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Kamdar P, Geetha TS, Palocaren T, Kandagaddala M, Chinniah PK, Murugan S, Vedam R, Danda S. Diagnostic exome identifies a novel PRKG2 mutation in a proband with skeletal dysplasia. Clin Genet 2024; 105:453-454. [PMID: 38072398 DOI: 10.1111/cge.14465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/29/2023] [Accepted: 11/22/2023] [Indexed: 03/07/2024]
Abstract
This graphic abstract combines pedigree, dysmorphology features, radiographs, and the PRKG2 protein domain, specifically the CNB-A regulatory domain, which harbors a mutation resulting in premature protein termination.
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Affiliation(s)
- Payal Kamdar
- Clinical Genetics, Christian Medical College, Vellore, India
| | | | - Thomas Palocaren
- Paediatric Orthopaedics, Christian Medical College, Vellore, India
| | | | | | | | | | - Sumita Danda
- Clinical Genetics, Christian Medical College, Vellore, India
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Andrews SV, Kukkle PL, Menon R, Geetha TS, Goyal V, Kandadai RM, Kumar H, Borgohain R, Mukherjee A, Wadia PM, Yadav R, Desai S, Kumar N, Joshi D, Murugan S, Biswas A, Pal PK, Oliver M, Nair S, Kayalvizhi A, Samson PL, Deshmukh M, Bassi A, Sandeep C, Mandloi N, Davis OB, Roberts MA, Leto DE, Henry AG, Di Paolo G, Muthane U, Das SK, Peterson AS, Sandmann T, Gupta R, Ramprasad VL. The Genetic Drivers of Juvenile, Young, and Early-Onset Parkinson's Disease in India. Mov Disord 2024; 39:339-349. [PMID: 38014556 DOI: 10.1002/mds.29676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/18/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Recent studies have advanced our understanding of the genetic drivers of Parkinson's disease (PD). Rare variants in more than 20 genes are considered causal for PD, and the latest PD genome-wide association study (GWAS) identified 90 independent risk loci. However, there remains a gap in our understanding of PD genetics outside of the European populations in which the vast majority of these studies were focused. OBJECTIVE The aim was to identify genetic risk factors for PD in a South Asian population. METHODS A total of 674 PD subjects predominantly with age of onset (AoO) ≤50 years (encompassing juvenile, young, or early-onset PD) were recruited from 10 specialty movement disorder centers across India over a 2-year period; 1376 control subjects were selected from the reference population GenomeAsia, Phase 2. We performed various case-only and case-control genetic analyses for PD diagnosis and AoO. RESULTS A genome-wide significant signal for PD diagnosis was identified in the SNCA region, strongly colocalizing with SNCA region signal from European PD GWAS. PD cases with pathogenic mutations in PD genes exhibited, on average, lower PD polygenic risk scores than PD cases lacking any PD gene mutations. Gene burden studies of rare, predicted deleterious variants identified BSN, encoding the presynaptic protein Bassoon that has been previously associated with neurodegenerative disease. CONCLUSIONS This study constitutes the largest genetic investigation of PD in a South Asian population to date. Future work should seek to expand sample numbers in this population to enable improved statistical power to detect PD genes in this understudied group. © 2023 Denali Therapeutics and The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Shan V Andrews
- Denali Therapeutics, South San Francisco, California, USA
| | - Prashanth L Kukkle
- Manipal Hospital, Bangalore, India
- Parkinson's Disease and Movement Disorders Clinic, Bangalore, India
| | | | | | - Vinay Goyal
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
- Medanta Hospital, New Delhi, India
- Medanta, The Medicity, Gurgaon, India
| | - Rukmini Mridula Kandadai
- Nizams Institute of Medical Sciences (NIMS), Hyderabad, India
- Citi Neuro Centre, Hyderabad, India
| | | | - Rupam Borgohain
- Nizams Institute of Medical Sciences (NIMS), Hyderabad, India
- Citi Neuro Centre, Hyderabad, India
| | - Adreesh Mukherjee
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Ravi Yadav
- National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Soaham Desai
- Department of Neurology, Shree Krishna Hospital and Pramukhaswami Medical College, Bhaikaka University, Anand, India
| | - Niraj Kumar
- All India Institute of Medical Sciences, Rishikesh, India
- All India Institute of Medical Sciences, Bibinagar (Hyderabad Metropolitan Region), Bibinagar, India
| | - Deepika Joshi
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | | | - Atanu Biswas
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | - Pramod K Pal
- National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | | | | | | | | | | | | | | | | | - Oliver B Davis
- Denali Therapeutics, South San Francisco, California, USA
| | | | - Dara E Leto
- Denali Therapeutics, South San Francisco, California, USA
| | | | | | - Uday Muthane
- Parkinson and Ageing Research Foundation, Bangalore, India
| | - Shymal K Das
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
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Srinivas SM, Dhar S, Gowdra A, Saha A, Sundararajan L, Geetha TS, Banerjee R, Malakar R, Sil A, Lakshminarayana Shyam Prasad A. Filaggrin gene polymorphisms in Indian children with atopic dermatitis: A cross-sectional multicentre study. Indian J Dermatol Venereol Leprol 2023; 89:819-827. [PMID: 37067103 DOI: 10.25259/ijdvl_37_2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 10/15/2022] [Indexed: 04/18/2023]
Abstract
Background Filaggrin (FLG) gene encoding the protein filaggrin plays an important role in barrier function of the skin and its alteration is a predisposing factor for atopic dermatitis. FLG gene variants result in absent or decreased filaggrin protein. Worldwide, the prevalence of FLG variants ranges from 14 to 56%. FLG null variants are distinct in each population. Objectives To study the FLG gene polymorphisms in Indian children and attempt a genotype-phenotype correlation in atopic dermatitis. Methods This was a cross-sectional, multicentre study conducted on 75 Indian children. Demographic details, clinical features and identified FLG null variants were recorded. We performed a whole gene sequencing of the entire FLG coding region using next-generation sequencing technology. Results The prevalence of FLG null variants was 34.7%. A total of 20 different FLG loss of function variants in 26 children were documented. Sixteen (80%) variants were novel and four (20%) were previously reported in Asian and European populations. We found a statistically significant association between FLG variants with early age of onset of atopic dermatitis (P = 0.016) and elevated serum IgE levels (P = 0.051). There was no significant difference between atopic dermatitis phenotypes in children having one variant as compared to children harbouring two or more null variants. Limitation Small sample size. Conclusion Our study reports a unique set of FLG variants different from Asian and European populations, with these variants being significantly associated with an early age of onset of atopic dermatitis and elevated serum IgE levels.
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Affiliation(s)
- Sahana M Srinivas
- Department of Pediatric Dermatology, Indira Gandhi Institute of Child Health, Bengaluru, Karnataka, India
| | - Sandipan Dhar
- Department of Pediatric Dermatology, Institute of Child Health, Kolkata, West Bengal, India
| | - Aruna Gowdra
- Department of Microbiology, Indira Gandhi Institute of Child Health, Bengaluru, Karnataka, India
| | - Abhijit Saha
- Department of Pediatric Dermatology, Institute of Child Health, Kolkata, West Bengal, India
| | | | | | - Raghubir Banerjee
- Department of Pediatric Dermatology, Institute of Child Health, Kolkata, West Bengal, India
| | - Rajib Malakar
- Department of Pediatric Dermatology, Institute of Child Health, Kolkata, West Bengal, India
| | - Amrita Sil
- Department of Pharmacology, Rampurhat Government Medical College and Hospital, Birbhum, West Bengal, India
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Sanga S, Chakraborty S, Bardhan M, Polavarapu K, Kumar VP, Bhattacharya C, Nashi S, Vengalil S, Geetha TS, Ramprasad V, Nalini A, Basu A, Acharya M. Identification of a shared, common haplotype segregating with an SGCB c.544 T > G mutation in Indian patients affected with sarcoglycanopathy. Sci Rep 2023; 13:15095. [PMID: 37699968 PMCID: PMC10497502 DOI: 10.1038/s41598-023-41487-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/28/2023] [Indexed: 09/14/2023] Open
Abstract
Sarcoglycanopathy is the most frequent form of autosomal recessive limb-girdle muscular dystrophies caused by mutations in SGCB gene encoding beta-sarcoglycan proteins. In this study, we describe a shared, common haplotype co-segregating in 14 sarcoglycanopathy cases from 13 unrelated families from south Indian region with the likely pathogenic homozygous mutation c.544 T > G (p.Thr182Pro) in SGCB. Haplotype was reconstructed based on 10 polymorphic markers surrounding the c.544 T > G mutation in the cases and related family members as well as 150 unrelated controls from Indian populations using PLINK1.9. We identified haplotype H1 = G, A, G, T, G, G, A, C, T, G, T at a significantly higher frequency in cases compared to related controls and unrelated control Indian population. Upon segregation analysis within the family pedigrees, H1 is observed to co-segregate with c.544 T > G in a homozygous state in all the pedigrees of cases except one indicating a probable event of founder effect. Furthermore, Identical-by-descent and inbreeding coefficient analysis revealed relatedness among 33 new pairs of seemingly unrelated individuals from sarcoglycanopathy cohort and a higher proportion of homozygous markers, thereby indicating common ancestry. Since all these patients are from the south Indian region, we suggest this region to be a primary target of mutation screening in patients diagnosed with sarcoglycanopathy.
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Affiliation(s)
- Shamita Sanga
- National Institute of Biomedical Genomics, P.O: N.S.S, Kalyani, West Bengal, 741251, India
| | - Sudipta Chakraborty
- National Institute of Biomedical Genomics, P.O: N.S.S, Kalyani, West Bengal, 741251, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Mainak Bardhan
- National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Kiran Polavarapu
- National Institute of Mental Health and Neurosciences, Bangalore, India
| | | | - Chandrika Bhattacharya
- National Institute of Biomedical Genomics, P.O: N.S.S, Kalyani, West Bengal, 741251, India
| | - Saraswati Nashi
- National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Seena Vengalil
- National Institute of Mental Health and Neurosciences, Bangalore, India
| | | | | | - Atchayaram Nalini
- National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Analabha Basu
- National Institute of Biomedical Genomics, P.O: N.S.S, Kalyani, West Bengal, 741251, India
| | - Moulinath Acharya
- National Institute of Biomedical Genomics, P.O: N.S.S, Kalyani, West Bengal, 741251, India.
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Joshi G, Arthur NBJ, Geetha TS, Datari PVR, Modak K, Roy D, Chaudhury AD, Sundaraganesan P, Priyanka S, Na F, Ramprasad V, Abraham A, Srivastava VM, Srivastava A, Kulkarni UP, George B, Velayudhan SR. Comprehensive laboratory diagnosis of Fanconi anaemia: comparison of cellular and molecular analysis. J Med Genet 2023; 60:801-809. [PMID: 36894310 PMCID: PMC10423531 DOI: 10.1136/jmg-2022-108714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/03/2022] [Indexed: 03/11/2023]
Abstract
BACKGROUND Fanconi anaemia (FA) is a rare inherited bone marrow failure disease caused by germline pathogenic variants in any of the 22 genes involved in the FA-DNA interstrand crosslink (ICL) repair pathway. Accurate laboratory investigations are required for FA diagnosis for the clinical management of the patients. We performed chromosome breakage analysis (CBA), FANCD2 ubiquitination (FANCD2-Ub) analysis and exome sequencing of 142 Indian patients with FA and evaluated the efficiencies of these methods in FA diagnosis. METHODS We performed CBA and FANCD2-Ub analysis in the blood cells and fibroblasts of patients with FA. Exome sequencing with improved bioinformatics to detect the single number variants and CNV was carried out for all the patients. Functional validation of the variants with unknown significance was done by lentiviral complementation assay. RESULTS Our study showed that FANCD2-Ub analysis and CBA on peripheral blood cells could diagnose 97% and 91.5% of FA cases, respectively. Exome sequencing identified the FA genotypes consisting of 45 novel variants in 95.7% of the patients with FA. FANCA (60.2%), FANCL (19.8%) and FANCG (11.7%) were the most frequently mutated genes in the Indian population. A FANCL founder mutation c.1092G>A; p.K364=was identified at a very high frequency (~19%) in our patients. CONCLUSION We performed a comprehensive analysis of the cellular and molecular tests for the accurate diagnosis of FA. A new algorithm for rapid and cost-effective molecular diagnosis for~90% of FA cases has been established.
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Affiliation(s)
- Gaurav Joshi
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, India
| | | | | | | | - Kirti Modak
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Debanjan Roy
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anurag Dutta Chaudhury
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | | | - Sweety Priyanka
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Fouzia Na
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | | | - Aby Abraham
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Vivi M Srivastava
- Department of Cytogenetics, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Alok Srivastava
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
- Center for Stem Cell Research, Vellore, Tamil Nadu, India
| | - Uday Prakash Kulkarni
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Biju George
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Shaji R Velayudhan
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
- Center for Stem Cell Research, Vellore, Tamil Nadu, India
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Varshney K, Narayanachar SG, Girisha KM, Bhavani GS, Narayanan D, Phadke S, Nampoothiri S, Udupi GA, Raghupathy P, Nair M, Geetha TS, Bhat M. Clinical, radiological and molecular studies in 24 individuals with Dyggve-Melchior-Clausen dysplasia and Smith-McCort dysplasia from India. J Med Genet 2023; 60:204-211. [PMID: 35477554 DOI: 10.1136/jmedgenet-2021-108098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 04/10/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Dyggve-Melchior-Clausen dysplasia (DMC) and Smith-McCort dysplasia (SMC types 1 and 2) are rare spondyloepimetaphyseal dysplasias with identical radiological findings. The presence of intellectual disability in DMC and normal intellect in SMC differentiates the two. DMC and SMC1 are allelic and caused by homozygous or compound heterozygous variants in DYM. SMC2 is caused by variations in RAB33B. Both DYM and RAB33B are important in intravesicular transport and function in the Golgi apparatus. METHODS Detailed clinical phenotyping and skeletal radiography followed by molecular testing were performed in all affected individuals. Next-generation sequencing and Sanger sequencing were used to confirm DYM and RAB33B variants. Sanger sequencing of familial variants was done in all parents. RESULTS 24 affected individuals from seven centres are described. 18 had DMC and 6 had SMC2. Parental consanguinity was present in 15 of 19 (79%). Height <3 SD and gait abnormalities were seen in 20 and 14 individuals, respectively. The characteristic radiological findings of lacy iliac crests and double-humped vertebral bodies were seen in 96% and 88% of the affected. Radiological findings became attenuated with age. 23 individuals harboured biallelic variants in either DYM or RAB33B. Fourteen different variants were identified, out of which 10 were novel. The most frequently occurring variants in this group were c.719 C>A (3), c.1488_1489del (2), c.1484dup (2) and c.1563+2T>C (2) in DYM and c.400C>T (2) and c.186del (2) in RAB33B. The majority of these have not been reported previously. CONCLUSION This large cohort from India contributes to the increasing knowledge of clinical and molecular findings in these rare 'Golgipathies'.
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Affiliation(s)
- Kruti Varshney
- Department of Clinical Genetics, Centre for Human Genetics, Bangalore, Karnataka, India
| | | | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Dhanyalakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shubha Phadke
- Department of Medical Genetics, SGPGIMS, Lucknow, Uttar Pradesh, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Reseacrh Centre, Kochi, Kerala, India
| | - Gautham Arunachal Udupi
- Department of Human Genetics, National Institute of Mental Health and Neurosciences, Bangalore, Karnataka, India
| | - Palany Raghupathy
- Department of Paediatric Endocrinology, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | - Mohandas Nair
- Department of Paediatrics, Government Medical College, Kozhikode, Kerala, India
| | | | - Meenakshi Bhat
- Department of Clinical Genetics, Centre for Human Genetics, Bangalore, Karnataka, India
- Department of Paediatric Genetics, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
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Nashi S, Polavarapu K, Bardhan M, Anjanappa RM, Preethish-Kumar V, Vengalil S, Padmanabha H, Geetha TS, Prathyusha PV, Ramprasad V, Joshi A, Chawla T, Unnikrishnan G, Sharma P, Huddar A, Uppilli B, Thomas A, Baskar D, Mathew S, Menon D, Arunachal G, Faruq M, Thangaraj K, Nalini A. Genotype-phenotype correlation and natural history study of dysferlinopathy: a single-centre experience from India. Neurogenetics 2023; 24:43-53. [PMID: 36580222 DOI: 10.1007/s10048-022-00707-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/15/2022] [Indexed: 12/30/2022]
Abstract
Dysferlinopathies are a group of limb-girdle muscular dystrophies causing significant disability in the young population. There is a need for studies on large cohorts to describe the clinical, genotypic and natural history in our subcontinent. To describe and correlate the clinical, genetic profile and natural history of genetically confirmed dysferlinopathies. We analysed a retrospective cohort of patients with dysferlinopathy from a single quaternary care centre in India. A total of 124 patients with dysferlinopathy were included (40 females). Median age at onset and duration of illness were 21 years (range, 13-50) and 48 months (range, 8-288), respectively. The average follow-up period was 60 months (range, 12-288). Fifty-one percent had LGMD pattern of weakness at onset; 23.4% each had Miyoshi and proximo-distal type while isolated hyperCKemia was noted in 1.6%. About 60% were born to consanguineous parents and 26.6% had family history of similar illness. Twenty-three patients (18.6%) lost ambulation at follow-up; the median time to loss of independent ambulation was 120 months (range, 72-264). Single-nucleotide variants (SNVs) constituted 78.2% of patients; INDELs 14.5% and 7.3% had both SNVs and INDELs. Earlier age at onset was noted with SNVs. There was no correlation between the other clinical parameters and ambulatory status with the genotype. Thirty-seven (45.7%) novel pathogenic/likely pathogenic (P/LP) variants were identified out of a total of 81 variations. The c.3191G > A variant was the most recurrent mutation. Our cohort constitutes a clinically and genetically heterogeneous group of dysferlinopathies. There is no significant correlation between the clinico-genetic profile and the ambulatory status.
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Affiliation(s)
- Saraswati Nashi
- Department of Neurology, Neuroscience Faculty Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | - Kiran Polavarapu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - Mainak Bardhan
- Department of Neurology, Neuroscience Faculty Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | - Ram Murthy Anjanappa
- Department of Neurology, Neuroscience Faculty Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | - Veeramani Preethish-Kumar
- Department of Neurology, Neuroscience Faculty Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | - Seena Vengalil
- Department of Neurology, Neuroscience Faculty Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | - Hansashree Padmanabha
- Department of Neurology, Neuroscience Faculty Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | | | - P V Prathyusha
- Department of Biostatistics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | | | - Aditi Joshi
- CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi, India
| | - Tanushree Chawla
- Department of Neurology, Neuroscience Faculty Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | - Gopikirshnan Unnikrishnan
- Department of Neurology, Neuroscience Faculty Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | - Pooja Sharma
- CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi, India
| | - Akshata Huddar
- Department of Neurology, Neuroscience Faculty Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | | | - Abel Thomas
- Department of Neurology, Neuroscience Faculty Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | - Dipti Baskar
- Department of Neurology, Neuroscience Faculty Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | - Susi Mathew
- CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi, India
| | - Deepak Menon
- Department of Neurology, Neuroscience Faculty Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | - Gautham Arunachal
- Department of Human Genetics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi, India
| | | | - Atchayaram Nalini
- Department of Neurology, Neuroscience Faculty Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India.
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8
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Mandal A, Khandelwal P, Geetha TS, Murugan S, Meena J, Jana M, Sinha A, Kumar R, Seth A, Hari P, Bagga A. Metabolic and Genetic Evaluation in Children with Nephrolithiasis. Indian J Pediatr 2022; 89:1243-1250. [PMID: 35819704 DOI: 10.1007/s12098-022-04234-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/07/2022] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To evaluate metabolic and genetic abnormalities in children with nephrolithiasis attending a referral center in North India. METHODS The patients aged 1-18 y old with nephrolithiasis underwent biochemical evaluation and whole-exome sequencing. The authors evaluated for monogenic variants in 56 genes and compared allele frequency of 39 reported polymorphisms between patients and 1739 controls from the GenomeAsia 100 K database. RESULTS Fifty-four patients, aged 9.1 ± 3.7 y were included. Stones were bilateral in 42.6%, familial in 33.3%, and recurrent in 25.9%. The most common metabolic abnormalities were hypercalciuria (35.2%), hyperoxaluria (24.1%), or both (11.1%), while xanthinuria (n = 3), cystinuria (n = 1), and hyperuricosuria (n = 1) were rare. Exome sequencing identified an etiology in 6 (11.1%) patients with pathogenic/likely pathogenic causative variants. Three variants in MOCOS and one in ATP7B were pathogenic; likely pathogenic variants included MOCOS (n = 2), AGXT, and SLC7A9 (n = 1, each). Causality was not attributed to two SLC34A1 likely pathogenic variants, due to lack of matching phenotype and dominant family history. Compared to controls, allele frequency of the polymorphism TRPV5 rs4252402 was significantly higher in familial stone disease (allele frequency 0.47 versus 0.53; OR 3.2, p = 0.0001). CONCLUSION The chief metabolic abnormalities were hypercalciuria and hyperoxaluria. A monogenic etiology was identified in 11% with pathogenic or likely pathogenic variants using a gene panel for nephrolithiasis. Heterozygous missense variants in the sodium-phosphate cotransporter SLC34A1 were common and required evaluation for attributing pathogenicity. Rare polymorphisms in TRPV5 might increase the risk of familial stones. These findings suggest that a combination of metabolic and genetic evaluation is useful for determining the etiology of nephrolithiasis.
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Affiliation(s)
- Anita Mandal
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Kidney Diseases, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Priyanka Khandelwal
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Kidney Diseases, All India Institute of Medical Sciences, New Delhi, 110029, India
| | | | | | - Jitendra Meena
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Kidney Diseases, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Manisha Jana
- Department of Radiodiagnosis, All India Institute of Medical Sciences, New Delhi, India
| | - Aditi Sinha
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Kidney Diseases, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Rajeev Kumar
- Department of Urology, All India Institute of Medical Sciences, New Delhi, India
| | - Amlesh Seth
- Department of Urology, All India Institute of Medical Sciences, New Delhi, India
| | - Pankaj Hari
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Kidney Diseases, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Arvind Bagga
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Kidney Diseases, All India Institute of Medical Sciences, New Delhi, 110029, India.
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9
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Kukkle PL, Geetha TS, Chaudhary R, Sathirapongsasuti JF, Goyal V, Kandadai RM, Kumar H, Borgohain R, Mukherjee A, Oliver M, Sunil M, Mootor MFE, Kapil S, Mandloi N, Wadia PM, Yadav R, Desai S, Kumar N, Biswas A, Pal PK, Muthane UB, Das SK, Sakthivel Murugan SM, Peterson AS, Stawiski EW, Seshagiri S, Gupta R, Ramprasad VL, Prai PRAOI. Genome-Wide Polygenic Score Predicts Large Number of High Risk Individuals in Monogenic Undiagnosed Young Onset Parkinson's Disease Patients from India. Adv Biol (Weinh) 2022; 6:e2101326. [PMID: 35810474 DOI: 10.1002/adbi.202101326] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 05/15/2022] [Indexed: 01/28/2023]
Abstract
Parkinson's disease (PD) is a genetically heterogeneous neurodegenerative disease with poorly defined environmental influences. Genomic studies of PD patients have identified disease-relevant monogenic genes, rare variants of significance, and polygenic risk-associated variants. In this study, whole genome sequencing data from 90 young onset Parkinson's disease (YOPD) individuals are analyzed for both monogenic and polygenic risk. The genetic variant analysis identifies pathogenic/likely pathogenic variants in eight of the 90 individuals (8.8%). It includes large homozygous coding exon deletions in PRKN and SNV/InDels in VPS13C, PLA2G6, PINK1, SYNJ1, and GCH1. Eleven rare heterozygous GBA coding variants are also identified in 13 (14.4%) individuals. In 34 (56.6%) individuals, one or more variants of uncertain significance (VUS) in PD/PD-relevant genes are observed. Though YOPD patients with a prioritized pathogenic variant show a low polygenic risk score (PRS), patients with prioritized VUS or no significant rare variants show an increased PRS odds ratio for PD. This study suggests that both significant rare variants and polygenic risk from common variants together may contribute to the genesis of PD. Further validation using a larger cohort of patients will confirm the interplay between monogenic and polygenic variants and their use in routine genetic PD diagnosis and risk assessment.
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Affiliation(s)
- Prashanth Lingappa Kukkle
- Department of Neurology, Manipal Hospital, Miller Road, Bangalore, 560052, India.,Department of Neurology, Parkinson's Disease and Movement Disorders Clinic, Bangalore, 560010, India.,Department of Neurology, All India Institute of Medical Sciences, Rishikesh, 249201, India
| | - Thenral S Geetha
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
| | - Ruchi Chaudhary
- Research Department, MedGenome Inc., 348 Hatch Drive, Foster City, CA, 94404, USA
| | | | - Vinay Goyal
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), New Delhi, 110608, India.,Department of Neurology, Medanta Hospital, New Delhi, 110047, India.,Department of Neurology, Medanta, The Medicity, Gurgaon, 122006, India
| | | | - Hrishikesh Kumar
- Department of Neurology, Institute of Neurosciences Kolkata, Kolkata, 700007, India
| | - Rupam Borgohain
- Department of Neurology, Nizams Institute of Medical Sciences (NIMS), Hyderabad, 500082, India
| | - Adreesh Mukherjee
- Department of Neurology, Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, 700020, India
| | - Merina Oliver
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
| | - Meeta Sunil
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
| | | | - Shruti Kapil
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
| | - Nitin Mandloi
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
| | - Pettarusp M Wadia
- Department of Neurology, Jaslok Hospital and Research Centre, Mumbai, 400026, India
| | - Ravi Yadav
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India
| | - Soaham Desai
- Department of Neurology, Shree Krishna Hospital and Pramukhswami Medical College, Bhaikaka University, Karamsad, 388325, India
| | - Niraj Kumar
- Department of Neurology, All India Institute of Medical Sciences, Rishikesh, 249201, India
| | - Atanu Biswas
- Department of Neurology, Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, 700020, India
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India
| | - Uday B Muthane
- Department of Neurology, Parkinson and Ageing Research Foundation, Bangalore, 560095, India
| | - Shymal Kumar Das
- Department of Neurology, Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, 700020, India
| | | | - Andrew S Peterson
- Research Department, MedGenome Inc., 348 Hatch Drive, Foster City, CA, 94404, USA
| | - Eric W Stawiski
- Research Department, MedGenome Inc., 348 Hatch Drive, Foster City, CA, 94404, USA
| | | | - Ravi Gupta
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
| | - Vedam L Ramprasad
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
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10
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Yadav N, Kirola L, Geetha TS, Mittal K, Kadandale J, Yogev Y, Birk OS, Gupta N, Balakrishnan P, Jana M, Gupta M, Kabra M, Thelma BK. A novel leaky splice variant in centromere protein J (CENPJ)-associated Seckel syndrome. Ann Hum Genet 2022; 86:245-256. [PMID: 35451063 DOI: 10.1111/ahg.12469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/12/2022] [Accepted: 03/31/2022] [Indexed: 11/29/2022]
Abstract
Primary microcephaly and Seckel syndrome are rare genetically and clinically heterogenous brain development disorders. Several exonic/splicing mutations are reported for these disorders to date, but ∼40% of all cases remain unexplained. We aimed to uncover the genetic correlate(s) in a family of multiple siblings with microcephaly. A novel homozygous intronic variant (NC_000013.10:g.25459823T>C) in CENPJ (13q12) segregating with all four affected male siblings was identified by exome sequencing and validated by targeted linkage approach (logarithm of the odds score 1.8 at θ 0.0). RT-PCR of CENPJ in affected siblings using their EBV derived cell lines showed aberrant transcripts suggestive of exon skipping confirmed by Sanger sequencing. Significantly reduced wild type transcript/protein in the affected siblings having the splice variant indicates a leaky gene expression of pathological relevance. Based on known CENPJ function, assessing for mitotic alterations revealed defect in centrosome duplication causing mono/multicentrosome(s) at prophase, delayed metaphase, and unequal chromosomal segregation in patient cells. Clinical features witnessed in this study expand the spectrum of CENPJ-associated primary microcephaly and Seckel syndrome. Furthermore, besides the importance of regulatory variants in classical monogenic disorders these findings provide new insights into splice site biology with possible implications for ASO-based therapies.
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Affiliation(s)
- Navneesh Yadav
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Laxmi Kirola
- Department of Genetics, University of Delhi South Campus, New Delhi, India.,Department of Molecular and Human Genetics, Banaras Hindu University, Uttar Pradesh, India
| | - Thenral S Geetha
- Department of Genetics, University of Delhi South Campus, New Delhi, India.,Medgenome, Labs, Bangalore, India
| | - Kirti Mittal
- Department of Genetics, University of Delhi South Campus, New Delhi, India.,Lunenfeld-Tanenbaum, Research Institute, Toronto, Canada
| | | | - Yuval Yogev
- The Morris Kahn Laboratory of Human Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Neerja Gupta
- Division of Genetics, Department of Paediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Prahlad Balakrishnan
- Division of Genetics, Department of Paediatrics, All India Institute of Medical Sciences, New Delhi, India.,Genes2me, Haryana, India
| | - Manisha Jana
- Department of Radiodiagnosis, All India Institute of Medical Sciences, New Delhi, India
| | - Meena Gupta
- Department of Neurology, Institute of Human Behaviour and Allied Sciences, New Delhi, India.,Department of Neurology, Paras Hospitals, Haryana, India
| | - Madhulika Kabra
- Division of Genetics, Department of Paediatrics, All India Institute of Medical Sciences, New Delhi, India
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11
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Olszewska DA, Shetty R, Geetha TS, Ramprasad VL, Lang AE, Prashanth L. Oculogyric crisis phenotype of levodopa‐induced ocular dyskinesia. Mov Disord Clin Pract 2022; 9:390-393. [PMID: 36989007 PMCID: PMC8974885 DOI: 10.1002/mdc3.13416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/04/2021] [Accepted: 01/22/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Diana A. Olszewska
- Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital Toronto Ontario Canada
| | | | | | | | - Anthony E. Lang
- Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital Toronto Ontario Canada
| | - L.K. Prashanth
- Center for Parkinson’s Disease and Movement Disorders Clinic, Vikram Hospital (Unit of Manipal Hospitals) Bangalore India
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12
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Shankar S, Pande A, Geetha TS, Raichurkar K, Sakpal M, Lochan R, Asthana S. A New Variant of an Old Itch: Novel Missense Variant in ABCB4 Presenting with Intractable Pruritus. J Clin Exp Hepatol 2022; 12:701-704. [PMID: 35535055 PMCID: PMC9077154 DOI: 10.1016/j.jceh.2021.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/21/2021] [Indexed: 12/12/2022] Open
Abstract
We report a novel homozygous missense variant in ABCB4 gene in a Yemeni child born to consanguineous parents, with a significant family history of liver disease-related deaths, resulting in a progressive familial intrahepatic cholestasis (PFIC) type 3 phenotype requiring liver transplantation for intractable pruritus.
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Key Words
- ABCB11, ATP binding cassette subfamily B member 11
- ABCB4 mutation
- ABCB4, ATP-binding cassette subfamily B member 4
- ALT, Alanine aminotransferase
- AST, Aspartate aminotransferase
- ATP8B1, ATPase phospholipid transporting 8B1
- BSEP, bile salt export pump
- FXR, farnesoid X receptor
- GGT, Gamma Glutamyl- Transpeptidase
- ICP, Intrahepatic cholestasis of pregnancy
- MDR3, multidrug resistance p-glycoprotein 3
- MYO5B, Myosin 5B
- PFIC
- PFIC, Progressive familial intrahepatic cholestasis
- TJP2, Tight junction protein 2
- congenital liver disease
- liver transplantation
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Affiliation(s)
- Sahana Shankar
- Division of Pediatric Gastroenterology, Department of Pediatrics, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, India
| | - Apurva Pande
- Aster Integrated Liver Care, Aster CMI Hospital, Bangalore, India
| | - Thenral S. Geetha
- Medgenome Labs Pvt Ltd, 3rd Floor, Narayana Netralaya Building, # 258/A, Bommasandra, Hosur Road, Narayana Health City, Bangalore, 560 099, India
| | | | | | - Rajiv Lochan
- Aster Integrated Liver Care, Aster CMI Hospital, Bangalore, India
| | - Sonal Asthana
- Aster Integrated Liver Care, Aster CMI Hospital, Bangalore, India,Address for correspondence: Dr. Sonal Asthana, Aster Integrated Liver Care, Aster CMI Hospital, New Airport Road, Hebbal, Bangalore, 560092, India.
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13
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Rajan S, Chockalingam P, Koneti NR, Geetha TS, Mishra S, Narasimhan C. Initial experience and results of a cardiogenetic clinic in a tertiary cardiac care center in India. Ann Pediatr Cardiol 2021; 14:443-448. [PMID: 34667425 PMCID: PMC8457287 DOI: 10.4103/apc.apc_123_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/11/2021] [Accepted: 07/18/2021] [Indexed: 11/04/2022] Open
Affiliation(s)
- Saileela Rajan
- Department of Pediatric Cardiology, MIOT Centre for Children's Cardiac Care, MIOT Hospitals, Chennai, Tamil Nadu, India E-mail:
| | | | - Nageswara Rao Koneti
- Department of Pediatric Cardiology, Rainbow Children's Heart Institute, Hyderabad, Telangana, India
| | | | | | - Calambur Narasimhan
- Department of Cardiology, Division of Cardiac Electrophysiology, AIG Hospital, Hyderabad, Telangana, India
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14
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Khandelwal P, Mahesh V, Mathur VP, Raut S, Geetha TS, Nair S, Hari P, Sinha A, Bagga A. Phenotypic variability in distal acidification defects associated with WDR72 mutations. Pediatr Nephrol 2021; 36:881-887. [PMID: 33033857 DOI: 10.1007/s00467-020-04747-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/21/2020] [Accepted: 08/26/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Distal renal tubular acidosis (RTA) is typically caused by defects in ATP6V0A4, ATP6V1B1, and SLC4A1, accounting for 60-80% of patients. Genes recently implicated include FOXI1, ATP6V1C2, and WDR72, of which WDR72 is associated with dental enamel defects. METHODS We describe 4 patients, from three unrelated consanguineous families, with RTA and amelogenesis imperfecta. Distal tubular acidification was evaluated by furosemide-fludrocortisone test, urine-to-blood PCO2 gradient and fractional excretion of bicarbonate. Exome sequencing was performed using a panel of genes implicated in human disease. RESULTS Patients had polyuria, hypokalemia, hypercalciuria, and nephrocalcinosis, but metabolic acidosis varied in severity. Although all patients acidified urine to pH < 5.3 during furosemide-fludrocortisone test, urine-to-blood PCO2 gradient was < 20 mmHg during bicarbonate loading. All patients had transient proximal tubular dysfunction with urinary losses of phosphate and beta-2-microglobulin, and generalized aminoaciduria. Homozygous pathogenic truncating variants in WDR72 was detected in all probands. CONCLUSION Patients with WDR72 mutations show mild rate-dependent distal RTA with variable metabolic acidosis, and intact ability to acidify the urine on provocative testing. Concomitant proximal tubular dysfunction may be present. Mutations in WDR72 should be considered in patients with suspected distal RTA, especially if associated with dental defects.
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Affiliation(s)
- Priyanka Khandelwal
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Nephrology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Mahesh V
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Nephrology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Vijay Prakash Mathur
- Center for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, India
| | - Sumantra Raut
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Nephrology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | | | | | - Pankaj Hari
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Nephrology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Aditi Sinha
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Nephrology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
| | - Arvind Bagga
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Nephrology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
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15
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Patel V, Udwadia-Hegde A, Hajirnis O, Nemani T, Pandrowala A, Desai M, Geetha TS, Ramprasad V, Kashikar R. A Rare Neurological Presentation of Familial Hemophagocytic Lymphohistiocytosis. Journal of Pediatric Neurology 2021. [DOI: 10.1055/s-0040-1712471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractIn this case report, we described a 15-year-old boy who presented with intermittent episodes of ataxia and diplopia since 6.5 years of age. Extensive workup done over several years was negative. Brain biopsy showed a neuroinflammatory disorder, and hence, differential diagnosis of chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids, central nervous system (CNS) lymphoma, and small vessel CNS vasculitis were considered. A final diagnosis of familial hemophagocytic lymphohistiocytosis was made when the patient developed episodes of prolonged fever with pancytopenia much later in the course of illness and genetic workup revealed pathogenic mutations in the PRF1 gene.
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Affiliation(s)
- Vishal Patel
- Department of Pediatric Neurology, Jaslok Hospital & Research Centre, Mumbai, Maharashtra, India
| | - Anaita Udwadia-Hegde
- Department of Pediatric Neurology, Jaslok Hospital & Research Centre, Mumbai, Maharashtra, India
| | - Omkar Hajirnis
- Synapses Child Neurology & Development Center, Thane, Maharashtra, India
| | - Tarishi Nemani
- Department of Pediatric Neurology, Jaslok Hospital & Research Centre, Mumbai, Maharashtra, India
| | - Ambreen Pandrowala
- Department of Immunology, Narayana Health SRCC Children's Hospital, Mumbai, Maharashtra, India
| | - Mukesh Desai
- Department of Immunology, Narayana Health SRCC Children's Hospital, Mumbai, Maharashtra, India
| | - Thenral S. Geetha
- Department of Genetics, MedGenome Labs Ltd, Bangalore, Karnataka, India
| | - Vedam Ramprasad
- Department of Genetics, MedGenome Labs Ltd, Bangalore, Karnataka, India
| | - Ritu Kashikar
- Department of Radiology, Jaslok Hospital & Research Centre, Mumbai, Maharashtra, India
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16
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Polavarapu K, Bardhan M, Anjanappa RM, Vengalil S, Preethish-Kumar V, Shingavi L, Chawla T, Nashi S, Mohan D, Arunachal G, Geetha TS, Ramprasad V, Nalini A. Nemaline Rod/Cap Myopathy Due to Novel Homozygous MYPN Mutations: The First Report from South Asia and Comprehensive Literature Review. J Clin Neurol 2021; 17:409-418. [PMID: 34184449 PMCID: PMC8242322 DOI: 10.3988/jcn.2021.17.3.409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 11/17/2022] Open
Abstract
Background and Purpose Pathogenic variants in the myopalladin gene (MYPN) are known to cause mildly progressive nemaline/cap myopathy. Only nine cases have been reported in the English literature. Methods A detailed evaluation was conducted of the clinical, muscle magnetic resonance imaging (MRI), and genetic findings of two unrelated adults with MYPN-related cap myopathy. Genetic analysis was performed using whole-exome sequencing. MRI was performed on a 1.5-T device in patient 1. Results Two unrelated adults born to consanguineous parents, a 28-year-old male and a 23-year-old female, were diagnosed with pathogenic variants in MYPN that cause cap myopathy. Both patients presented with early-onset, insidiously progressive, and minimally disabling proximodistal weakness with mild ptosis, facial weakness, and bulbar symptoms. Patient 1 had a prominent foot drop from the onset. Both patients were followed up at age 30 years, at which point serum creatine kinase concentrations were minimally elevated. There were no cardiac symptoms; electrocardiograms and two-dimensional echocardiograms were normal in both patients. Muscle MRI revealed preferential involvement of the glutei, posterior thigh muscles, and anterior leg muscles. Whole-exome sequencing revealed significant homozygous splice-site variants in both of the probands, affecting intron 10 of MYPN: c.1973+1G>C (patient 1) and c.1974-2A>C (patient 2). Conclusions This study elaborates on two patients with homozygous MYPN pathogenic variants, presenting as slowly progressive congenital myopathy. These patients are only the tenth and eleventh cases reported in the English literature, and the first from South Asia. The clinical phenotype reiterates the mild form of nemaline rod/cap myopathy. A comprehensive literature review is presented.
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Affiliation(s)
- Kiran Polavarapu
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India.,Children's Hospital of Eastern Ontario Research Institute; Division of Neurology, Department of Medicine, The Ottawa Hospital; Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Mainak Bardhan
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ram Murthy Anjanappa
- Department of Human Genetics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | | | - Leena Shingavi
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Tanushree Chawla
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Saraswati Nashi
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Dhaarini Mohan
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Gautham Arunachal
- Department of Human Genetics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | | | | | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India.
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17
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Kukkle PL, Geetha TS, Mahadevan A, Ramprasad VL. Reply to: Fatal Familial Insomnia: A Rare Disease with Unique Clinico-Neurophysiological Features. Mov Disord Clin Pract 2021; 8:164-165. [PMID: 33426176 PMCID: PMC7780938 DOI: 10.1002/mdc3.13115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 11/11/2022] Open
Affiliation(s)
- Prashanth L. Kukkle
- Center for Parkinson's Disease and Movement Disorders Clinic, Vikram HospitalsBangaloreIndia
- Parkinson's Disease and Movement Disorders ClinicBangaloreIndia
| | | | - Anita Mahadevan
- Department of NeuropathologyNational Institute of Mental Health and NeurosciencesBangaloreIndia
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18
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Kukkle PL, Geetha TS, Mahadevan A, Ramprasad VL. A Case of Autosomal Dominant Ataxia with Vocal Cord Palsy Attributed to a Mutation in the PRNP Gene. Mov Disord Clin Pract 2020; 7:688-692. [PMID: 32775516 DOI: 10.1002/mdc3.12999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/14/2020] [Accepted: 05/23/2020] [Indexed: 01/21/2023] Open
Affiliation(s)
- Prashanth L Kukkle
- Center for Parkinson's Disease and Movement Disorders Clinic Vikram Hospitals Bangalore India.,Parkinson's Disease and Movement Disorders Clinic Bangalore India
| | | | - Anita Mahadevan
- Department of Neuropathology National Institute of Mental Health and Neurosciences Bangalore India
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19
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Pandey S, Sankhla CS, Ramprasad VL, Geetha TS. Novel GNAL mutation in an Indian patient with generalized dystonia and response to deep brain stimulation. Parkinsonism Relat Disord 2019; 62:246-247. [PMID: 30660597 DOI: 10.1016/j.parkreldis.2019.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 12/27/2018] [Accepted: 01/11/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Sanjay Pandey
- Department of Neurology, Academic Block, Room No 503, Department of Neurology, Govind Ballabh Pant Postgraduate Institute of Medical Education and Research, New Delhi, 110 002, India
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20
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Geetha TS, Lingappa L, Jain AR, Govindan H, Mandloi N, Murugan S, Gupta R, Vedam R. A novel splice variant in EMC1 is associated with cerebellar atrophy, visual impairment, psychomotor retardation with epilepsy. Mol Genet Genomic Med 2017; 6:282-287. [PMID: 29271071 PMCID: PMC5902391 DOI: 10.1002/mgg3.352] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/30/2017] [Accepted: 10/23/2017] [Indexed: 11/09/2022] Open
Abstract
Background Several genes have been implicated in a highly variable presentation of developmental delay with psychomotor retardation. Mutations in EMC1 gene have recently been reported. Herein, we describe a proband born of a consanguineous marriage, who presented with early infantile onset epilepsy, scaphocephaly, developmental delay, central hypotonia, muscle wasting, and severe cerebellar and brainstem atrophy. Methods Genetic testing in the proband was performed using custom clinical exome and targeted next‐generation sequencing. This was followed by segregation analysis of the variant in the parents by Sanger sequencing and evaluation of the splice variant by RNA sequencing. Results Clinical exome sequencing identified a novel homozygous intronic splice variant in the EMC1 gene (chr1:19564510C>T, c.1212 + 1G>A, NM_015047.2). Neither population databases (ExAC and 1000 genomes) nor our internal database (n = 1,500) had reported this rare variant, predicted to affect the splicing. RNA sequencing data from the proband confirmed aberrant splicing with intron 11 retention, thereby introducing a stop codon in the resultant mRNA. This nonsense mutation is predicted to result in the premature termination of protein synthesis leading to loss of function of the EMC1 protein. Conclusion We report, for the first time the role of aberrant EMC1RNA splicing as a potential cause of disease pathogenesis. The severe epilepsy observed in our study expands the disease‐associated phenotype and also emphasizes the need for comprehensive screening of intronic splice mutations.
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Affiliation(s)
| | | | | | | | | | | | - Ravi Gupta
- Medgenome Labs, Bommasandra, Bangalore, India
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Geetha TS, Michealraj KA, Kabra M, Kaur G, Juyal RC, Thelma BK. Targeted deep resequencing identifies MID2 mutation for X-linked intellectual disability with varied disease severity in a large kindred from India. Hum Mutat 2014; 35:41-4. [PMID: 24115387 DOI: 10.1002/humu.22453] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 09/19/2013] [Indexed: 11/11/2022]
Abstract
We report a novel missense mutation (c.1040G>A, p.Arg347Gln) in MID2, which encodes ubiquitin ligase E3, as the likely cause of X-linked mental retardation in a large kindred. The mutation was observed in all affected and obligate carriers but not in any unaffected males of the family or in population controls (n = 200). When transiently expressed in HEK293T cell line, the mutation was found to abolish the function of the COS domain in the protein. The GFP-tagged mutant protein accumulated in the cytoplasm instead of binding to the cytoskeleton resulting in its altered subcellular localization. Screening of coding exons of this gene in additional 480 unrelated individuals with idiopathic intellectual disability identified another novel variation p.Asn343Ser. This study highlights the growing role of the ubiquitin pathway in intellectual disability and also, the difference in MID2 determined phenotype observed in this study compared with that of its paralogue MID1 reported in literature.
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Affiliation(s)
- Thenral S Geetha
- Department of Genetics, University of Delhi South Campus, New Delhi, India
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