Dataset Information

Transcription factor SOX3 is involved in X-linked mental retardation with growth hormone deficiency.

ABSTRACT: Physical mapping of the breakpoints of a pericentric inversion of the X chromosome (46,X,inv[X][p21q27]) in a female patient with mild mental retardation revealed localization of the Xp breakpoint in the IL1RAPL gene at Xp21.3 and the Xq breakpoint near the SOX3 gene (SRY [sex determining region Y]-box 3) (GenBank accession number NM_005634) at Xq26.3. Because carrier females with microdeletion in the IL1RAPL gene do not present any abnormal phenotype, we focused on the Xq breakpoint. However, we were unable to confirm the involvement of SOX3 in the mental retardation in this female patient. To validate SOX3 as an X-linked mental retardation (XLMR) gene, we performed mutation analyses in families with XLMR whose causative gene mapped to Xq26-q27. We show here that the SOX3 gene is involved in a large family in which affected individuals have mental retardation and growth hormone deficiency. The mutation results in an in-frame duplication of 33 bp encoding for 11 alanines in a polyalanine tract of the SOX3 gene. The expression pattern during neural and pituitary development suggests that dysfunction of the SOX3 protein caused by the polyalanine expansion might disturb transcription pathways and the regulation of genes involved in cellular processes and functions required for cognitive and pituitary development.

SUBMITTER: Laumonnier F

PROVIDER: S-EPMC420004 | biostudies-literature | 2002 Dec

REPOSITORIES: biostudies-literature

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Transcription factor SOX3 is involved in X-linked mental retardation with growth hormone deficiency.

Laumonnier Frédéric F Ronce Nathalie N Hamel Ben C J BC Thomas Paul P Lespinasse James J Raynaud Martine M Paringaux Christine C Van Bokhoven Hans H Kalscheuer Vera V Fryns Jean-Pierre JP Chelly Jamel J Moraine Claude C Briault Sylvain S

American journal of human genetics 20021108 6

Physical mapping of the breakpoints of a pericentric inversion of the X chromosome (46,X,inv[X][p21q27]) in a female patient with mild mental retardation revealed localization of the Xp breakpoint in the IL1RAPL gene at Xp21.3 and the Xq breakpoint near the SOX3 gene (SRY [sex determining region Y]-box 3) (GenBank accession number NM_005634) at Xq26.3. Because carrier females with microdeletion in the IL1RAPL gene do not present any abnormal phenotype, we focused on the Xq breakpoint. However, w ...[more]

PMID: 12428212

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Project description:A novel X-linked mental retardation (XLMR) syndrome was recently identified, resulting from creatine deficiency in the brain caused by mutations in the creatine transporter gene, SLC6A8. We have studied the prevalence of SLC6A8 mutations in a panel of 290 patients with nonsyndromic XLMR archived by the European XLMR Consortium. The full-length open reading frame and splice sites of the SLC6A8 gene were investigated by DNA sequence analysis. Six pathogenic mutations, of which five were novel, were identified in a total of 288 patients with XLMR, showing a prevalence of at least 2.1% (6/288). The novel pathogenic mutations are a nonsense mutation (p.Y317X) and four missense mutations. Three missense mutations (p.G87R, p.P390L, and p.P554L) were concluded to be pathogenic on the basis of conservation, segregation, chemical properties of the residues involved, as well as the absence of these and any other missense mutation in 276 controls. For the p.C337W mutation, additional material was available to biochemically prove (i.e., by increased urinary creatine : creatinine ratio) pathogenicity. In addition, we found nine novel polymorphisms (IVS1+26G-->A, IVS7+37G-->A, IVS7+87A-->G, IVS7-35G-->A, IVS12-3C-->T, IVS2+88G-->C, IVS9-36G-->A, IVS12-82G-->C, and p.Y498) that were present in the XLMR panel and/or in the control panel. Two missense variants (p.V629I and p.M560V) that were not highly conserved and were not associated with increased creatine : creatinine ratio, one translational silent variant (p.L472), and 10 intervening sequence variants or untranslated region variants (IVS6+9C-->T, IVS7-151_152delGA, IVS7-99C-->A, IVS8-35G-->A, IVS8+28C-->T, IVS10-18C-->T, IVS11+21G-->A, IVS12+15C-->T, *207G-->C, IVS12+32C-->A) were found only in the XLMR panel but should be considered as unclassified variants or as a polymorphism (p.M560V). Our data indicate that the frequency of SLC6A8 mutations in the XLMR population is close to that of CGG expansions in FMR1, the gene responsible for fragile-X syndrome.

Project description:Abstract SOX3 (SRY-related HMG-box gene 3), located in the X chromosome, spans only one exon and is expressed in the infundibulum, diencephalon and hypothalamus. Alterations in SOX3, mainly deletions or insertions in the polyalanine tract, were associated with mental retardation, isolated GH deficiency (IGHD) or combined pituitary hormone deficiencies (CPHD). Missense variants are rare and only two were reported. Our aim was to find a molecular cause in patients with pituitary hormone deficiency and determine genotype-phenotype correlation. Twenty-eight patients (15F:13M) 24 CPHD:4 IGHD were selected for the study. Whole blood DNA was extracted using the Salting Out method. Library preparation was performed following Agilent’s SureSelectXT customized gene panel protocol containing 654 genes known to cause endocrine diseases. Illumina NextSeq 500 platform was used for sequencing at SELA. Alignment to genome reference hg19 was performed using BWA-MEM. Variants were called with FreeBayes and annotated by Annovar. Allele frequency ?1% for exonic regions was considered in 1000 Genomes, gnomAD, ABraOM and SELA populational databases for variant filtering. Family segregation was done using Sanger sequencing. RNA and protein analysis were performed using mfold and YASARA, respectively. Protein models were made by I-Tasser. SOX3 missense variant (c.912G>A/p.M304I) was found in one male patient, without mental retardation, diagnosed with IGHD at the age of 7 years. After GH replacement, he reached final height at the age of 18 within family target height. Pituitary image showed an ectopic posterior pituitary, hypoplastic anterior pituitary and thin pituitary stalk. SOX3 (c.912G>A/p.M304I) variant in hemizygous state was absent in populational data banks. In silico prediction algorithms SIFT, PolyPhen, and Mutation Assessor were predicted as damaging. Family segregation showed normal mother and sister carriers of the variant, while father, brother and uncle (from mother’s side), all phenotypically normal, did not harbor the variant. RNA In silico analysis pointed that the variant causes mRNA structure change. Protein stability dropped from 677.46 kcal/mol in wild type to 666.69 kcal/mol in p.M304I, making it less stable. Protein Interaction analysis with DNA binding motif (PDB 2LE4) required two times less energy in mutant (376.19 kcal/mol) than wild type protein (646.77 kcal/mol), leading to a less stable interaction. We conclude that one among 28 patients presented a rare novel variant in SOX3 associated to IGHD in a patient without mental retardation and compatible with an X-linked inheritance pattern.

Dataset Information

Transcription factor SOX3 is involved in X-linked mental retardation with growth hormone deficiency.

Publications

Transcription factor SOX3 is involved in X-linked mental retardation with growth hormone deficiency.

Similar Datasets

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