Shazia Khan

Background: Neurodevelopmental disorders (NDDs) are clinically heterogeneous conditions with complex etiologies and limited therapeutic options. Here, we investigated a proband presenting global developmental delay (GDD), tonic seizures, failure to thrive, mild microcephaly, intellectual disability (ID), and hypotonia. Methods: Exome sequencing (ES), followed by Sanger sequencing, was performed for molecular diagnosis. Gene expression was assessed by reverse‐transcriptase quantitative PCR (RT‐qPCR), and 3D protein modeling was performed. Results: ES revealed a novel de novo (heterozygous) missense variant [c.2660C>T; p.(Pro887Leu)], in LRRC7 (NM_001370785.2) gene, located in exon 18, which may contribute to the proband's phenotype. The identified variant was classified as variant of uncertain significant (VUS) according to the American College of Medical Genetics and Genomics Guidelines (ACMG). RT‐qPCR showed reduced LRRC7 mRNA expression in the proband compared to control samples, while and 3D protein modeling revealed substantial changes in the LRRC7‐secondary structure. Conclusion: Using genetic, molecular, in silico, and expression analysis, we characterize a novel de novo‐ LRRC7 variant and describe its association with an NDD phenotype.

Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function; they are characterized by extensive genetic and clinical variability. We performed clinical, genetic, biochemical, and molecular analyses on two consanguineous families with microcephaly exhibiting an NDD. Detailed clinical investigation and molecular diagnosis were performed using whole-exome sequencing (WES), followed by Sanger sequencing for the affected families. WES revealed disease-causing homozygous variants in two families associated with microcephaly and NDDs. In family A and family B, we identified two previously reported homozygous variants (c.3978G>A; Trp1326* and c.4309C>A; p.Arg1437Ser) in the ASPM gene. Both the variants were further confirmed using bi-directional Sanger sequencing. In the present study, we presented literature review regarding the NDDs and microcephaly associated with ASPM pathogenesis. These findings contribute to studies of genotype–phenotype correlation, genetic counseling of the families, inclusion of ASPM in newborn screening, and further understanding of human brain function and development.

Bardet–Biedl syndrome (BBS) is a rare clinically and genetically heterogeneous autosomal recessive multi-systemic disorder with 22 known genes. The primary clinical and diagnostic features include six different hallmarks, such as rod–cone dystrophy, learning difficulties, renal abnormalities, male hypogonadism, post-axial polydactyly, and obesity. Here, we report nine consanguineous families and a non-consanguineous family with several affected individuals presenting typical clinical features of BBS. In the present study, 10 BBS Pakistani families were subjected to whole exome sequencing (WES), which revealed novel/recurrent gene variants, including a homozygous nonsense mutation (c.94C>T; p.Gln32Ter) in the IFT27 (NM_006860.5) gene in family A, a homozygous nonsense mutation (c.160A>T; p.Lys54Ter) in the BBIP1 (NM_001195306.1) gene in family B, a homozygous nonsense variant (c.720C>A; p.Cys240Ter) in the WDPCP (NM_015910.7) in family C, a homozygous nonsense variant (c.505A>T; p.Lys169Ter) in the LZTFL1 (NM_020347.4) in family D, pathogenic homozygous 1 bp deletion (c.775delA; p.Thr259Leufs*21) in the MKKS/BBS5 (NM_170784.3) gene in family E, a pathogenic homozygous missense variant (c.1339G>A; p.Ala447Thr) in BBS1 (NM_024649.4) in families F and G, a pathogenic homozygous donor splice site variant (c.951+1G>A; p?) in BBS1 (NM_024649.4) in family H, a pathogenic bi-allelic nonsense variant in MKKS (NM_170784.3) (c.119C>G; p.Ser40*) in family I, and homozygous pathogenic frameshift variants (c.196delA; p.Arg66Glufs*12) in BBS5 (NM_152384.3) in family J. Our findings extend the mutation and phenotypic spectrum of four different types of ciliopathies causing BBS and also support the importance of these genes in the development of multi-systemic human genetic disorders.

Background: Population diversity is important and rare disease isolates can frequently reveal novel homozygous or biallelic mutations that lead to expanded clinical heterogeneity, with diverse clinical presentations.Methods: The present study describes two consanguineous families with a total of seven affected individuals suffering from a clinically similar severe syndromic neurological disorder, with abnormal development and central nervous system (CNS) and peripheral nervous system (PNS) abnormalities. Whole exome sequencing (WES) and Sanger sequencing followed by 3D protein modeling was performed to identify the disease‐causing gene. RNA was extracted from the fresh blood of both families affected and healthy individuals.Results: The families were clinically assessed in the field in different regions of Khyber Pakhtunkhwa. Magnetic resonance imagining was obtained in the probands and blood was collected for DNA extraction and WES was performed. Sanger sequencing confirmed a homozygous, likely pathogenic mutation (GRCh38: chr17:42684199G>C; (NM_003632.3): c.333G>C);(NP_003623.1): p.(Trp111Cys) in the CNTNAP1 gene in family A, previously associated with Congenital Hypo myelinating Neuropathy 3 (CHN3; OMIM # 618186) and a novel nonsense variant in family B, (GRCh38: chr16: 57654086C>T; NC_000016.10 (NM_001370440.1): c.721C>T); (NP_001357369.1): p.(Gln241Ter) in the ADGRG1 gene previously associated with bilateral frontoparietal polymicrogyria (OMIM # 606854); both families have extended CNS and PNS clinical manifestations. In addition, 3D protein modeling was performed for the missense variant, p.(Trp111Cys), identified in the CNTNAP1, suggesting extensive secondary structure changes that might lead to improper function or downstream signaling. No RNA expression was observed in both families affected and healthy individuals hence showing that these genes are not expressed in blood.Conclusions: In the present study, two novel biallelic variants in the CNTNAP1 and ADGRG1 genes in two different consanguineous families with a clinical overlap in the phenotype were identified. Thus, the clinical and mutation spectrum is expanded to provide further evidence that CNTNAP1 and ADGRG1 are very important for widespread neurological development.

Objective: To identify genetic causes of Shabbir syndrome in two patients of Pakistani origin. Methods: In the present study, we have investigated a Pakistani family with two affected members segregating Laryngo-onycho-cutaneous (LOC) syndrome. The patients were diagnosed as suspected cases of LOC based on phenotypes including abnormal larynx, nails, and hyperpigmentation in patients’ eyes. Genetic investigation was done by performing whole exome sequencing (WES) using DNA of the patients. Sanger sequencing was performed to validate WES findings and segregation analysis in the family. Results: Data analysis of exomes and Sanger sequencing of patients revealed a homozygous one base pair duplication (NM_000227.6; LAMA3; c.151dup; p.Val51GlyfsTer4) in LAMA3 in the patients. Parents of the patients were heterozygous for the identified variant. Conclusion: Previously, the same variant has been found in most of the Pakistani Punjabi patients affected with LOC. Therefore, Pakistani Punjabi families affected with Shabbir Syndrome may be screened for c.151dup variant in LAMA3 using targeted sequencing. Sanger sequencing is a cost-effective and time-saving technique as compared to whole exome/genome sequencing. Hence, developing ethnicity-specific LAMA3 targeted molecular diagnostic test would be cost-effective. Further, the study would assist in carrier testing and prenatal diagnosis of the affected families. doi: https://doi.org/10.12669/pjms.39.4.6926 How to cite this: Ullah A, Syed F, Khan S. c.151dup variant in LAMA3 in Pakistani patients affected with Shabbir Syndrome but showing mild symptoms. Pak J Med Sci. 2023;39(4):1124-1128. doi: https://doi.org/10.12669/pjms.39.4.6926 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

The highly evolutionarily conserved transport protein particle (TRAPP) complexes (TRAPP II and III) perform fundamental roles in subcellular trafficking pathways. Here we identified biallelic variants in TRAPPC10, a component of the TRAPP II complex, in individuals with a severe microcephalic neurodevelopmental disorder. Molecular studies revealed a weakened interaction between mutant TRAPPC10 and its putative adaptor protein TRAPPC2L. Studies of patient lymphoblastoid cells revealed an absence of TRAPPC10 alongside a concomitant absence of TRAPPC9, another key TRAPP II complex component associated with a clinically overlapping neurodevelopmental disorder. The TRAPPC9/10 reduction phenotype was recapitulated in TRAPPC10^-/- knockout cells, which also displayed a membrane trafficking defect. Notably, both the reduction in TRAPPC9 levels and the trafficking defect in these cells could be rescued by wild type but not mutant TRAPPC10 gene constructs. Moreover, studies of Trappc10^-/- knockout mice revealed neuroanatomical brain defects and microcephaly, paralleling findings seen in the human condition as well as in a Trappc9^-/- mouse model. Together these studies confirm autosomal recessive TRAPPC10 variants as a cause of human disease and define TRAPP-mediated pathomolecular outcomes of importance to TRAPPC9 and TRAPPC10 mediated neurodevelopmental disorders in humans and mice.

Background: Limb‐girdle muscular dystrophy (LGMD) comprises a heterogeneous group of diseases, affecting different muscles, predominantly skeletal muscles and cardiac muscles of the body. LGMD is classified into two main subtypes A and B, which are further subclassified into eight dominant and thirty recessive subtypes. Three genes, namely POPDC1, POPDC2 and POPDC3, encode popeye domain‐containing protein (POPDC), and the variants of POPDC1 and POPDC3 genes have been associated with LGMD.Methods: In the present study, we performed whole‐exome sequencing (WES) analysis on a single‐family to investigate the hallmark features of LGMD. The results of WES were further confirmed by Sanger sequencing and 3D protein modeling was also conducted.Results: WES data analysis and Sanger sequencing revealed a homozygous missense variant (c.460A>G; p.Lys154Glu) at a highly conserved amino acid position in the POPDC3. Mutations in the POPDC3 gene have been previously associated with recessive limb‐girdle muscular dystrophy type 26. 3D protein modeling further suggested that the identified variant might affect the POPDC3 structure and proper function.Conclusions: The present study confirms the role of POPDC3 in LGMD, and will facilitate genetic counseling of the family to mitigate the risks of the carrier or affects on future pregnancies.

This research explores the seasonal evolution of sea surface salinity (SSS) in the Northwestern Indian Ocean (NWIO) over the Sea of Oman (SOO) and the Arabian Sea. For this study we used the datasets provided by the Argo floats within the timeframe from 2004 to 2019. For SSS, values of salinity are used nearest to the sea surface (depth ≤ 10 m), as it would be comparable to satellite SSS measurements. From the seasonal evolution of SSS, we investigated the co-existence of two water masses in the Arabian Sea region: 1) the Arabian Sea High Saline Water (ASHSW) that is in excess of salinity (> 36.9) and occupying the north and central basins of the Arabian Sea and 2) the Bay of Bengal Water (BBW) that is inferior in salinity (˂ 35) and occupying the south basin of the Arabian Sea.

Distal arthrogryposis (DA) is a heterogeneous sub-group of arthrogryposis multiplex congenita (AMC), mostly characterized by having congenital contractures affecting hands, wrists, feet, and ankles. Distal arthrogryposis is mostly autosomal dominantly inherited, while only one sub-type DA type 5D is inherited in an autosomal recessive manner. Clinically, DA5D is described having knee extension contractures, micrognathia, distal joint contractures, clubfoot, ptosis, contractures (shoulders, elbows, and wrists), and scoliosis. Using whole exome sequencing (WES) followed by Sanger sequencing, we report on a first familial case of DA5D from Pakistani population having a novel biallelic missense mutation (c.158C>A, p.Pro53Leu) in the ECEL1 gene. Our result support that homozygous mutations in ECEL1 causes DA5D and expands the clinical and allelic spectrum of ECEL1 related contracture syndromes.

Ciliopathies are a clinically and genetically heterogeneous group of disorders often exhibiting phenotypic overlap and caused by abnormalities in the structure or function of cellular cilia. As such, a precise molecular diagnosis is important for guiding clinical management and genetic counseling. In the present study, two Pakistani families comprising individuals with overlapping clinical features suggestive of a ciliopathy syndrome, including intellectual disability, obesity, congenital retinal dystrophy, and hypogonadism (in males), were investigated clinically and genetically. Whole‐exome sequencing identified the likely causes of disease as a novel homozygous frameshift mutation (NM_152384.2: c.196delA; p.(Arg66Glufs*12); family 1) in BBS5, and a nonsense mutation (NM_019892.5:c.1879C>T; p.Gln627*; family 2) in INPP5E, previously reported in an extended Pakistani family with MORM syndrome. Our findings expand the molecular spectrum associated with BBS5 mutations in Pakistan and provide further supportive evidence that the INPP5E mutation is a common cause of ciliopathy in Northern Pakistan, likely representing a regional founder mutation. This study also highlights the value of genomic studies in Pakistan for families affected by rare heterogeneous developmental disorders and where clinical phenotyping may be limited by geographical and financial constraints. The identification of the spectrum and frequency of disease‐causing variants within this setting enables the development of population‐specific genetic testing strategies targeting variants common to the local population and improving health care outcomes.