Indentification of Genes Responsible for Intellectual Disability in Consanguineous Families

Abstract

Intellectual disability (ID) or cognitive impairment is clinically and genetically a heterogeneous disorder. The extreme genetic heterogeneity is evident from the identification of approximately 2500 ID genes (also include autosomal recessive ID genes) but despite this recent progress underlying genes are still unknown in the large number of ID patients/families. Here we present 8 consanguineous Pakistani families which have multiple individuals with autosomal recessive ID. Affected members of these families mainly presented ID, but detailed clinical evaluations also showed the presence of additional features in some ID patients including facial dysmorphism, microcephaly, polydactyly, hypopigmented skin, strabismus, hypotonia, cerebellar ataxia, myotonic dystrophy, cerebral palsy and micrognathia. DNA samples collected from all available members of these eight families were used for whole genome genotyping and homozygosity mapping was performed to identify the homozygosity by descent (HBD) regions. Homozygosity mapping led to the identification of single HBD region in family G, but all other families have multiple HBD regions. Majority of the detected HBD regions do not overlap with each other and thus ruled out the involvement of the same gene in these families. Subsequently, DNA samples from one patient from each family was used for exome sequencing to identify the ID causing variant. However, the analysis and filtering of variants obtained by exome sequencing identified 28 potentially pathogenic variants, which were tested for segregation in the respective families. Further analysis of these 28 variants and segregation tests helped to reduce the list of 28 variant to nine potential variants. The potential variants were identified in TRAPPC10 (Family A), RAB11FIP1 (Family B), CWF19L1 (Family C), WDR19 (Family D), SYNE1 (Family E), ALG3 (Family F), AP4M1 (Family G), DUOX2 (Family H) and ZNF54 (Family H) genes. Among the identified variants, variants in novel candidate genes were identified in family A and family B, but other variants were identified either in the known ID gene or in gene involved in ID spectrum disorders. In family A, a variant (c.C2786T; p.P929L) in TRAPPC10 was detected in the proband, which segregate with the ID phenotype in this family. This variant affects the C terminal region of TRAPPC10, and is predicted to affect its interaction with TRAPPC9 protein. Similarly, in family B a missense variant (c.451A>C; pAsn151His) in exon 2 was identified which is predicted to affects the C2 domain of the protein at N terminus end and probably decreases the GTP binding efficiency of this domain. Microscopic analysis of hair samples of proband from this family showed the irregular pattern of melanin indicating the improper transportation of proteins. The genes identified in both the families play role in the vesicle transport and it is anticipated that loss of function variant identified in family A and B probably compromise this role and thus may cause ID in the affected individuals of both families. In family C, a nonsense variant (c.C949T; p.Q317X ) was identified in CWF19L1 gene, whereas affected members of family D carry a missense variant (c. 3521G>A; p.R1174H) in WDR19 gene. Both these variants are novel but CWF19L1 and WDR19 genes are already known to cause ID. However, affected members of families E, F and G have pathogenic variants in SYNE1 (p.R82L), ALG3 (c.274G>T; p.Ser270Leu) and AP4M1 (c.193-194delTA; p.Y65FfsX50) genes, respectively and these genes are known to cause disorders which also include ID. The variants identified in these families are novel except the variant in AP4M1 gene which has been already reported in a Pakistani family. In family H, exome sequence analysis identifies two potential variants in DUOX2 and ZNF541 genes, but we could not establish the pathogenic nature of these potential variants with certainty. Though the variants in DUOX2 gene has recently been associated with ID in patients with congenital hypothyroidism but testing of thyroid function of two affected members of our family ruled out the thyroid abnormalities in these patients. After ruling out the involvement of DUOX2 variant in this family we looked for additional variants which resulted in the identification of a variant (p. K733N) in ZNF541 gene. However, based on the currently available data it is difficult to ascertain the functional effects of this variant and thus it can be considered as variant of unknown significance (VUS). This study results in the identification of two (TRAPPC10 and RAB11FIP1) ID genes and six reported genes that are associated with ID. The network analysis of the genes identified in this study showed the involvement of pathways involved in the modification of lipids and proteins, membrane trafficking, maintenance of nuclear integrity and flagellar movements. Together these processes are required for the proper development and functioning of the brain which is needed for higher level functioning such as cognition and the disturbances in these processes can result in ID or related disorder in humans.The work presented in this thesis results in the following publications: 1. Ricardo Harripaul, Nasim Vasli, Anna Mikhailov, Muhammad Arshad Rafiq, Kirti Mittal, Christian, Muhammad Ilyas, Falak Sher Khan, Valeed Khan, Mohammad Moradi, Muhammad Ayaz, Farooq Naeem, Abolfazl Heidari, Peter John, Iltaf Ahmed, Zehra Agha, Asif Mir, Muhammad Ansar, Leon French, Muhammad Ayub, John B. Vincent. Mapping autosomal recessive intellectual disability: Combined microarray and exome sequencing identifies 26 novel candidate genes in 192 consanguineous families. Molecular Psychiatry. 2017 Apr 11. doi: 10.1038/mp.2017.60. 2. Regie Lyn P Santos-Cortez*, Valeed Khan*, Falak Sher Khan, Zaib-un-Nisa Mughal, Imen Chakchouk, Kwanghyuk Lee, Memoona Rasheed, Ehsan Ullah, Muhammad Arif Nadeem Saqib, Izoduwa Abbe, Ghazanfar Ali, Saadullah Khan, Zahid Azeem, Irfan Ullah, Deborah, Wasim Ahmad, Muhammad Ansar, Suzanne M. Leal. Novel candidate genes and variants underlying autosomal recessive neurodevelopmental disorders with intellectual disability. Human Genetics 2018. DOI:10.1007/s00439-018-1928-6.