Detailed genetic and clinical analysis of a novel de novo variant in HPRT1: Case report of a female patient from Saudi Arabia with Lesch-Nyhan syndrome

Case report: Whole exome sequencing identifies a novel variant in the HPRT1 gene in a male with developmental delay

Lesch-Nyhan syndrome (LNS, OMIM #300322) is a rare X-linked genetic disorder caused by variants in the HPRT1 gene, which codes for the Hypoxanthine-guanine phosphoribosyltransferase (HGPRT). HPRT1 gene variants disrupt normal purine metabolism, leading to the involvement of multiple organ systems, primarily characterized by hyperuricemia, dystonia, and neurological abnormalities, which makes LNS clinically heterogeneous and diagnostically challenging. Here, we report a rare case of a 27-year-old Chinese male exhibiting severe lower limb motor disorders, hyperuricemia, and intellectual development delay. Blood tests showed hyperuricemia and whole exome sequencing (WES) identified a novel hemizygous variant in the HPRT1 (NM-000194.3) gene: c.104T > C in exon 2, respectively. Bioinformatics techniques indicated that the variant may disrupt the activity of HGPRT. According to the clinical presentation, diagnostic examination, and WES results, the patient was finally diagnosed with LNS. This study identified a previously unreported pathogenic variant in the HPRT1 gene. Although no curative therapy is currently available for HPRT1 gene variants at present, a definite diagnosis of its genetic etiology is of great significance for genetic counseling and family planning.

Whole Exome Sequencing Facilitates Early Diagnosis of Lesch-Nyhan Syndrome: A Case Series

BACKGROUND

Lesch-Nyhan syndrome (LNS) is a rare X-linked recessive metabolic disorder caused by mutations in the HPRT1 gene, resulting in hypoxanthine-guanine phosphoribosyltransferase (HPRT) deficiency. Early diagnosis is critical for optimizing management and improving outcomes. This study presents a case series of three Taiwanese patients diagnosed at a single medical center.

METHODS

Exome sequencing and biochemical testing were used to confirm the diagnoses. Early clinical manifestations, including hyperuricemia, hypotonia, and developmental delay, were documented during the initial stages of the disease.

RESULTS

All three patients had hyperuricemia, hypotonia, spasticity, and motor developmental delay. Pathogenic variants in the HPRT1 gene were identified in two patients, while the third was confirmed by biochemical testing. Two patients had orange-colored crystalline deposits in their diapers, indicative of hyperuricosuria. Self-injurious behavior had not yet developed in two patients due to their young age.

CONCLUSIONS

Early clinical features such as hyperuricemia, hypotonia, and motor delay may suggest LNS in infancy. Molecular genetic testing, particularly whole exome sequencing, can facilitate an early diagnosis before specific manifestations occur, enabling timely interventions and improving patient outcomes.

Genetically transitional disease: conceptual understanding and applicability to rheumatic disease

In genomic medicine, the concept of genetically transitional disease (GTD) refers to cases in which gene mutation is necessary but not sufficient to cause disease. In this Perspective, we apply this novel concept to rheumatic diseases, which have been linked to hundreds of genetic variants via association studies. These variants are in the 'grey zone' between monogenic variants with large effect sizes and common susceptibility alleles with small effect sizes. Among genes associated with rare autoinflammatory diseases, many low-frequency and/or low-penetrance variants are known to increase susceptibility to systemic inflammation. In autoimmune diseases, hundreds of HLA and non-HLA genetic variants have been revealed to be modest- to moderate-risk alleles. These diseases can be reclassified as GTDs. The same concept could apply to many other human diseases. GTD could improve the reporting of genetic testing results, diagnostic yields, genetic counselling and selection of therapy, as well as facilitating research using a novel approach to human genetic diseases.