1
|
Levy M, Elron E, Shohat M, Lifshitz S, Kahana S, Shani H, Grossman A, Amar S, Narkis G, Sagi-Dain L, Basel-Salmon L, Maya I. Exploring inheritance, and clinical penetrance of distal Xq28 duplication syndrome: insights from 47 new unpublished cases. J Hum Genet 2024; 69:337-343. [PMID: 38632380 PMCID: PMC11199134 DOI: 10.1038/s10038-024-01252-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Distal Xq28 duplication, or int22h1/int22h2-mediated Xq28 duplication syndrome, leads to cognitive impairment, neurobehavioral issues, and facial dysmorphisms. Existing literature has limited information on clinical traits and penetrance. METHODS We identified cases of distal Xq28 duplication (chrX: 154,126,575-154,709,680, GRCh37/hg19) through a review of clinical records and microarray reports from five centers, encompassing both postnatal and prenatal cases, with no prior family knowledge of the duplication. RESULTS Our search found 47 cases across 26 families, with duplications ranging from 208 to 935 Kb. In total, 8 out of 26 index cases featured a 200-300 kb partial duplication, mainly from Armenian/Caucasian Jewish backgrounds. Most prenatal cases showed no major fetal ultrasound malformations. Of cases with known inheritance mode (15 out of 26), maternal inheritance was more common (80%). The study identified seven male carriers of the duplication from six unrelated families, indicating partial penetrance in males. CONCLUSION Our study provides key insights into distal Xq28 duplication. Most prenatal tests showed no major fetal ultrasound issues. Maternal inheritance was common, with unaffected mothers. In the postnatal group, a balanced gender distribution was observed. Among male family members, two fathers had ADHD, one was healthy, and one brother had mild symptoms, indicating partial penetrance in males.
Collapse
Affiliation(s)
- Michal Levy
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel.
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Eyal Elron
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mordechai Shohat
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Maccabi Genetic Institute & Bioinformatics Unit, Sheba Cancer Research Center, Ramat Gan, Israel
| | - Shira Lifshitz
- Maccabi Genetic Institute & Bioinformatics Unit, Sheba Cancer Research Center, Ramat Gan, Israel
| | - Sarit Kahana
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Hagit Shani
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Ramat Gan, Israel
| | - Anat Grossman
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Ramat Gan, Israel
| | - Shirly Amar
- Genetic Institute, Soroka Medical Center & Ben Gurion University, Be'er Sheva, Israel
| | - Ginat Narkis
- Genetic Institute, Soroka Medical Center & Ben Gurion University, Be'er Sheva, Israel
| | - Lena Sagi-Dain
- Genetics Institute, Department of Obstetrics and Gynecology, Carmel Medical Center & The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Lina Basel-Salmon
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Idit Maya
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
2
|
Kingdom R, Tuke M, Wood A, Beaumont RN, Frayling TM, Weedon MN, Wright CF. Rare genetic variants in genes and loci linked to dominant monogenic developmental disorders cause milder related phenotypes in the general population. Am J Hum Genet 2022; 109:1308-1316. [PMID: 35700724 PMCID: PMC9300873 DOI: 10.1016/j.ajhg.2022.05.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/19/2022] [Indexed: 12/02/2022] Open
Abstract
Many rare monogenic diseases are known to be caused by deleterious variants in thousands of genes, however the same variants can also be found in people without the associated clinical phenotypes. The penetrance of these monogenic variants is generally unknown in the wider population, as they are typically identified in small clinical cohorts of affected individuals and families with highly penetrant variants. Here, we investigated the phenotypic effect of rare, potentially deleterious variants in genes and loci where similar variants are known to cause monogenic developmental disorders (DDs) in a large population cohort. We used UK Biobank to investigate phenotypes associated with rare protein-truncating and missense variants in 599 monoallelic DDG2P genes by using whole-exome-sequencing data from ∼200,000 individuals and rare copy-number variants overlapping known DD loci by using SNP-array data from ∼500,000 individuals. We found that individuals with these likely deleterious variants had a mild DD-related phenotype, including lower fluid intelligence, slower reaction times, lower numeric memory scores, and longer pairs matching times compared to the rest of the UK Biobank cohort. They were also shorter, had a higher BMI, and had significant socioeconomic disadvantages: they were less likely to be employed or be able to work and had a lower income and higher deprivation index. Our findings suggest that many genes routinely tested within pediatric genetics have deleterious variants with intermediate penetrance that may cause lifelong sub-clinical phenotypes in the general adult population.
Collapse
Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Marcus Tuke
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Andrew Wood
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Timothy M Frayling
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK.
| |
Collapse
|
3
|
Kherraf ZE, Cazin C, Bouker A, Fourati Ben Mustapha S, Hennebicq S, Septier A, Coutton C, Raymond L, Nouchy M, Thierry-Mieg N, Zouari R, Arnoult C, Ray PF. Whole-exome sequencing improves the diagnosis and care of men with non-obstructive azoospermia. Am J Hum Genet 2022; 109:508-517. [PMID: 35172124 DOI: 10.1016/j.ajhg.2022.01.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/19/2022] [Indexed: 12/12/2022] Open
Abstract
Non-obstructive azoospermia (NOA) is a severe and frequent cause of male infertility, often treated by testicular sperm extraction followed by intracytoplasmic sperm injection. The aim of this study is to improve the genetic diagnosis of NOA, by identifying new genes involved in human NOA and to better assess the chances of successful sperm extraction according to the individual's genotype. Exome sequencing was performed on 96 NOA-affected individuals negative for routine genetic tests. Bioinformatics analysis was limited to a panel of 151 genes selected as known causal or candidate genes for NOA. Only highly deleterious homozygous or hemizygous variants were retained as candidates. A likely causal defect was identified in 16 genes in a total of 22 individuals (23%). Six genes had not been described in man (DDX25, HENMT1, MCMDC2, MSH5, REC8, TDRKH) and 10 were previously reported (C14orf39, DMC1, FANCM, GCNA, HFM1, MCM8, MEIOB, PDHA2, TDRD9, TERB1). Seven individuals had defects in genes from piwi or DNA repair pathways, three in genes involved in post-meiotic maturation, and 12 in meiotic processes. Interestingly, all individuals with defects in meiotic genes had an unsuccessful sperm retrieval, indicating that genetic diagnosis prior to TESE could help identify individuals with low or null chances of successful sperm retrieval and thus avoid unsuccessful surgeries.
Collapse
Affiliation(s)
- Zine-Eddine Kherraf
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, 38000 Grenoble, France; CHU Grenoble Alpes, UM GI-DPI, Grenoble 38000, France
| | - Caroline Cazin
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, 38000 Grenoble, France; CHU Grenoble Alpes, UM GI-DPI, Grenoble 38000, France; Laboratoire Eurofins Biomnis, Département de Génétique Moléculaire, 69 007 Lyon, France
| | - Amine Bouker
- Polyclinique les Jasmins, Centre d'Aide Médicale à la Procréation, Centre Urbain Nord, 1003 Tunis, Tunisia
| | | | - Sylviane Hennebicq
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, 38000 Grenoble, France; CHU Grenoble Alpes, UM laboratoire d'aide à la procréation-CECOS, 38 000 Grenoble, France
| | - Amandine Septier
- Univ. Grenoble Alpes, CNRS, UMR5525, TIMC, 38000 Grenoble, France
| | - Charles Coutton
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, 38000 Grenoble, France; CHU Grenoble Alpes, UM de Génétique Chromosomique, 38000 Grenoble, France
| | - Laure Raymond
- Laboratoire Eurofins Biomnis, Département de Génétique Moléculaire, 69 007 Lyon, France
| | - Marc Nouchy
- Laboratoire Eurofins Biomnis, Département de Génétique Moléculaire, 69 007 Lyon, France
| | | | - Raoudha Zouari
- Polyclinique les Jasmins, Centre d'Aide Médicale à la Procréation, Centre Urbain Nord, 1003 Tunis, Tunisia
| | - Christophe Arnoult
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, 38000 Grenoble, France
| | - Pierre F Ray
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, 38000 Grenoble, France; CHU Grenoble Alpes, UM GI-DPI, Grenoble 38000, France.
| |
Collapse
|