Expanding the phenotypic spectrum of LHCGR signal peptide insertion variant: novel clinical and allelic findings causing Leydig cell hypoplasia type II

Abstract

Purpose: Leydig cell hypoplasia (LCH) type II is a rare disease with only a few cases reported. Patients presented with hypospadias, micropenis, undescended testes, or infertility. In this study, we report a new patient with compound heterozygous variants in the LHCGR gene and LCH type II phenotype.

Methods: Whole exome sequencing (WES) was performed followed by Sanger sequencing to confirm the detected variants in the patient and his parents.

Results: A novel missense variant (p.Phe444Cys) was identified in a highly conserved site and is verified to be in trans with the signal peptide's 33-bases insertion variant.

Conclusion: Our research provides a more comprehensive clinical and genetic spectrum of Leydig cell hypoplasia type II. It highlighted the importance of WES in the diagnosis of this uncommon genetic disorder as well as the expansion of the genotype of LCH type II.

Keywords: 33-bases insertion; 46,XY DSD; LCH type II; TMD; WES.

Fig. 1

Sequence chromatogram for exon 1 of the LHCGR gene showing the site of the insertion mutation. (A) the patient’s sequence, (B) the father’s sequence with heterozygous insertion of 33 bases c.55_56insTGCTGAAGCTGCTGCTGCTGCTGCAGCTGCAG, and (C) the mother’s sequence with heterozygous 6 bases insertion NM_000233.4:c.55_56insTGCAGC. The sequence of the two overlapping alleles (heterozygous insertion) is indicated above the sequence (the wild-type in green and the mutant in black). (D) The three detected alleles in exon 1 of the proband and his parents. The proband and his father had the wild type allele and the mutant allele, while the mother had the wild type allele and the polymorphic allele

Fig. 2

The detected missense variant in exon 11 (c.1331T > G; p.Phe444Cys). Sequence chromatogram for exon 11 of LHCGR gene showing the site of the variant (A) in the patient with heterozygous pattern, (B) in the father with wild-type sequence, and (C) in the mother with the heterozygous form. (D) A ribbon presentation of the protein by HOPE project showing the side chains of the wild-type and mutant residues, which are colored green and red, respectively

Fig. 3

Multiple sequence alignment of LHCGR (NP_000224.2), TSHR (NP_000360.2), and FSHR (NP_000136.2) proteins sequences using ClastalX2. The big arrow points to the site of the detected variant in the current study. Small arrows indicate the site of reported variants (variants in the upper section are inactivating causing thyroid-stimulating hormone resistance, resistant ovarian syndrome, and empty follicle syndrome, while variants in the lower section are activating ones, resulting in hyperthyroidism and male precocious puberty)