Prenatal diagnosis of short-rib polydactyly syndrome type III or short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3) associated with compound heterozygous mutations in DYNC2H1 in a fetus

Clinical features and genetic analysis of a case series of skeletal ciliopathies in a prenatal setting

BACKGROUND

Short-rib polydactyly syndrome (SRPS) refers to a group of lethal skeletal dysplasias that can be difficult to differentiate between subtypes or from other non-lethal skeletal dysplasias such as Ellis-van Creveld syndrome and Jeune syndrome in a prenatal setting. We report the ultrasound and genetic findings of four unrelated fetuses with skeletal dysplasias.

METHODS

Systemic prenatal ultrasound examination was performed in the second or third trimester. Genetic tests including GTG-banding, single nucleotide polymorphism (SNP) array and exome sequencing were performed with amniocytes or aborted fetal tissues.

RESULTS

The major and common ultrasound anomalies for the four unrelated fetuses included short long bones of the limbs and narrow thorax. No chromosomal abnormalities and pathogenic copy number variations were detected. Exome sequencing revealed three novel variants in the DYNC2H1 gene, namely NM_001080463.2:c.6809G > A p.(Arg2270Gln), NM_001080463.2:3133C > T p.(Gln1045Ter), and NM_001080463.2:c.337C > T p.(Arg113Trp); one novel variant in the IFT172 gene, NM_015662.3:4540-5 T > A; and one novel variant in the WDR19 gene, NM_025132.4:c.2596G > C p.(Gly866Arg). The genotypes of DYNC2H1, IFT172 and WDR19 and the phenotypes of the fetuses give hints for the diagnosis of short-rib thoracic dysplasia (SRTD) with or without polydactyly 3, 10, and 5, respectively.

CONCLUSION

Our findings expand the mutation spectrum of DYNC2H1, IFT172 and WDR19 associated with skeletal ciliopathies, and provide useful information for prenatal diagnosis and genetic counseling on rare skeletal disorders.

Genetic analysis and prenatal diagnosis of short-rib thoracic dysplasia 3 with or without polydactyly caused by compound heterozygous variants of DYNC2H1 gene in four Chinese families

Background: To describe the genetic variation of dynein cytoplasmic 2 heavy chain 1 (DYNC2H1) gene in four Chinese families affected with short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3), and to provide evidence for accurate prenatal diagnosis and genetic counseling.

Methods: The detailed clinical prenatal sonographic features of four fetuses with SRTD3 were carried out. Trio-whole exome sequencing (WES) and proband-WES sequencing was applied to filtrated causative variants in four families. The causative variants of each family were validated in by Sanger sequencing. Bioinformation analysis was applied to predict the harmfulness of these mutations and perform the protein-protein interaction network and Gene Ontology (GO) analysis. A vitro minigene splicing assay was conducted to assess the influence of the splice site variant.

Results: Typical characterization of the four fetuses included short long bones, short ribs, narrow chest, hand and foot posture abnormalities, femur short in diameter and slightly bowing, cardiac abnormalities, and so on. Moreover, eight compound heterozygous variants of DYNC2H1 (NM_001080463.2): c.3842A>C (p.Tyr1281Ser) and c.8833-1G>A, c.8617A>G (p.Met2873Val) and c.7053_7054del (p.Cys2351Ter), c.5984C>T (p.Ala1995Val) and c.10219C>T (p.Arg3407Ter), c.5256del (p.Ala1753GlnfsTer13) and c.9737C>T (p.Thr3246Ile), were identified. Among which, c.10219C>T (p.Arg3407Terp), c.5984C>T (p.Ala1995Val) and c.9737C>T (p.Thr3246Ile) were reported in ClinVar databases, and c.8617A>G (p.Met2873Val), c.10219C>T (p.Arg3407Ter), c.5984C>T (p.Ala1995Val) were found in HGMD databases. Four variants (c.3842A>C (p.Tyr1281Ser), c.8833-1G>A, c.7053_7054del (p.Cys2351Ter) and c.5256del (p.Ala1753GlnfsTer13) were first reported as novel mutations. According to the ACMG guidelines, c.8617A>G (p.Met2873Val), c.7053_7054del (p.Cys2351Ter), c.5984C>T (p.Ala1995Val), c.10219C>T (p.Arg3407Ter) and c.5256del (p.Ala1753GlnfsTer13) were rated as pathogenic or likely pathogenic variants, others variants were predicted to be variants of uncertain significance mutations. The minigene assay results indicated that c.8833-1G>A caused the skipping over exon 56, resulting in exon 56 loss.

Conclusion: In our study, we analyzed the genetic mutations in four fetuses with SRTD3 by whole exome sequencing and identified pathogenic variants causing SRTD3. Our results expand the mutation spectrum of DYNC2H1 in SRTD3, which is helpful for the accurate prenatal diagnosis of SRTD3 fetuses and provide useful strategies for genetic counseling.

Genetic variations in the DYNC2H1 gene causing SRTD3 (short-rib thoracic dysplasia 3 with or without polydactyly)

Background and aims: Short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3) represents a type of severe fetal skeletal dysplasia (SD) characterized by shortened limbs, narrow thorax with or without polydactyly, which is caused by the homozygous or compound heterozygous mutations in the DYNC2H1 gene. SRTD3 is a recessive disorder, identification of the responsible genetic variation would be beneficial to an accurate prenatal diagnosis and well-grounded counseling for the affected families. Material and methods: Two families having experienced recurrent fetal SDs were recruited and submitted to a multiplatform genetic investigation. Whole-exome sequencing (WES) was performed with samples collected from the probands. Sanger sequencing and fluorescent quantitative PCR (qPCR) were conducted as validation assays for suspected variations. Results: WES identified two compound heterozygous variations in the DYNC2H1(NM_001080463.2) gene, namely c.2386C>T (p.Arg796Trp) and c.7289T>C (p.Ile2430Thr) for one; and exon (64-83)del and c.8190G>T (p.Leu2730Phe) for the other, respectively. One variant in them, exon (64-83)del, was novelly identified. Conclusion: The study detected two compound heterozygous variation in DYNC2H1 including one novel deletion: exon (64-83) del. Our findings clarified the cause of fetal skeletal dysplasia in the subject families, provided guidance for their future pregnancies, and highlighted the value of WES in diagnosis of skeletal dysplasia with unclear prenatal indications.

A novel WDR60 variant contributes to a late diagnosis of Jeune asphyxiating thoracic dystrophy in a Chinese patient: A case report

We report a Chinese patient with JATD presenting a mild skeletal phenotype and with renal insufficiency as the initial symptom of the disease. A novel homozygous c.2789C>T (p.S930L) variant in the WDR60 gene was identified. Our report will help to improve awareness and diagnosability for this disease.

Identification of novel compound heterozygous mutations of the DYNC2H1 gene in a fetus with short-rib thoracic dysplasia 3 with or without polydactyly

A prenatal sonograph revealed a 26-week-old fetus with short limbs and a narrow chest in a 23-year-old woman with a history of fetal skeletal dysplasia. A single nucleotide polymorphism-based chromosomal microarray (CMA) indicated a normal karyotype, and no chromosomal segments with abnormal copy numbers were noted in the fetus. Whole exome sequencing identified compound heterozygous mutations in the DYNC2H1 gene responsible for a lethal type of bone growth disorder, short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3), and revealed a missense mutation c.515C>A (p. Pro172Gln) of paternal origin and a missense mutation c.5983G>A (p. Ala1995Thr) of maternal origin. These variants were further confirmed by Sanger sequencing. To the extent known, the c.515C>A (p. Pro172Gln) mutation is novel for SRTD3, and the site is conserved across species. This study found a novel mutation of the DYNC2H1 gene for SRTD3 and it has increased the number of reported cases and expanded the spectrum of mutations causing this rare disease.

Checking NEKs: Overcoming a Bottleneck in Human Diseases

In previous years, several kinases, such as phosphoinositide 3-kinase (PI3K), mammalian target of rapamycin (mTOR), and extracellular-signal-regulated kinase (ERK), have been linked to important human diseases, although some kinase families remain neglected in terms of research, hiding their relevance to therapeutic approaches. Here, a review regarding the NEK family is presented, shedding light on important information related to NEKs and human diseases. NEKs are a large group of homologous kinases with related functions and structures that participate in several cellular processes such as the cell cycle, cell division, cilia formation, and the DNA damage response. The review of the literature points to the pivotal participation of NEKs in important human diseases, like different types of cancer, diabetes, ciliopathies and central nervous system related and inflammatory-related diseases. The different known regulatory molecular mechanisms specific to each NEK are also presented, relating to their involvement in different diseases. In addition, important information about NEKs remains to be elucidated and is highlighted in this review, showing the need for other studies and research regarding this kinase family. Therefore, the NEK family represents an important group of kinases with potential applications in the therapy of human diseases.

Genetic Overview of Syndactyly and Polydactyly

Syndactyly and polydactyly-respectively characterized by fused and supernumerary digits-are among the most common congenital limb malformations, with syndactyly presenting at an estimated incidence of 1 in 2,000-3,000 live births and polydactyly at a frequency of 1 in approximately 700-1,000 live births. Despite their relatively regular manifestation in the clinic, the etiologies of syndactyly and polydactyly remain poorly understood because of their phenotypic and genetic diversity. Further, even though concrete knowledge of genotypic links has been established for some variants of syndactyly and polydactyly, there appears to be no single comprehensive published summary of all syndromic and nonsyndromic syndactyly and polydactyly presentations, and there is decidedly no resource that maps all syndromic and nonsyndromic syndactylies and polydactylies to their genetic bases. This gap in the literature problematizes comprehensive carrier screening and prenatal diagnosis and complicates novel diagnostic attempts. This review thus attempts to collect all that is known about the genetic bases of syndromic and nonsyndromic syndactylies and polydactylies, as well as to highlight the dactyly manifestations for which no genetic bases are as yet known. Then, having established a summation of existing and missing knowledge, this work briefly outlines the diagnostic techniques that a genetics-reinforced understanding of syndactyly and polydactyly could inform.