X-exome sequencing in Finnish families with intellectual disability--four novel mutations and two novel syndromic phenotypes

Abstract

Background: X-linked intellectual disability (XLID) is a group of genetically heterogeneous disorders characterized by substantial impairment in cognitive abilities, social and behavioral adaptive skills. Next generation sequencing technologies have become a powerful approach for identifying molecular gene mutations relevant for diagnosis.

Methods & objectives: Enrichment of X-chromosome specific exons and massively parallel sequencing was performed for identifying the causative mutations in 14 Finnish families, each of them having several males affected with intellectual disability of unknown cause.

Results: We found four novel mutations in known XLID genes. Two mutations; one previously reported missense mutation (c.1111C > T), and one novel frameshift mutation (c. 990_991insGCTGC) were identified in SLC16A2, a gene that has been linked to Allan-Herndon-Dudley syndrome (AHDS). One novel missense mutation (c.1888G > C) was found in GRIA3 and two novel splice donor site mutations (c.357 + 1G > C and c.985 + 1G > C) were identified in the DLG3 gene. One missense mutation (c.1321C > T) was identified in the candidate gene ZMYM3 in three affected males with a previously unrecognized syndrome characterized by unique facial features, aortic stenosis and hypospadia was detected. All of the identified mutations segregated in the corresponding families and were absent in > 100 Finnish controls and in the publicly available databases. In addition, a previously reported benign variant (c.877G > A) in SYP was identified in a large family with nine affected males in three generations, who have a syndromic phenotype.

Conclusions: All of the mutations found in this study are being reported for the first time in Finnish families with several affected male patients whose etiological diagnoses have remained unknown to us, in some families, for more than 30 years. This study illustrates the impact of X-exome sequencing to identify rare gene mutations and the challenges of interpreting the results. Further functional studies are required to confirm the cause of the syndromic phenotypes associated with ZMYM3 and SYP in this study.

Figure 1

Overview of the mutations reported in SLC16A2 gene in two Finnish families with Allan Herndon Dudley Syndrome. a) Family pedigree of L107 showing the inheritance of SLC16A2 mutation, open circles denote females; circles with a dot in the middle denote obligate carrier females, empty square denote males, the left half of the black squares denote affected males, the right half of the squares denote mutation positive males, crossed symbols denote deceased individuals, wt denote mutation negative subject, b) Sanger sequencing confirming the missense mutation c.1111C > T, c) Multiple species protein sequence alignment showing conservation of the mutated R371 residue, d) Family pedigree of D299 showing the inheritance of SLC16A2 mutation, e) Sanger sequencing confirming the frameshift insertion c.990_991insGCTGC.

Figure 2

Overview of the missense variant reported in GRIA3 in a Finnish Family with XLID. a) Family pedigree showing the inheritance of the GRIA3 mutation, open circles denote females; circles with a dot in the middle denote obligate carrier females, empty square denote males, the left half of the black squares denote affected males, the right half of the squares denote mutation positive males, crossed symbols denote deceased individuals, wt denote mutation negative subject, b) Photographs of the affected males, c) Sanger sequencing confirming the mutation, d) Multiple species protein sequence alignment showing conservation of the mutated G630 residue.

Figure 3

Overview of the two splice donor mutations identified in DLG3 in two Finnish families. a) Pedigree of family D172 showing the inheritance of the DLG3 splice donor mutation c.357 + 1G > C, open circles denote females; circles with a dot in the middle denote obligate carrier females, empty square show males, the left half of the black squares denote affected males, the right half of the squares denote mutation positive males, crossed symbols denote deceased individuals, wt denote mutation negative subject, b) Sanger sequencing result showing the mutation in one affected male, c) Pedigree of family D301 showing the inheritance of the DLG3 splice donor mutation c.985 + 1G > C, d) Sanger sequencing result showing the mutation in one affected male, e) Schematic representation of the DLG3 gene, along with overview of previously reported mutations and mutations reported in the current study.

Figure 4

Clinical presentation of a novel syndrome in a Finnish family with XLID and segregation of the ZMYM3 missense mutation. a) Pedigree showing the inheritance of the ZMYM3 mutation in family D222, open circles show females, circles with a dot in the middle show obligate carrier females, empty square show males, the left half of the black squares show affected males, the right half of the squares show mutation positive males, crossed symbols denote deceased individuals, wt denote mutation negative subject, b) Photographs of the three affected males, c) Sanger sequencing confirming the mutation, d) Multiple species protein alignment showing conservation of the mutated R441 residue in ZMYM3.

Figure 5

A clinical presentation of a novel syndrome in a Finnish family (D175) with XLID. a) Family pedigree showing the inheritance of the benign variant in SYP, open circles denote females, circles with a dot in the middle denote obligate carrier females, empty square denote males, the left half of the black squares denote affected males, the right half of the squares denote mutation positive males, crossed symbols denote deceased individuals, wt denote mutation negative subject, b) Photographs of the six affected males, c) Sanger sequencing confirming the benign variant, d) Multiple species protein alignment showing conservation of the mutated Gly293 residue in SYP, e) Schematic presentation of the SYP protein domains, location of the published mutations and the polymorphism identified in this study.