allele frequencies. RESULT(S) We applied dominant and recessive models of inheritance, showing no association among T(H)2 [interleukin (IL) 10 (592 C/A) and transforming growth factor β] gene polymorphisms, while significant association was observed between T(H)2 [IL-4 (C590T), IL-6 (G174C), IL-10 (1082A/G and 819C/T)], and T(H)1 [interferon-γ (+874A/T)] with RM compared with control subjects. However, when classification and regression tree analysis was applied, this effect disappeared and demonstrated that IL-10 plays an important role in maintenance of pregnancy. CONCLUSION(S) Interleukin-10 acts as an immunosuppressive by keeping a balance of pro- and antiinflammatory signals that coordinate the satisfactory development of pregnancy, placental growth, and remodeling for favorable pregnancy outcome.

Biallelic Loss of Proprioception-Related PIEZO2 Causes Muscular Atrophy with Perinatal Respiratory Distress, Arthrogryposis, and Scoliosis

We report ten individuals of four independent consanguineous families from Turkey, India, Libya, and Pakistan with a variable clinical phenotype that comprises arthrogryposis, spontaneously resolving respiratory insufficiency at birth, muscular atrophy predominantly of the distal lower limbs, scoliosis, and mild distal sensory involvement. Using whole-exome sequencing, SNPchip-based linkage analysis, DNA microarray, and Sanger sequencing, we identified three independent homozygous frameshift mutations and a homozygous deletion of two exons in PIEZO2 that segregated in all affected individuals of the respective family. The mutations are localized in the N-terminal and central region of the gene, leading to nonsense-mediated transcript decay and consequently to lack of PIEZO2 protein. In contrast, heterozygous gain-of-function missense mutations, mainly localized at the C terminus, cause dominant distal arthrogryposis 3 (DA3), distal arthrogryposis 5 (DA5), or Marden-Walker syndrome (MWKS), which encompass contractures of hands and feet, scoliosis, ophthalmoplegia, and ptosis. PIEZO2 encodes a mechanosensitive ion channel that plays a major role in light-touch mechanosensation and has recently been identified as the principal mechanotransduction channel for proprioception. Mice ubiquitously depleted of PIEZO2 are postnatally lethal. However, individuals lacking PIEZO2 develop a not life-threatening, slowly progressive disorder, which is likely due to loss of PIEZO2 protein in afferent neurons leading to disturbed proprioception causing aberrant muscle development and function. Here we report a recessively inherited PIEZO2-related disease and demonstrate that depending on the type of mutation and the mode of inheritance, PIEZO2 causes clinically distinguishable phenotypes.

Clinical utility of fetal autopsy and its impact on genetic counseling.

We aimed to analyze the utility of fetal autopsy in terms of its contribution to establishing a definitive diagnosis and its impact on genetic counseling.

Novel and recurrent mutations in WISP3 and an atypical phenotype

Novel and Recurrent Mutations in WISP3 and an Atypical Phenotype Gandham SriLakshmi Bhavani, Hitesh Shah, Ashwin B. Dalal, Anju Shukla, Sumita Danda, Shagun Aggarwal, Shubha R. Phadke, Neerja Gupta, Madhulika Kabra, Kalpana Gowrishankar, Anju Gupta, Meenakshi Bhat, Ratna D. Puri, Sunita Bijarnia-Mahay, Sheela Nampoothiri, Kavitha M. Mohanasundaram, S. Rajeswari, Akhil M. Kulkarni, Muralidhar L. Kulkarni, Prajnya Ranganath, A. Radha Ramadevi, Sankar V. Hariharan, and Katta Mohan Girisha* Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India Department of Orthopedics, Pediatric Orthopedics Services, Kasturba Medical College, Manipal University, Manipal, India Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, India Department of Medical Genetics, Nizam’s Institute of Medical Sciences, Hyderabad, India Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India Department of Pediatrics, Division of Genetics, All India Institute of Medical Science, New Delhi, India Department of Medical Genetics, Kanchi Kamakoti Childs Trust Hospital, Chennai, Tamil Nadu, India Department of Pediatrics, Post Graduate Institute of Medical Education and Research, Chandigarh, India Centre for Human Genetics, Bangalore, India Centre of Medical Genetics, Sir Ganga Ram Hospital, New Delhi, India Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Ponekkara, Cochin, Kerala, India Department of Rheumatology, Madras Medical College, Chennai, India Department of Radiodiagnosis, SS Institute of Medical Sciences and Research Centre, Davangere, India Department of Pediatrics, Jagadguru Jayadeva Murugarajendra Medical College, Davangere, India Department of Clinical Genetics, Genetics Unit, Rainbow Children Hospital, Hyderabad, India Department of Pediatrics, Sree Avittom Thirunal Hospital, Government Medical College, Trivandrum, India

Noonan syndrome in diverse populations

Noonan syndrome (NS) is a common genetic syndrome associated with gain of function variants in genes in the Ras/MAPK pathway. The phenotype of NS has been well characterized in populations of European descent with less attention given to other groups. In this study, individuals from diverse populations with NS were evaluated clinically and by facial analysis technology. Clinical data and images from 125 individuals with NS were obtained from 20 countries with an average age of 8 years and female composition of 46%. Individuals were grouped into categories of African descent (African), Asian, Latin American, and additional/other. Across these different population groups, NS was phenotypically similar with only 2 of 21 clinical elements showing a statistically significant difference. The most common clinical characteristics found in all population groups included widely spaced eyes and low‐set ears in 80% or greater of participants, short stature in more than 70%, and pulmonary stenosis in roughly half of study individuals. Using facial analysis technology, we compared 161 Caucasian, African, Asian, and Latin American individuals with NS with 161 gender and age matched controls and found that sensitivity was equal to or greater than 94% for all groups, and specificity was equal to or greater than 90%. In summary, we present consistent clinical findings from global populations with NS and additionally demonstrate how facial analysis technology can support clinicians in making accurate NS diagnoses. This work will assist in earlier detection and in increasing recognition of NS throughout the world.