A novel mutation in neurofibromatosis type 1
How to cite this article: Luo Z, Tao X, Jin Z, Wang Z. A novel mutation in neurofibromatosis type 1. Indian J Dermatol Venereol Leprol doi: 10.25259/IJDVL_480_2022
Neurofibromatosis type 1 (NF1) is an autosomal dominant disorder with a global prevalence of about 0.03% caused by mutations in the neurofibromatosis type 1 gene at 17q11.2, which encodes neurofibromin. Approximately half of the patients have family history and the others have sporadic mutations.1 Typical symptoms of neurofibromatosis type 1 include café-au-lait macules, cutaneous neurofibroma or plexiform neurofibroma, axillary or inguinal freckles, iris Lisch nodules, optic pathway gliomas, skeletal dysplasia, behavioural defects and cognitive impairment.
The proband was a 21-year-old woman. There were many café-au-lait macules of different sizes all over the body since one month after birth. The number of the café-au-lait macules in the waist and abdomen gradually increased and fused with age. At around 16-years of age, subcutaneous mass appeared on her both sides of the lumbar ribs and gradually increased in size [Figure 1]. Pathology of subcutaneous mass biopsy showed tumours formed by spindle cells [Figure 1]. neurofibromatosis type 1 was diagnosed by the diagnostic criteria formulated by the National Institutes of Health. The proband’s mother also had café-au-lait macules, tumours and freckles [Figure 2], and a biopsy was performed on her posterior dorsal tumours [Figure 2]. The proband’s maternal grandmother and second aunt also had café-au-lait macules. Her father and sister were normal.
We collected blood samples from the proband, her parents and sister after the informed consent. This study was approved by the hospital ethics committee. The DNA of the proband’s mother was sent to the company (Shanghai SARO Biotechnology Co., Ltd.) for panel-targeted capture sequencing. The novel mutation was verified in the proband, her father and sister by Sanger sequencing.
A point mutation (c.T1664>G) in exon 15 of the neurofibromatosis type 1 gene (NM_001042492) was found, which caused the cDNA from T to G at position 1664, resulting in premature termination of protein translation at position 555 and abnormal structure of neurofibromin. The mutation was detected in the proband but not in her sister and father by Sanger sequencing [Figure 3]. Mutation Taster predicted this mutation to be “D” (disease causing) and the Likelihood Ratio Test predicts deleterious. It is not described in gnomAD exomes and any other databases. According to the American College of Medical Genetics and Genomics guidelines, this variant is a nonsense mutation and can be interpreted as a pathogenic variant of neurofibromatosis type 1 (PVS1+PM2+PP1).2
More than 3000 pathogenic mutations have been identified in the neurofibromatosis type 1 gene, including missense, nonsense, splicing, microdeletion, microinsertion, total deletion (>20 bp), total insertion (>20 bp) and complex rearrangement. The penetrance of neurofibromatosis type 1 is 100%, but the expression of the neurofibromatosis type 1 gene is highly variable and age-dependent. Even within the same family, the clinical manifestations can be variable in different patients. As in this case, though the proband and her mother held the same mutation, the mother mainly presented with cutaneous neurofibroma, while the proband mainly had giant type plexiform neurofibroma. Phenotype differences may be related to allelic and nonallelic heterogeneity, cell heterogeneity, epigenetics, modified loci, environmental and random factors.
In our case, the mutation is a premature termination codon mutation. Depending on the differences of the clinical manifestations of the proband and her mother, it is not possible to judge whether the mutation causes serious phenotypes, which may require a comprehensive physical examination and long-term follow-up. So far, we have found that five genotypes are clinically identified to be associated with the phenotypes, and there is no correlation between premature termination codon mutations and specific phenotypes. It is only suggested that neurofibromatosis type 1 gene microdeletion and total deletion are associated with severe phenotypes. The number of plexiform and spinal neurofibromas increases, and intellectual and skeletal abnormalities can occur.3 Different phenotypes were found in mutations with different locations. The missense change of codon 1809 (p. Arg1809 Cys) mainly manifested as café-au-lait macules and freckles, macrocephaly, growth retardation and learning problems;4 the missense mutations affecting codons 844–848 are related to the severe phenotypes, which can be manifested as high risk of plexiform neurofibroma, spinal neurofibroma and even malignant transformation.5 Mild phenotype is associated with in-frame deletion of codon 992 (p.Met992del) mainly characterised by pigmentation-like features without cutaneous neurofibroma.6 Therefore, there was no significant phenotypic difference in the mutation types.
In summary, we have identified a novel nonsense mutation in the neurofibromatosis type 1 gene causing different phenotypes of neurofibromatosis in family lines, and our findings expand the spectrum of mutations causing neurofibromatosis type 1 and provide information for genetic counselling.
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