Excess of de novo variants in genes involved in chromatin remodelling in patients with marfanoid habitus and intellectual disability

PURPOSE

Marfanoid habitus (MH) combined with intellectual disability (ID) (MHID) is a clinically and genetically heterogeneous presentation. The combination of array CGH and targeted sequencing of genes responsible for Marfan or Lujan-Fryns syndrome explain no more than 20% of subjects.

METHODS

To further decipher the genetic basis of MHID, we performed exome sequencing on a combination of trio-based (33 subjects) or single probands (31 subjects), of which 61 were sporadic.

RESULTS

We identified eight genes with de novo variants (DNVs) in at least two unrelated individuals (ARID1B, ATP1A1, DLG4, EHMT1, NFIX, NSD1, NUP205 and ZEB2). Using simulation models, we showed that five genes (DLG4, NFIX, EHMT1, ZEB2 and ATP1A1) met conservative Bonferroni genomewide significance for an excess of the observed de novo point variants. Overall, at least one pathogenic or likely pathogenic variant was identified in 54.7% of subjects (35/64). These variants fell within 27 genes previously associated with Mendelian disorders, including NSD1 and NFIX, which are known to be mutated in overgrowth syndromes.

CONCLUSION

We demonstrated that DNVs were enriched in chromatin remodelling (p=2×10^-4) and genes regulated by the fragile X mental retardation protein (p=3×10^-8), highlighting overlapping genetic mechanisms between MHID and related neurodevelopmental disorders.

Nager syndrome: confirmation of SF3B4 haploinsufficiency as the major cause

Nager syndrome belongs to the group of acrofacial dysostosis, which are characterized by the association of craniofacial and limb malformations. Recently, exome sequencing studies identified the SF3B4 gene as the cause of this condition in most patients. SF3B4 encodes a highly conserved protein implicated in mRNA splicing and bone morphogenic protein (BMP) signaling. We performed SF3B4 sequencing in 14 families (18 patients) whose features were suggestive of Nager syndrome and found nine mutations predicted to result in loss-of-function. SF3B4 is the major gene responsible for autosomal dominant Nager syndrome. All mutations reported predict null alleles, therefore precluding genotype-phenotype correlations. Most mutation-negative patients were phenotypically indistinguishable from patients with mutations, suggesting genetic heterogeneity.

Clinical and molecular spectrum of renal malformations in Kabuki syndrome

OBJECTIVE

To determine the frequency and types of renal malformations, and to evaluate renal function in a cohort of patients with Kabuki syndrome (KS).

STUDY DESIGN

Renal ultrasound scans and plasma creatinine measurements were collected from a French cohort of 94 patients with genotyped KS. Renal function was evaluated based on the estimated glomerular filtration rate. A genotype-phenotype study was conducted for renal and urinary tract malformations.

RESULTS

Renal malformations were present in 22% of cases, and urinary tract anomalies were present in 15%. Renal malformations were observed in 28% of the MLL2 mutation-positive group and in 0% of the MLL2 mutation-negative group (P = .015). No correlation was found between the presence or absence of renal or urinary tract malformations and the location or type of MLL2 mutation. Renal function was normal except for 1 patient with a MLL2 mutation diagnosed in the first days of life and severe renal disease due to unilateral renal agenesia and controlateral severe hypoplasia that progressed to the terminal stage at age 2 years.

CONCLUSION

Our study emphasizes the need for ultrasound and renal function screening in children diagnosed with KS.

Systematic molecular and cytogenetic screening of 100 patients with marfanoid syndromes and intellectual disability

The association of marfanoid habitus (MH) and intellectual disability (ID) has been reported in the literature, with overlapping presentations and genetic heterogeneity. A hundred patients (71 males and 29 females) with a MH and ID were recruited. Custom-designed 244K array-CGH (Agilent®; Agilent Technologies Inc., Santa Clara, CA) and MED12, ZDHHC9, UPF3B, FBN1, TGFBR1 and TGFBR2 sequencing analyses were performed. Eighty patients could be classified as isolated MH and ID: 12 chromosomal imbalances, 1 FBN1 mutation and 1 possibly pathogenic MED12 mutation were found (17%). Twenty patients could be classified as ID with other extra-skeletal features of the Marfan syndrome (MFS) spectrum: 4 pathogenic FBN1 mutations and 4 chromosomal imbalances were found (2 patients with both FBN1 mutation and chromosomal rearrangement) (29%). These results suggest either that there are more loci with genes yet to be discovered or that MH can also be a relatively non-specific feature of patients with ID. The search for aortic complications is mandatory even if MH is associated with ID since FBN1 mutations or rearrangements were found in some patients. The excess of males is in favour of the involvement of other X-linked genes. Although it was impossible to make a diagnosis in 80% of patients, these results will improve genetic counselling in families.

Association of ectrodactyly and distal phocomelia

Ectrodactyly and phocomelia are well known limbs malformations. They can be a part of various syndromes, and are more often transmitted with dominant autosomal Inheritance with variable expression and Incomplete penetrance. Different loci have been Identified for ectrodactyly (SHFM1 at 7q21.3q22.1, SHFM2 at Xq26, SHFM3 at 10q24q25, SHFM4 at 3q27), and two genes are known (DSS1 for SHFM1, p63 for SHFM4). We report the case of a 33 year-old female affected with the association of ectrodactyly and phocomelia. It could be a "new" association, or a mild or partial expression of the syndrome Including ectrodactyly, phocomelia, deafness and sinusal arythmia.

[Costello syndrome: clinical aspects and tumor risk]

Costello syndrome is a sporadic development anomaly suggesting a genetic determinism. Main features include characteristic facial features, mental retardation, growth retardation, cutis laxa, heart malformation, and peri-orificial papillomata. In previous reported cases, the frequency of tumors is 15%, which argues for a screening protocol. The occurrence of a tumor in a child with growth retardation and cutis laxa must be reminiscent of Costello syndrome. The determinism of this syndrome is still unknown, and the hypothesis of an inactivation of a tumor suppressor gene is to be considered.