[A child with Fructose-1,6-bisphosphatase deficiency due to variant of FBP1 gene: Genetic and clinical analysis and literature review]

Abstract

Objective: To explore the clinical characteristics and variant of FBP1 gene in a child with Fructose-1,6-bisphosphatase deficiency (FBP1D), and review the literature on the clinical characteristics and gene mutations of FBP1D in the Chinese population.

Methods: A FBP1D proband due to variant of FBP1 gene who was admitted to Women and Children's Hospital of Ningbo University on August 10, 2021 due to "vomiting for 1 day" was selected as the study subject. Clinical data of the child were retrospectively collected. Whole exome sequencing (WES) was performed on the child, and candidate variants identified in the child were validated by Sanger sequencing in both the child and his parents. The difference between wild type and variant FBP1 protein were compared using AlphaFold v3.0.1 and PyMOL v2.5.6. The pathogenicity of candidate variant was rated according to the Standards and Guidelines for the Interpretation of Sequence Variants released by American College of Medical Genetics and Genomics (ACMG) (hereinafter referred to as ACMG guidelines). Using keywords such as "FBP1 gene" and "fructose-1,6-bisphosphatase deficiency" both in Chinese and English, relevant literature on FBP1D patients caused by FBP1 gene variants in the Chinese population were retrieved from the PubMed database, CNKI, and Wanfang Data Knowledge Service Platform, and the genetic variant and clinical phenotypes of FBP1D patients reported in the literature were analyzed. The literature retrieval time was set from the establishment of each database to October 31st, 2024. This study was approved by the Women and Children's Hospital of Ningbo University (Ethics No.: 2020-048).

Results: The proband was presented with repeated infections, nausea, vomiting, and mental illness. The auxiliary examination revealed hypoglycemia, acidosis, liver and kidney dysfunction, hyperlipidemia and hepatomegaly. WES and Sanger sequencing revealed that the child has harbored compound heterozygous variants of the FBP1 gene, including a de novo nonsense variant c.778G>T (p.G260*) in exon 6 and a maternally derived missense variant c.923C>G (p.P308R) in exon 7. The c.923C>G was known as a likely pathogenic variant, while c.778G>T has not been included in the databases such as HGMD, ClinVar, 1000 Genomes, ExAC, dbSNP, and gnomAD. Protein structure prediction shows that the c.778G>T (p.G260*) variant may result in a premature termination codon, resulting in loss of a β-fold in a core region, which may significantly reduce the stability of its protein product and affect its function. Based on the ACMG guidelines, the c.778G>T (p.G260*) variant was rated as likely pathogenic (PVS1_Strong+PM2_Supporting+PP4+PM6). Literature review has identified 32 patients from 23 Chinese families with FBP1D due to FBP1 gene variants. Together with the case reported in this study, in total 33 patients were analyzed. Among them, 22 cases were males (66.7%) with hypoglycemia, metabolic acidosis, vomiting, seizures, hyperlactatemia, and ketosis as the primary clinical phenotypes. After treatment, only 1 case (3.0%) died due to cerebral hernia, while the remaining 32 (97.0%) had favorable outcomes. Four cases (12.1%) exhibited developmental delay. A total of 66 FBP1 gene variant sites were identified, which involved 22 variant types, predominantly missense mutations (31 gene variant sites). These variants were mainly located in exon 7 of the gene (25 variant sites), with c.490G>A (16.7%, 11/66), c.960_961insG (19.7%, 13/66), c.355G>A (12.1%, 8/66), and c.704delC (9.1%, 6/66) being the most common variants.

Conclusion: The heterozygous variant of the FBP1 gene probably underlay the FBP1D in this child. Above finding has enriched the phenotypic and mutational spectrum of the FBP1 gene and provided a basis for genetic counseling and clinical decision-making.