Mosaic Intronic NIPBL Variant in a Family With Cornelia de Lange Syndrome

Abstract

Cornelia de Lange Syndrome (CdLS) is a well described multiple malformation syndrome caused by alterations in genes encoding subunits or regulators of the cohesin complex. In approximately 70% of CdLS patients, pathogenic NIPBL variants are detected and 15% of them are predicted to affect splicing. Moreover, a large portion of genetic variants in NIPBL was shown to be somatic mosaicism. Here we report two family members with different expression of the CdLS phenotype. In both individuals, a c.869-2A>G (r.869_1495del) substitution was detected, affecting a conserved splice-acceptor site. Deep sequencing revealed the presence of somatic mosaicism in the mother. The substitution was detected in 23% of the sequencing reads using DNA derived from blood samples and 51% in DNA from buccal swabs. The analysis of blood DNA of the son excluded the presence of somatic mosaicism. Correlation of molecular and clinical data revealed that various distribution of genetic alteration in different cell types had an impact on the expression of observed clinical features in both individuals.

Recurrence and Familial Inheritance of Intronic NIPBL Pathogenic Variant Associated With Mild CdLS

“…Interestingly despite only a tiny fraction of the total NIPBL mRNA seems represented by the alternative transcripts, likely undergoing degradation, their occurrence is sufficient for recognition of the CdLS phenotype. In conclusion, our data corroborates the previously reported case with the same branch site pathogenic variant ( 11 ) highlighting the significance and diagnostic impact of non-canonical intronic variants of NIPBL gene in CdLS patients and the graded clinical presentation of CdLS with detection of extremely mild adult cases through their progeny ( 10 ). It is well-known that the approximate detection rate of NIPBL pathogenic variants (~70%) also implemented by the recent widespread application of multigene panel and WES NGS ( 9 ), underestimates the fraction of cases with mild phenotype.…”

“…Although the estimated frequency of NIPBL splicing defects is consistent ( 9 , 10 ), only two non-canonical splice variants are recorded in HGMD database: NM_133433:c.459-9G>A which effect is only predicted ( 4 ) and the branch site variant NM_133433:c.5329-15A>G, recurring in our patients and the previously described case ( 11 ). Sequencing of the proband's cDNA showed two aberrant transcripts a-Tr1 and a-Tr2, a finding consistent with the frequent detection of multiple mRNA species, widely reported for variants deeply located within an intron as those affecting the branch point ( 15 ).…”

“…Mildly affected CdLS subjects are rare ( 1 ) and often they remain molecularly unsolved. Whenever they display suggestive clinical features they should be accurately investigated, also in the non-coding sequence, considering the 50% risk of generating affected progeny ( 10 , 16 ).…”

“…Splicing alterations account for 17% NIPBL pathogenic variants ( 9 ) but are likely underestimated, as almost all those detected affect canonical splice sites or flanking consensus sequences (LOVD NIPBL ). A familial case where a canonical NIPBL splice variant segregating from a mosaic mother to her son was recently reported to be associated to heterogeneous phenotype expression ( 10 ). The prevalence of pauci-symptomatic NIPBL- mutated cases is difficult to estimate as these patients are often overlooked and do not receive molecular diagnosis.…”

Genetic Mosaicism in a Group of Patients With Cornelia de Lange Syndrome

“…Unfortunately, the blood sample of this patient was not available for the study. In the patient CdLS02M, substitution (c.869-2A>G, p.Gly290_Lys498del) was detected in 23% (251/1115) and 51% (74/148) of reads in DNA extracted from blood and buccal swab samples, respectively (13). Finally, a novel intronic and mosaic variant of KMT2A (c.4012+1G>A) was found in 48% (349/823) of reads of DNA extracted from buccal swab sample of patient CdLS09.…”