Hemizygous pathogenic variants in MBTPS2 located at Xp22.12 cause IFAP syndrome, which is characterized by the triad of ichthyosis, alopecia and photophobia. Here we identified a hemizygous intronic variant in MBTPS2 (NM_015884: c.970+5G>A) in a patient with alopecia, follicular keratinization, developmental delay and epilepsy which were compatible with IFAP syndrome. The variant has been reported to cause skipping of 20 bases in exon 7, leading to the premature termination codon. To further investigate the consequence of the variant, we performed long-read RNA sequencing using RNA extracted from fibroblasts cultured from the patient's skin. Long-read RNA sequencing revealed skipping of exons 6 and 7, in addition to the previously reported 20-base skipping in exon 7. Furthermore, the expression of normal transcripts, as observed in healthy skin, was markedly reduced. Long-read RNA sequencing is a powerful tool for simultaneously identifying diverse transcript isoforms, making it highly valuable for elucidating the effects of splice-altering variants.

Microcephaly with or without chorioretinopathy, lymphedema or mental retardation is a rare KIF11-related disorder. Here we report the case of a patient with microcephaly, lymphedema, nystagmus and familial exudative vitreoretinopathy carrying a novel de novo KIF11 nonsense variant (NM_004523.4:p.Glu123Ter), which is considered pathogenic. This case expands the phenotypic range of KIF11 pathogenic variants and highlights the importance of early ophthalmological evaluation, genetic counseling and family assessment.

Autosomal dominant polycystic kidney disease (ADPKD) is a hereditary disorder

MINAR2 is essential for normal hearing by regulating cholesterol localization in stereocilia in hair cells. MINAR2 knockout results in rapidly progressive sensorineural hearing loss (SNHL) in mice and zebrafish models. Recently, biallelic variants in MINAR2 have been reported to cause SNHL in four unrelated families with nonsyndromic severe to profound SNHL. Here we provide a second report of an additional family with SNHL. The index patient presented with nonsyndromic severe to profound SNHL. The family history was remarkable for a 20-year-old male sibling with nonsyndromic severe to profound SNHL. Both patients did not have any neurological involvement. Trio whole-exome sequencing of the index and his parents revealed a homozygous nonsense variant in MINAR2 (NM_001257308.2:c.319A>T; p.(Lys107*) in the index. Parents were heterozygous for the same variant. This variant introduces an early stop codon and probably results in a loss of function because of the predicted nonsense-mediated decay. Our study provides the first independent confirmation of the MINAR2-related SNHL.

Tricho-hepato-enteric syndrome (THES), a rare autosomal recessive disorder caused by variants in the SKIC3 or SKIC2 gene, is characterized by intractable diarrhea, woolly hair, growth restriction and liver disease. Here we report a neonatal case of THES with neonatal hemochromatosis, in which the novel compound heterozygous SKIC3 variants NM_014639.4:c.815_816del p.(Gly272AlafsTer9) and NM_014639.4:c.2284G>A p.(Gly762Arg) were identified. Further research is needed to elucidate the mechanisms underlying iron metabolism dysregulation in THES.

Spastic paraplegia (SPG)10 is an autosomal dominant SPG caused by kinesin family member 5A (KIF5A) gene variants. We describe a Japanese patient with SPG whose deceased mother and maternal uncle also exhibited SPG. Exome analysis identified a rare KIF5A nonsense variant (NM_004984.4:c.2590C>T (p.Arg864Ter)) in the patient, regarded as pathogenic. As KIF5A mRNA expression was significantly decreased compared with that of a healthy control, the variant was deemed causative of SPG.

DSG2, encoding desmoglein-2, is one of the causative genes of arrhythmogenic cardiomyopathy. We previously identified a homozygous DSG2 p.Arg119Ter stop-gain variant in a patient with juvenile-onset cardiomyopathy and advanced biventricular heart failure. However, the pathological significance and prevalence of the heterozygous DSG2 p.Arg119Ter variant remains uncertain. Here, we identified four unrelated patients with cardiomyopathy with heterozygous DSG2 p.Arg119Ter variants among 808 patients with nonischemic cardiomyopathy; the allele frequency was 0.0037, which is more than 50-fold greater than that reported in the general Japanese population. These patients were clinically diagnosed with arrhythmogenic right ventricular cardiomyopathy (Pt-1), dilated cardiomyopathy (DCM) after ventricular septum defect closure surgery (Pt-2), DCM (Pt-3), and end-stage hypertrophic cardiomyopathy (Pt-4). The patients also exhibited reduced left ventricular contractile function and varying clinical courses. Genetic analysis identified additional possible causative variants, DSG2 p.Arg292Cys in Pt-1 and BAG3 p.His166SerfsTer6 in Pt-3. Immunohistochemical analysis of endomyocardial biopsy samples revealed that the expression of not only desmoglein-2 but also desmoplakin was markedly reduced. Transmission electron microscopy revealed pale and fragmented desmosomes and widened gaps between intercalated discs in the myocardium. A microforce test using human cardiomyocytes differentiated from induced pluripotent stem cells (iPSC-CMs) demonstrated reduced contractility in iPSC-CMs carrying a heterozygous truncating variant in DSG2. These data suggest that the DSG2 p.Arg119Ter variant is concealed in patients with cardiomyopathy with heart failure, and desmosome impairment may be a latent exacerbating factor of contractile dysfunction and disease progression.

Cockayne syndrome (CS) is a progressive multisystem disorder characterized by growth failure, microcephaly, developmental delay, and photosensitivity. The characteristic symptoms appear during early childhood in most patients with CS. Herein, we report a mild case of CS with a novel start-loss variant in ERCC8 that did not show the characteristic symptoms of CS during early childhood and exhibited sudden growth failure after the age of 10 years.

Recently, heterozygous loss-of-function NFKB1 variants were identified as the primary cause of common variable immunodeficiency (CVID) in the European population. However, pathogenic NFKB1 variants have never been reported in the Japanese population. We present a 29-year-old Japanese woman with CVID. A novel variant, c.136 C > T, p.(Gln46*), was identified in NFKB1. Her mother and daughter carried the same variant, demonstrating the first Japanese pedigree with an NFKB1 pathogenic variant.

HCN1 is one of four genes encoding hyperpolarization-activated cyclic nucleotide-gated channels. The phenotypic spectrum associated with HCN1 variants ranges from neonatal developmental and epileptic encephalopathy to idiopathic generalized epilepsy. We report a Japanese patient with repetitive focal seizures and super-refractory status epilepticus since early infancy caused by a de novo HCN1 variant, NM_021072.4, c.1195T>C, p.(Ser399Pro). This variant might have a dominant-negative effect on channel function, leading to severe epileptic encephalopathy.