Identification of a new missense mutation (Gly95Glu) in a highly conserved codon within the high-mobility group box of the sex-determining region Y gene: report on a 46,XY female with gonadal dysgenesis and yolk-sac tumor

Evolutionary Landscape of SOX Genes to Inform Genotype-to-Phenotype Relationships

The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype-phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in combination with structural dynamics to interpret 3999 gnomAD, 485 ClinVar, 1174 Geno2MP, and 4313 COSMIC human variants. We identified, within the HMG (High Mobility Group)- box, twenty-seven amino acids with changes in multiple SOX proteins annotated to clinical pathologies. These sites were screened through Geno2MP medical phenotypes, revealing novel SOX15 R104G associated with musculature abnormality and SOX8 R159G with intellectual disability. Within gnomAD, SOX18 E137K (rs201931544), found within the HMG box of ~0.8% of Latinx individuals, is associated with seizures and neurological complications, potentially through blood-brain barrier alterations. A total of 56 highly conserved variants were found at sites outside the HMG-box, including several within the SOX2 HMG-box-flanking region with neurological associations, several in the SOX9 dimerization region associated with Campomelic Dysplasia, SOX14 K88R (rs199932938) flanking the HMG box associated with cardiovascular complications within European populations, and SOX7 A379V (rs143587868) within an SOXF conserved far C-terminal domain heterozygous in 0.716% of African individuals with associated eye phenotypes. This SOX data compilation builds a robust genotype-to-phenotype association for a gene family through more robust ortholog data integration.

Identification of a novel mutation (Ala66Thr) of SRY gene causes XY pure gonadal dysgenesis by affecting DNA binding activity and nuclear import

Sex-determining region of the Y chromosome (SRY) gene plays a crucial role in male sexual differentiation and development. Several mutations in the SRY gene have been reported in the high mobility group (HMG) box domain and can cause gonadal dysgenesis symptoms. In this study, we report that a novel missense mutation in the SRY gene, a G to A transition within the HMG box, causes the Ala66Thr amino acid substitution in a female patient presenting 46,XY karyotype with pure gonadal dysgenesis. The G to A base transition was not found in the SRY sequence after the screening of 100 normal males. Furthermore, Ala66Thr mutation drastically reduced the binding capacity of SRY to DNA sequences, whereas wild-type SRY protein showed the normal binding capacity to DNA sequences in vitro. We also found that the mutant SRY protein was partly localized in cytoplasm, whereas wild-type SRY protein was strictly localized in cell nucleus. In addition, we analyzed the three-dimensional structure of SRY protein by homology modeling methods. In conclusion, we identified a novel SRY mutation in a 46,XY female patient with pure gonadal dysgenesis, demonstrating the importance of the Ala66Thr mutation in DNA binding activity and nuclear transport.

Perspectives in Pediatric Pathology, Chapter 5. Gonadal Dysgenesis

One of the most challenging areas in pediatric testicular pathology is the appropriate understanding and pathological diagnosis of disorders of sexual development (DSD), and in particular, the issue of gonadal dysgenesis. Here we present the main concepts necessary for their understanding and appropriate classification, with extensive genetic correlations.

Primary amenorrhea in a 46,XY adolescent girl with partial gonadal dysgenesis: identification of a new SRY gene mutation

OBJECTIVE

To determine the genetic cause of primary amenorrhea in a 46,XY adolescent girl.

DESIGN

Case report.

SETTING

Pediatric endocrinology and gynecologic unit of an academic hospital.

PATIENT(S)

A 16-year-old adolescent referred for primary amenorrhea.

INTERVENTION(S)

Endocrine and surgical investigation, SRY mutational analysis.

MAIN OUTCOME MEASURE(S)

Plasma gonadotropin levels, estradiol and testosterone levels, and pathologic findings.

RESULT(S)

We report a new mutation of the SRY gene in a 46,XY sex-reversed patient. We observed two unusual features. First, partial pubertal development has rarely been described in association with SRY gene mutation. Second, the location of the mutation was in the HMG box region of the SRY gene, in contrast to the other partial cases of 46,XY gonadal dysgenesis. In addition, the presence of a gonadoblastoma underlines the necessity of removing the gonads quickly in 46,XY sex-reversal cases, and raises several questions about the role of the SRY gene in the development of such tumors.

CONCLUSION(S)

Partial pubertal development in a 46,XY sex-reversed patient does not exclude SRY gene mutation.

A Novel Frame Shift Mutation in the HMG Box of the SRY Gene in a Patient With Complete 46,XY Pure Gonadal Dysgenesis

Pure gonadal dysgenesis or Swyer syndrome is a sex-reversal disorder resulting from embryonic testicular regression sequences especially during the first few weeks of fetal life and is induced by mutations in the SRY gene. In the present report, we describe a nonmosaic XY sex-reversed female with pure gonadal dysgenesis. Molecular analysis using sequential PCR to detect Y chromosomal microdeletions showed the presence of SRY, ZFY and AZFa, b and c regions. Automated sequencing of the SRY region revealed a new mutation (deletion of A (adenine) in codon 82 at position +244), leading to a frame shift mutation within the helix I of the HMG-box domain. This mutation generates a truncated protein and is very likely to produce an impairment of SRY DNA binding activity. The present findings further support the functional importance of the putative DNA binding activity of the SRY HMG-box domain.

Mutations in the desert hedgehog (DHH) gene in patients with 46,XY complete pure gonadal dysgenesis

Mutations of SRY are the cause of complete pure gonadal dysgenesis (PGD) in 10-15% of patients. In the remaining individuals, it has been suggested that mutations in other genes involved in the testis-determining pathway could be causative. We describe the first report in which three cases of 46,XY complete PGD are attributed to mutations of the Desert hedgehog (DHH) gene. DHH was sequenced using genomic DNA from paraffin-embedded gonadal tissue from six patients with complete 46,XY PGD. Mutations were found in three patients: a homozygous mutation in exon 2, responsible for a L162P, and a homozygous 1086delG in exon 3. Mutated individuals displayed 46,XY complete PGD, differentiating from the only previously described patient with a homozygous DHH mutation, who exhibited a partial form of PGD with polyneuropathy, suggesting that localization of mutations influence phenotypic expression. This constitutes the first report where mutations of DHH are associated with the presence of 46,XY complete PGD, demonstrating that the genetic origin of this entity is heterogeneous and that disorders in other genes, different from SRY, involved in the testis-determining pathway are implicated in abnormal testicular differentiation in humans. These data extend previous reports demonstrating DHH is a key gene in gonadal differentiation.

A de novo phe671eu mutation in the SRY gene in a patient with complete 46,XY gonadal dysgenesis

The sex-determining region of the Y chromosome (SRY) gene initiates the process of male sex differentiation in mammalians. In humans, mutations in the SRY gene have been reported to account for 10-15% of the XY sex reversal cases. In this report we describe the clinical, endocrinological and molecular data of a patient with complete 46,XY gonadal dysgenesis caused by a de novo mutation affecting SRY amino acid phenylalanine at position 67 (F67L), located within the highly conserved high mobility group (HMG) box coding region of the gene.

Equilibrium binding assays reveal the elevated stoichiometry and salt dependence of the interaction between full-length human sex-determining region on the Y chromosome (SRY) and DNA

In an effort to better define the molecular mechanism of the functional specificity of human sex-determining region on the Y chromosome (SRY), we have carried out equilibrium binding assays to study the interaction of the full-length bacterial-expressed protein with a DNA response element derived from the CD3epsilon gene enhancer. These assays are based on the observation of the fluorescence anisotropy of a fluorescein moiety covalently bound to the target oligonucleotide. The low anisotropy value due to the fast tumbling of the free oligonucleotide in solution increases substantially upon binding the protein to the labeled target DNA. Our results indicate that the full-length human wild-type SRY (SRY(WT)) forms a complex of high stoichiometry with its target DNA. Moreover, we have demonstrated a strong salt dependence of both the affinity and specificity of the interaction. We have also addressed the DNA bending properties of full-length human SRY(WT) in solution by fluorescence resonance energy transfer and revealed that maximal bending is achieved with a protein to DNA ratio significantly higher than the classical 1:1. Oligomerization thus appears, at least in vitro, to be tightly coupled to SRY-DNA interactions. Alteration of protein-protein interactions observed for the mutant protein SRY(Y129N), identified in a patient presenting with 46,XY sex reversal, suggests that oligomerization may play an important role in vivo as well.

Molecular dissection of the human Y-chromosome

Human Y chromosome, earlier thought to be gene deficient, has attracted a great deal of attention owing to its supremacy in male sex determination and unique haplotype status in the genome. Studies on Y chromosome have shown the presence of different types of satellite DNA and several genes implicated with a variety of physical and physiological functions. The interaction of these repetitive DNA with genes in normal individuals and in patients with Y-chromosome-related genetic anomalies is still an unresolved issue and is actively being pursued. The fast changing scenario of the human genome project is likely to effect our overall understanding of the Y chromosome and Y-linked genetic anomalies in a big way. We provide a brief overview of the organization of Y chromosome with respect to several important loci encompassing both the arms and their likely involvement/modulation in genetic anomalies. The experimental approaches discussed here are envisaged to be of clinical relevance for the molecular diagnosis of the Y-linked disorders.