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Dantas NCB, Funari MFA, Lerário AM, Andrade NLM, Rezende RC, Cellin LP, Alves C, Crisostomo LG, Arnhold IJP, Mendonca B, Scalco RC, Jorge AAL. Identification of a second genetic alteration in patients with SHOX deficiency individuals: a potential explanation for phenotype variability. Eur J Endocrinol 2023; 189:387-395. [PMID: 37695807 DOI: 10.1093/ejendo/lvad128] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/13/2023]
Abstract
OBJECTIVE Our study aimed to assess the impact of genetic modifiers on the significant variation in phenotype that is observed in individuals with SHOX deficiency, which is the most prevalent monogenic cause of short stature. DESIGN AND METHODS We performed a genetic analysis in 98 individuals from 48 families with SHOX deficiency with a target panel designed to capture the entire SHOX genomic region and 114 other genes that modulate growth and/or SHOX action. We prioritized rare potentially deleterious variants. RESULTS We did not identify potential deleterious variants in the promoter or intronic regions of the SHOX genomic locus. In contrast, we found eight heterozygous variants in 11 individuals from nine families in genes with a potential role as genetic modifiers. In addition to a previously described likely pathogenic (LP) variant in CYP26C1 observed in two families, we identified LP variants in PTHLH and ACAN, and variants of uncertain significance in NPR2, RUNX2, and TP53 in more affected individuals from families with SHOX deficiency. Families with a SHOX alteration restricted to the regulatory region had a higher prevalence of a second likely pathogenic variant (27%) than families with an alteration compromising the SHOX coding region (2.9%, P = .04). CONCLUSION In conclusion, variants in genes related to the growth plate have a potential role as genetic modifiers of the phenotype in individuals with SHOX deficiency. In individuals with SHOX alterations restricted to the regulatory region, a second alteration could be critical to determine the penetrance and expression of the phenotype.
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Affiliation(s)
- Naiara C B Dantas
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 01246-903 Sao Paulo, SP, Brazil
| | - Mariana F A Funari
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular LIM/42, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 05403-900 Sao Paulo, SP, Brazil
| | - Antonio M Lerário
- Department of Internal Medicine, Division of Endocrinology, Metabolism and Diabetes, University of Michigan, Ann Arbor, MI 48105, United States
| | - Nathalia L M Andrade
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 01246-903 Sao Paulo, SP, Brazil
| | - Raíssa C Rezende
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 01246-903 Sao Paulo, SP, Brazil
| | - Laurana P Cellin
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 01246-903 Sao Paulo, SP, Brazil
| | - Crésio Alves
- Pediatric Endocrinology Unit, Hospital Universitario Prof. Edgard Santos, Faculdade de Medicina, Universidade Federal da Bahia, 40026-010 Salvador, BA, Brazil
| | - Lindiane G Crisostomo
- Department of Pediatrics, Centro Universitário Sao Camilo, 04263-200 Sao Paulo SP, Brazil
| | - Ivo J P Arnhold
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular LIM/42, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 05403-900 Sao Paulo, SP, Brazil
| | - Berenice Mendonca
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular LIM/42, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 05403-900 Sao Paulo, SP, Brazil
| | - Renata C Scalco
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 01246-903 Sao Paulo, SP, Brazil
- Disciplina de Endocrinologia, Faculdade de Ciencias Medicas da Santa Casa de Sao Paulo, 01221-020 Sao Paulo SP, Brazil
| | - Alexander A L Jorge
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 01246-903 Sao Paulo, SP, Brazil
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Santana LS, Caetano LA, Costa-Riquetto AD, Quedas EPS, Nery M, Collett-Solberg P, Boguszewski MCS, Vendramini MF, Crisostomo LG, Floh FO, Zarabia ZI, Kohara SK, Guastapaglia L, Passone CGB, Sewaybricker LE, Jorge AAL, Teles MG. Clinical application of ACMG-AMP guidelines in HNF1A and GCK variants in a cohort of MODY families. Clin Genet 2017; 92:388-396. [PMID: 28170077 DOI: 10.1111/cge.12988] [Citation(s) in RCA: 14] [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: 11/18/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 01/05/2023]
Abstract
Maturity-onset diabetes of the young (MODY) is a form of monogenic diabetes with autosomal dominant inheritance. GCK -MODY and HNF1A -MODY are the prevalent subtypes. Currently, there is growing concern regarding the correct interpretation of molecular genetic findings. The American College of Medical Genetics and Genomics (ACMG) updated guidelines to interpret and classify molecular variants. This study aimed to determine the prevalence of MODY ( GCK / HNF1A ) in a large cohort of Brazilian families, to report variants related to phenotype, and to classify them according to ACMG guidelines. One hundred and nine probands were investigated, 45% with clinical suspicion of GCK -MODY and 55% with suspicion of HNF1A -MODY. Twenty-five different variants were identified in GCK gene (30 probands-61% of positivity), and 7 variants in HNF1A (10 probands-17% of positivity). Fourteen of them were novel (12- GCK /2- HNF1A ). ACMG guidelines were able to classify a large portion of variants as pathogenic (36%- GCK /86%- HNF1A ) and likely pathogenic (44%- GCK /14%- HNF1A ), with 16% (5/32) as uncertain significance. This allows us to determine the pathogenicity classification more efficiently, and also reinforces the suspected associations with the phenotype among novel variants.
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Affiliation(s)
- L S Santana
- Monogenic Diabetes Group, Genetic Endocrinology Unit and Laboratory of Molecular & Cellular Endocrinology/LIM25, School of Medicine, University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | - L A Caetano
- Monogenic Diabetes Group, Genetic Endocrinology Unit and Laboratory of Molecular & Cellular Endocrinology/LIM25, School of Medicine, University of Sao Paulo (USP), Sao Paulo, SP, Brazil.,Diabetes Unit, Clinics Hospital, School of Medicine, University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | - A D Costa-Riquetto
- Monogenic Diabetes Group, Genetic Endocrinology Unit and Laboratory of Molecular & Cellular Endocrinology/LIM25, School of Medicine, University of Sao Paulo (USP), Sao Paulo, SP, Brazil.,Diabetes Unit, Clinics Hospital, School of Medicine, University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | - E P S Quedas
- Monogenic Diabetes Group, Genetic Endocrinology Unit and Laboratory of Molecular & Cellular Endocrinology/LIM25, School of Medicine, University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | - M Nery
- Diabetes Unit, Clinics Hospital, School of Medicine, University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | - P Collett-Solberg
- Department of Endocrinology, University of Rio de Janeiro State (UERJ), Rio de Janeiro, RJ, Brazil
| | - M C S Boguszewski
- Departamento de Pediatria, Universidade Federal do Paraná (UFPR), Curitiba, PR, Brazil
| | - M F Vendramini
- Serviço de Endocrinologia, Hospital do Servidor Público Estadual de São Paulo (HSPE-SP), Sao Paulo, SP, Brazil
| | - L G Crisostomo
- Serviço de Endocrinologia, Hospital Israelita Albert Eisntein, Sao Paulo, SP, Brazil.,Faculdade de Medicina, Centro Universitário São Camilo, Sao Paulo, SP, Brazil
| | - F O Floh
- Serviço de Endocrinologia, Hospital Israelita Albert Eisntein, Sao Paulo, SP, Brazil
| | - Z I Zarabia
- Serviço de Endocrinologia, Hospital Infantil Dr. Jeser Amarante Faria, Joinville, SC, Brazil
| | - S K Kohara
- Serviço de Endocrinologia, Universidade da Região de Joinville (UNIVILLE), Joinville, SC, Brazil
| | - L Guastapaglia
- Serviço de Endocrinologia, Hospital do Servidor Público Municipal de São Paulo (HSPM-SP), Sao Paulo, SP, Brazil
| | - C G B Passone
- Instituto da Criança, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (USP), Sao Paulo, SP, Brazil
| | - L E Sewaybricker
- Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - A A L Jorge
- Monogenic Diabetes Group, Genetic Endocrinology Unit and Laboratory of Molecular & Cellular Endocrinology/LIM25, School of Medicine, University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | - M G Teles
- Monogenic Diabetes Group, Genetic Endocrinology Unit and Laboratory of Molecular & Cellular Endocrinology/LIM25, School of Medicine, University of Sao Paulo (USP), Sao Paulo, SP, Brazil.,Diabetes Unit, Clinics Hospital, School of Medicine, University of Sao Paulo (USP), Sao Paulo, SP, Brazil
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