PMC9715973_01
PMC9715973_02
Laparoscopic findings and pathological examination. (A) Laparoscopy showed testicular gonads between the lower pole of the right kidney and the opening of the inner ring in the right pelvic cavity. (B) Laparoscopy showed muscular tissue in the space between the bladder and rectum in the left pelvic cavity, accompanied by vascular tissue with a slightly enlarged end. (C) Pathological examination revealed that the right gonadal tissue was consistent with testicular tissue (x50). (D) Pathological examination revealed that the left abdominal mass was consistent with an accessory middle renal duct cyst (x50).
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PMC9715973_02_fped-10-1027832-g001.jpg
F1
There was no vas deferens in the right pelvic cavity, a testicular gonad was found between the lower pole of the right kidney and the opening of the inner ring, not well developed, approximately 1.2 x 0.3 cm (Figures 1A,B). Pathological examination revealed that the left abdominal mass was an accessory middle renal duct cyst, and the right gonadal tissue was testicular (Figures 1C,D).
Genetic test results. (A,B) Suggests that the patient has a male karyotype (46,XY, carrying SRY). (C) c.2817G > A (p.W939*) de novo heterozygous mutation in the MYRF gene by WES.
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F2
Copy number variation analysis confirmed the karyotype of 46,XY, carrying SRY (Figures 2A,B). One de novo heterozygous variant in MYRF was identified, namely c.2817G > A (NM_001127392.3) (Figure 2C), which resulted in early termination (p.
The protein sequence from several organisms and the predicted 3D structure of the variant. (A) Comparison of MYRF protein sequences from several organisms. (B) Normal 3D structure of MYRF protein. (C) The predicted 3D structure of MYRF protein residues 890-1,138 was modeled by Genome3D (residues 890-939 are colored white, and residues 940-1,138 are colored gray). As we could see from the predicted 3D structure, the variant caused a premature termination codon, resulting in protein truncation (approximately 15% of protein length is missing), and damaging the protein structure (region colored in gray).
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F3
ACMG Classification Standards and Guidelines for Genetic Variations, the variant showed strong evidence of pathogenicity because it was a nonsense variant (PVS1), and a de novo variant (PS2), and was not included in 1,000 Genomes, GnomAD, LOVD, and HGVD (PM2). Analysis of conserved sequences suggested that this variant was located in highly conserved sequences across several species (PP3) (Figure 3).