Uncovering Hidden Genetic Contributors to 46,XY Disorders of Sex Development Through Phenotype-Driven Rare Variant...

Despite advances in genetic testing, many 46,XY Disorders of sex development (DSD) cases remain unsolved after whole-exome sequencing (WES). This study intended to explore rare variants in patients with micropenis, cryptorchidism, or hypospadias using bioinformatics analysis to identify potential pathogenic contributors and pathways underlying 46,XY DSD.

A total of 35 patients with specific phenotypes (micropenis/cryptorchidism/hypospadias) and negative whole-exome sequencing results were enrolled. Bioinformatics analysis methods (SKAT-O test and GO enrichment) were applied to identify the putative loss-of-function (pLoF) variation, including nonsense, frameshift, and canonical splice-site variants, and predicted deleterious missense variants (CADD Phred > 20). Literature was reviewed to explore the correlation of detected candidate genes/pathways and 46,XY disorder of sex development.

After variant quality filtering, we identified 307,638 pLoF variants and 127,857 predicted deleterious missense variants across all samples. In subgroup A (micropenis, n = 21), we identified 146,268 pLoF variants and 104,746 predicted deleterious missense variants. In subgroup B (cryptorchidism, n = 10), we identified 111,172 pLoF variants and 77,244 predicted deleterious missense variants. In subgroup C (hypospadias, n = 4), we identified 50,198 pLoF variants and 23,111 predicted deleterious missense variants. Using SKAT-O with an initial screening threshold of p < 0.005 (FDR q < 0.05), we obtained 67 candidate genes from the pLoF variant set and 59 candidate genes from the predicted deleterious missense variant set in subgroup A; 81 and 11 candidate genes, respectively, in subgroup B; and 17 and 0 candidate genes, respectively, in subgroup C.

Assessment of rare variants helps further explore the genetic contributors to 46,XY disorder of sex development and provide potential candidate genes and associated pathways.