A novel NFIA gene nonsense mutation in a Chinese patient with macrocephaly, corpus callosum hypoplasia, developmental delay, and dysmorphic features

Prenatal diagnosis of non-typical Chiari malformation type I associated with de novo Nuclear Factor I A gene mutation: a case report

BACKGROUND

Chiari malformation is one of the most common Central nervous system (CNS) abnormalities that can be detected in routine fetal scanning. Chiari malformation type I (CMI) is a congenital defect characterized by a displacement of the cerebellar tonsils through the foramen magnum. The etiology of CMI has not been well established and suggested having multifactorial contributions, especially genetic deletion. Clinical characteristics of this anomaly may express in different symptoms from neurological dysfunction and/or skeletal abnormalities in the later age, but it is rarely reported in pregnancy.

CASE PRESENTATION

We present a case in which the Chiari malformation type I was diagnosed with comorbidities of facial anomalies (flatting forehead and micrognathia) and muscular-skeletal dysmorphologies (clenched hands and clubfeet) at the 24+6 weeks of gestation in a 29-year-old Vietnamese pregnant woman. The couple refused an amniocentesis, and the pregnancy was followed up every 4 weeks until a spontaneous delivery occurred at 38 weeks. The newborn had a severe asphyxia and seizures at birth required to have an emergency resuscitation at delivery. He is currently being treated in the intensive neonatal care unit. He carries the novel heterozygous NFIA gene mutation confirmed after birth. No further postnatal malformation detected.

CONCLUSION

CMI may only represent with facial abnormalities and muscle-skeletal malformations at the early stage of pregnancy, which may also alert an adverse outcome. A novel heterozygous NFIA gene mutation identified after birth helps to confirm prenatal diagnosis of CMI and to provide an appropriate consultation.

Significant phenotypic variability in a multigenerational family with an NFIA missense mutation: Case series and review of the literature

We report the first multigenerational family with NFIA-related disorder from a missense variant. This case highlights the condition's phenotypic variability and the need for genetic testing when an initial diagnosis fails to explain all symptoms.

NFIA haploinsufficiency: case series and literature review

Background

NFIA-related disorder (OMIM #613735) is an autosomal dominant neurodevelopmental disorder characterized by a variable degree of cognitive impairment and non-specific dysmorphic features. To date, fewer than thirty patients affected by this disorder have been described.

Methods

Our study included three children with NFIA haploinsufficiency recruited from three medical genetics centers. Clinical presentations were recorded on a standardized case report form.

Results

All patients presented a variable degree of intellectual disability. None of the individuals in our cohort had urinary tract malformations. Three novel mutations, c.344G>A, c.261T>G, and c.887_888del are reported here.

Conclusion

NFIA haploinsufficiency can be suspected through careful observation of specific dysmorphisms, including macrocephaly and craniofacial abnormalities. Instrumental tests such as MRI and renal ultrasound provide further diagnostic clues, while genetic testing can confirm the diagnosis.

Phenotypic Spectrum of NFIA Haploinsufficiency: Two Additional Cases and Review of the Literature

The NFIA (nuclear factor I/A) gene encodes for a transcription factor belonging to the nuclear factor I family and has key roles in various embryonic differentiation pathways. In humans, NFIA is the major contributor to the phenotypic traits of "Chromosome 1p32p31 deletion syndrome". We report on two new cases with deletions involving NFIA without any other pathogenic protein-coding gene alterations. A cohort of 24 patients with NFIA haploinsufficiency as the sole anomaly was selected by reviewing the literature and public databases in order to analyze all clinical features reported and their relative frequencies. This process was useful because it provided an overall picture of the phenotypic outcome of NFIA haploinsufficiency and helped to define a cluster of phenotypic traits that can facilitate clinicians in identifying affected patients. NFIA haploinsufficiency can be suspected by a careful observation of the dysmorphisms (macrocephaly, craniofacial, and first-finger anomalies), and this potential diagnosis is strengthened by the presence of intellectual and developmental disabilities or other neurodevelopmental disorders. Further clues of NFIA haploinsufficiency can be provided by instrumental tests such as MRI and kidney urinary tract ultrasound and confirmed by genetic testing.

A 1p31.3 deletion encompassing the nuclear factor 1A gene presenting as possible temporal lobe epilepsy in association with schizoaffective disorder

Chromosome 1p32-p31 deletion syndrome, which is characterized by a variety of neurodevelopmental abnormalities, is thought to occur as a result of nuclear factor 1A (NFIA) haploinsufficiency. We present a case of a right-handed 40-year-old female with a 1p31.3 deletion, who exhibited numerous common features of this syndrome, in addition to treatment resistant schizoaffective disorder and possible temporal lobe epilepsy, making her presentation unique. While neither psychosis nor temporal lobe epilepsy has been described in this syndrome previously, these conditions likely occurred in our patient as a result of NFIA haploinsufficiency.

The p.Thr395Met missense variant of NFIA found in a patient with intellectual disability is a defective variant

Nuclear factor one A (NFIA) is a transcription factor that regulates the development of the central nervous system. Haploinsufficiency of the NFIA gene causes NFIA-related disorder, which includes brain abnormalities and intellectual disability, with or without urinary tract defects. Intragenic deletions, nonsense variants, frameshift variants, and missense variants in one allele of the NFIA gene have been reported to cause various neurological and urogenital symptoms. Here we report a 10-year-old male patient with developmental delay, coarctation of the aorta, and distinctive facial features. Exome analysis identified a rare de novo heterozygous missense variant p.Thr395Met in NFIA. We employed zebrafish as a model organism in our NFIA analysis and found that nfia^-/- zebrafish initially showed a loss of commissural axons in the brain, and eventually underwent growth retardation resulting in premature death. Impairment of the commissural neurons in nfia^-/- zebrafish embryos could be restored by the expression of wild-type human NFIA protein, but not of mutant human protein harboring the p.Thr395Met substitution, indicating that this variant affects the function of NFIA protein. Taken together, we suggest that the p.Thr395Met allele in the NFIA gene is relevant to the pathogenesis of NFIA-related disorder.

Recurrent NFIA K125E substitution represents a loss-of-function allele: Sensitive in vitro and in vivo assays for nontruncating alleles

Nuclear factor I A (NFIA) is a transcription factor that belongs to the NFI family. Truncating variants or intragenic deletion of the NFIA gene are known to cause the human neurodevelopmental disorder known as NFIA‐related disorder, but no patient heterozygous for a missense mutation has been reported. Here, we document two unrelated patients with typical phenotypic features of the NFIA‐related disorder who shared a missense variant p.Lys125Glu (K125E) in the NFIA gene. Patient 1 was a 6‐year‐old female with global developmental delay, corpus callosum anomaly, macrocephaly, and dysmorphic facial features. Patient 2 was a 14‐month‐old male with corpus callosum anomaly and macrocephaly. By using Drosophila and zebrafish models, we functionally evaluated the effect of the K125E substitution. Ectopic expression of wild‐type human NFIA in Drosophila caused developmental defects such as eye malformation and premature death, while that of human NFIA K125E variant allele did not. nfia‐deficient zebrafish embryos showed defects of midline‐crossing axons in the midbrain/hindbrain boundary. This impairment of commissural neurons was rescued by expression of wild‐type human NFIA, but not by that of mutant variant harboring K125E substitution. In accordance with these in vivo functional analyses, we showed that the K125E mutation impaired the transcriptional regulation of HES1 promoter in cultured cells. Taken together, we concluded that the K125E variant in the NFIA gene is a loss‐of‐function mutation.

A novel NFIA gene nonsense mutation in a Chinese patient with macrocephaly, corpus callosum hypoplasia, developmental delay, and dysmorphic features

BACKGROUND

NFIA gene (OMIM*600727) has been shown to be associated with a syndrome of central nervous system malformations (corpus callosum and ventriculomegaly) with or without urinary tract defects(BRMUTD) (OMIM#613735) with a low incidence. METHODS AND RESULTS:   We presented the clinical data of a 3-month-old Chinese infant with clinical features such as thin corpus callosum, ventriculomegaly, development delay, and dysmorphic features (macrocephaly, hypertelorism, slightly pointed chin, broad forehead, and large ears). Genomic DNA was extracted for Trio Whole Exome Sequencing. Preliminary genetic tests revealed one de novo heterozygous nonsense mutation c.220 C>T (p.Arg74Ter) of the NFIA gene (NM_005595).

CONCLUSION

Genetic DNA sequencing is a crucial method for diagnosing BRMUTD. This approach enriches the genotype and spectrum of BRMUTD syndrome and the outcome of the patient.