Identification of Disease Causing Genes in Intellectually Disabled Pakistani Families

Abstract

Development of nervous system is a complex biological process that is tightly controlled and any abnormality in this process may result in different types of neurodevelopmental disorders (NDDs). Intellectual disability (ID) is a specific type of NDD which is characterized by less than average intelligence and compromised adaptive behavior. ID affects 1-3% population worldwide and its prevalence is much higher in certain populations. ID is genetically heterogeneous with over 1500 genes are currently known. The presence of ID with different co-morbidities further adds to the complexity of the underlying genetics. This study aims to identify disease-causing variants in 15 Pakistani families with autosomal recessive and X linked ID inheritance. Fifteen families (A-O), with total 47 affected individuals, were collected from various remote villages from three provinces of Pakistan. ID was inherited in autosomal recessive pattern in 12 (A-C, F-L, N-O) families while X-linked recessive inheritance was observed in 3 families (D, E, M). The clinical investigation of the families revealed presence of additional clinical features in some families such as seizures (Family A, B, G, M), hypotonia (Family A), facial dysmorphism (Family A, C, G, H, J, M), camptodactyly (Family B), autistic features (Family F), behavioral abnormality (Family A, E, F, H, J, K, M, N), speech impairment (Family A, B, C, D, F, G, H, I, M, N), lethargy (Family F, G), microcephaly (Family I), ataxia (Family A, I), short stature (Family L), self-harm (Family M) and ambulation delay (Family J, N). The genetic analysis helped in the identification of homozygous missense variants in three novel genes, ZBTB11 (p.H880Q), ELFN1 (p.P50H) and CCS (p.117A), in family A, B and G(b), respectively. ZBTB11 acts as a transcription factor which is localized in nucleolus and novel variant, p.H880Q, identified in family A results in its mislocalization and loss of function. ELFN1 functions as trans-regulator of mGluR7 in excitatory post synaptic sites and Elfn1 knockout mice exhibits seizures and hyperactivity and these clinical features were also observed in our patients of family B. In family C and F, novel non-sense homozygous variants were identified in previously known ID genes i.e. METTL4 (p.R84*) and C5orf42 (p.Q2871*). In family E and I, a 9 bp and a 4 bp homozygous deletions were identified in ARX (p.R483fs*46) and BCKDK Abstract Identification of disease causing genes in intellectually disabled Pakistani Families ix (p.D216Lfs*65), respectively. The frameshift variant (p.D216Lfs*65) identified in BCKDK probably results in the constitutive activation of enzyme complex in the affected members of family I. In family D, a novel homozygous ~0.2 Mb deletion was identified which resulted in the deletion of exon 6 of IL1RAPL1. This deletion was confirmed by DNA walking, Sanger sequencing and real time PCR. In family G(a), H and J, recurrent mutations were identified in GNE (p.Y156H), RSRC1 (c.532-1G>A) and LRP2 (p.D3779N). The GNE missense variant, p.Y156H, is previously reported to cause hereditary inclusion body myopathy however the clinical profile in family G(a) was ID with seizures. The variants identified in these RSRC1 and LRP2 are already known to cause ID in Pakistani families. This study helped in identification of three novel genes and five novel putative disease causing mutations in ID genes and two recurrent mutations. Furthermore, this study also reports a recurrent mutation with a phenotypic expansion. The genetic cause of ID in five families (K-O) could not be identified and additional work is needed to unravel the ID associated genes in these families. The work presented here is part of these publications;  Rasheed M, Khan V, Harripaul R, Siddiqui M, Malik MA, Zahid M, Vincent JB, Ansar M. Exome sequencing identifies novel mutations in six families with intellectual disability. BMC Medical Genomics 2021, Aug 27;14(1):211. doi: 10.1186/s12920-021-01066-y  Santos-Cortez RLP, Khan V, Khan FS, Mughal ZU, Chakchouk I, Lee K, Rasheed M, Hamza R, Acharya A, Ullah E, Saqib MAN, Abbe I, Ali G, Hassan MJ, Khan S, Azeem Z, Ullah I, Bamshad MJ, Nickerson DA, Schrauwen I, Ahmad W, Ansar M, Leal SM. Novel candidate genes and variants underlying autosomal recessive neurodevelopmental disorders with intellectual disability. Human Genetics 2018;137(9):735-752.  Fattahi Z, Sheikh TI, Musante L, Rasheed M, Taskiran II, Harripaul R, Hu H, Kazeminasab S, Alam MR, Hosseini M, Larti F, Ghaderi Z, Celik A, Ayub M, Ansar M, Haddadi M, Wienker TF, Ropers HH, Kahrizi K, Vincent JB, Najmabadi H. Biallelic missense variants in ZBTB11 can cause intellectual disability in humans. Human Molecular Genetics 2018;27(18):3177-3188