X-exome sequencing in Finnish families with intellectual disability--four novel mutations and two novel syndromic phenotypes.
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.
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.
Anju K
AK
Philips
Auli
A
Sirén
Kristiina
K
Avela
Mirja
M
Somer
Maarit
M
Peippo
Minna
M
Ahvenainen
Fatma
F
Doagu
Maria
M
Arvio
Helena
H
Kääriäinen
Hilde
H
Van Esch
Guy
G
Froyen
Stefan A
SA
Haas
Hao
H
Hu
Vera M
VM
Kalscheuer
Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland. irma.jarvela@helsinki.fi.
Irma
I
Järvelä
D000293:Adolescent; D000328:Adult; D059472:Exome / Q000235:genetics*; D005260:Female; D050172:Genes, X-Linked; D006801:Humans; D008607:Intellectual Disability / Q000235:genetics*; D008297:Male; D009154:Mutation; D010375:Pedigree; D055815:Young Adult