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Mhaske A, Dileep K, Kumar M, Poojary M, Pandhare K, Zhang KY, Scaria V, Binukumar B. ATP7A Clinical Genetics Resource - A comprehensive clinically annotated database and resource for genetic variants in ATP7A gene. Comput Struct Biotechnol J 2020; 18:2347-2356. [PMID: 32994893 PMCID: PMC7501406 DOI: 10.1016/j.csbj.2020.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/21/2022] Open
Abstract
ATP7A is a critical copper transporter involved in Menkes Disease, Occipital horn Syndrome and X-linked distal spinal muscular atrophy type 3 which are X linked genetic disorders. These are rare diseases and their genetic epidemiology of the diseases is unknown. A number of genetic variants in the genes have been reported in published literature as well as databases, however, understanding the pathogenicity of variants and genetic epidemiology requires the data to be compiled in a unified format. To this end, we systematically compiled genetic variants from published literature and datasets. Each of the variants were systematically evaluated for evidences with respect to their pathogenicity and classified as per the American College of Medical Genetics and the Association of Molecular Pathologists (ACMG-AMP) guidelines into Pathogenic, Likely Pathogenic, Benign, Likely Benign and Variants of Uncertain Significance. Additional integrative analysis of population genomic datasets provides insights into the genetic epidemiology of the disease through estimation of carrier frequencies in global populations. To deliver a mechanistic explanation for the pathogenicity of selected variants, we also performed molecular modeling studies. Our modeling studies concluded that the small structural distortions observed in the local structures of the protein may lead to the destabilization of the global structure. To the best of our knowledge, ATP7A Clinical Genetics Resource is one of the most comprehensive compendium of variants in the gene providing clinically relevant annotations in gene.
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Affiliation(s)
- Aditi Mhaske
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
| | - K.V. Dileep
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mukesh Kumar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Mukta Poojary
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Kavita Pandhare
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Kam Y.J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
- Corresponding author at: CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar, New Delhi 110025, India.
| | - B.K. Binukumar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
- Corresponding author at: CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar, New Delhi 110025, India.
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Characterization of ATP7A missense mutants suggests a correlation between intracellular trafficking and severity of Menkes disease. Sci Rep 2017; 7:757. [PMID: 28389643 PMCID: PMC5428812 DOI: 10.1038/s41598-017-00618-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/06/2017] [Indexed: 12/12/2022] Open
Abstract
Menkes disease (MD) is caused by mutations in ATP7A, encoding a copper-transporting P-type ATPase which exhibits copper-dependent trafficking. ATP7A is found in the Trans-Golgi Network (TGN) at low copper concentrations, and in the post-Golgi compartments and the plasma membrane at higher concentrations. Here we have analyzed the effect of 36 ATP7A missense mutations identified in phenotypically different MD patients. Nine mutations identified in patients with severe MD, virtually eliminated ATP7A synthesis, in most cases due to aberrant RNA splicing. A group of 21 predominantly severe mutations led to trapping of the protein in TGN and displayed essentially no activity in a yeast-based functional assay. These were predicted to inhibit the catalytic phosphorylation of the protein. Four mutants showed diffuse post-TGN localization, while two displayed copper dependent trafficking. These six variants were identified in patients with mild MD and typically displayed activity in the yeast assay. The four post-TGN located mutants were presumably affected in the catalytic dephosphorylation of the protein. Together these results indicate that the severity of MD correlate with cellular localization of ATP7A and support previous studies indicating that phosphorylation is crucial for the exit of ATP7A from TGN, while dephosphorylation is crucial for recycling back to TGN.
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Møller LB, Schönewolf-Greulich B, Rosengren T, Larsen LJ, Ostergaard JR, Sommerlund M, Ostenfeldt C, Stausbøl-Grøn B, Linnet KM, Gregersen PA, Jensen UB. Development of hypomelanotic macules is associated with constitutive activated mTORC1 in tuberous sclerosis complex. Mol Genet Metab 2017; 120:384-391. [PMID: 28336152 DOI: 10.1016/j.ymgme.2017.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 02/25/2017] [Accepted: 02/27/2017] [Indexed: 10/20/2022]
Abstract
TSC1 and TSC2 are genes mutated in the syndrome TSC (tuberous sclerosis complex). We describe a 3-generation family with 17 affected members, all presenting classic TSC features except renal manifestations. The disease segregates with a silent substitution in TSC2, c.4149C>T, p.(Ser1383Ser), which leads to the formation of an active donor splice site, resulting in three shorter alternatively spliced transcripts with premature stop codons. However a small amount of normal spliced transcript is apparently produced from the mutated allele, which might explain the milder phenotype. The gene products of TSC1/2 form a complex which at energy limiting states, down-regulates the activity of the regulator of protein synthesis, the mammalian target of rapamycin complex1 (mTORC1). As expected, in contrast to cultured control fibroblasts, starvation of cultured patient fibroblasts obtained from a hypomelanotic macule did not lead to repression of mTORC1, whereas partial repression was observed in patient fibroblasts obtained from non-lesional skin. The findings indicate that the development of hypomelanotic macules is associated with constitutive activated mTORC1, whereas mild deregulation of mTORC1 allows the maintenance of normal skin. Furthermore, the finding establishes the pathogenic effect of the "silent" c.4149C>T substitution and emphasizes the need for awareness when interpreting silent substitutions in general.
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Affiliation(s)
- Lisbeth Birk Møller
- Applied Human Molecular Genetics, Clinical Genetics Clinic, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark; Department of Science and Environment, Roskilde University, Roskilde, Denmark.
| | - Bitten Schönewolf-Greulich
- Applied Human Molecular Genetics, Clinical Genetics Clinic, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark
| | - Thomas Rosengren
- Applied Human Molecular Genetics, Clinical Genetics Clinic, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark
| | - Lasse Jonsgaard Larsen
- Applied Human Molecular Genetics, Clinical Genetics Clinic, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark
| | - John R Ostergaard
- Centre for Rare Disorders, Department of Pediatrics, Aarhus University Hospital, Aarhus, Denmark
| | - Mette Sommerlund
- Department of Dermatology, Aarhus University Hospital, Aarhus, Denmark
| | - Caroline Ostenfeldt
- Applied Human Molecular Genetics, Clinical Genetics Clinic, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark
| | - Brian Stausbøl-Grøn
- Department of Radiology/MR Centre, Aarhus University Hospital, Aarhus, Denmark
| | | | - Pernille Axél Gregersen
- Centre for Rare Disorders, Department of Pediatrics, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
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Hunt RC, Simhadri VL, Iandoli M, Sauna ZE, Kimchi-Sarfaty C. Exposing synonymous mutations. Trends Genet 2014; 30:308-21. [PMID: 24954581 DOI: 10.1016/j.tig.2014.04.006] [Citation(s) in RCA: 231] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 04/16/2014] [Accepted: 04/17/2014] [Indexed: 12/12/2022]
Abstract
Synonymous codon changes, which do not alter protein sequence, were previously thought to have no functional consequence. Although this concept has been overturned in recent years, there is no unique mechanism by which these changes exert biological effects. A large repertoire of both experimental and bioinformatic methods has been developed to understand the effects of synonymous variants. Results from this body of work have provided global insights into how biological systems exploit the degeneracy of the genetic code to control gene expression, protein folding efficiency, and the coordinated expression of functionally related gene families. Although it is now clear that synonymous variants are important in a variety of contexts, from human disease to the safety and efficacy of therapeutic proteins, there is no clear consensus on the approaches to identify and validate these changes. Here, we review the diverse methods to understand the effects of synonymous mutations.
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Affiliation(s)
- Ryan C Hunt
- Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD, USA.
| | - Vijaya L Simhadri
- Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD, USA
| | - Matthew Iandoli
- Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD, USA
| | - Zuben E Sauna
- Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD, USA.
| | - Chava Kimchi-Sarfaty
- Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD, USA.
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