Amelogenesis Imperfecta (AI) is a set of hereditary diseases affecting enamel development, leading to various types of enamel defects, potentially impacting oral health unassociated with other generalized defects. AI manifests in syndromic and non-syndromic forms and can be inherited through autosomal recessive, autosomal dominant, or X-linked inheritance patterns. Genetic studies have identified sequence variants in a number of genes (≥ 70) linked to both syndromic and non-syndromic AI, highlighting the genetic diversity underlying the condition. The current study involved clinical evaluation and exome sequencing, aimed at identifying the causative variants in four unrelated consanguineous Pakistani families presenting AI phenotypes. The exome sequencing results revealed a novel homozygous frameshift variant FAM20A : NM_017565.4, c.188dupA; p.(Asp63Glufs*17) in families A, B, and C while a nonsense homozygous variant WDR72 : NM_182758.4, c.2686C > T; p. (Arg896*) in family D. The segregation of both variants was confirmed by Sanger sequencing. Bioinformatics analysis predicted the pathogenicity of these genetic variants. These alterations suggest functional consequences, potentially impairing the FAM20A and WDR72 proteins and causing dental anomalies. This investigation significantly broadens our understanding of FAM20A and WDR72 ’s involvement in AI. Furthermore, this study highlights the genetic heterogeneity of AI (involving FAM20A and WDR72 in this study) within the Pakistani population.

ObjectiveThis study aims to clinically and genetically assess 30 unrelated consanguineous Pakistani families from various ethnic backgrounds, all exhibiting features of neurodevelopmental disorders (NDDs).MethodsWe conducted clinical, genetic, biochemical, and molecular analyses on 30 consanguineous families with NDDs enrolled from various regions of Pakistan. The likely molecular causes of primary microcephaly and NDDs were identified. Detailed clinical investigations and molecular diagnoses were performed using whole exome sequencing (WES) of the proband, followed by Sanger sequencing for validation and segregation in the available family members of the affected families.ResultsWES identified likely disease-causing homozygous variants in 30 unrelated consanguineous families. Six families presented newly described variants in known NDD-related genes: ABAT (c.1439 T > G; p.Phe480Cys) [OMIM613163], SLC12A6 (c.2865_2865insT; p.Glu955Asnfs*5) [OMIM 218000], SHANK3 (c.1305-3_1,305-2delTT; p.Gln29-_Gly305del) [OMIM 606232], BCKDK (c.356_356insC; p.Gly119Alafs*24) [OMIM 614923], DDHD2 (c.2065G > T; p.Asp689Tyr) [OMIM 615033], ERCC2 (c.1255G > A; p.Glu419Lys) [OMIM 610756]. Additionally, 12 families had previously reported disease-causing variants associated with different types of NDDs: ATRX (c.109C > T; p.Arg37*) [OMIM 309580], GPR56 [ADGRG1] (c.1423C > T; p.Arg475*) [OMIM 606854], NAGLU (c.1694G > A; p.Arg565Gln) [OMIM 252920], DOLK (c.3G > A; p.Met1Ile) [OMIM 610768], GPT2 (c.815C > T; p.Ser272Leu) [OMIM 616281], DYNC1I2 (c.607 + 1G > A; p.?) [OMIM 618492], FBXL3 (c.885delT; p.Leu295Phefs25*) [OMIM 606220], LINGO1 (c.869G > A; p.Arg290His) [OMIM 618103], and ASPM (c.3978G > A; Trp1326*, c.9557C > G; p.Ser3186*, c.6994C > T; p.Arg2332*) [OMIM 608716]. All the identified variants showed segregation compatible with autosomal recessive inheritance.ConclusionIn the present study, we observed a high frequency of ASPM variants in the genetic analysis of 30 consanguineous families exhibiting features of NDDs, particularly those associated with autosomal recessive primary microcephaly. These findings contribute to studies on genotype–phenotype correlation, genetic counseling for families, and a deeper understanding of human brain function and development.

A family of Pakistani origin, segregating polydactyly, and phalangeal synostosis in an autosomal dominant manner, has been investigated and presented in the present report. Whole-exome sequencing (WES), followed by segregation analysis using Sanger sequencing, revealed a heterozygous missense variant [c.G1696A, p.(Gly566Ser)] in the LRP4 gene located on human chromosome 11p11.2. Homology protein modeling revealed the mutant Ser566 generated new interactions with at least four other amino acids and disrupted protein folding and function. Our findings demonstrated the first direct evidence of involvement of LRP4 in causing polydactyly and phalangeal synostosis in the same family. This study highlighted the importance of inclusion of LRP4 gene in screening individuals presenting polydactyly in hands and feet, and phalangeal synostosis in the same family.

BACKGROUND:Congenital ichthyosis is a diverse group of keratinization disorders associated with generalized scaling of skin of varying severity. The non-syndromic forms of congenital ichthyosis are further grouped into common ichthyosis (ichthyosis vulgaris and X-linked ichthyosis), autosomal recessive congenital ichthyosis, and keratopathic ichthyosis.OBJECTIVE:To identify sequence variants involved in different forms of hereditary ichthyoses.METHODS:We studied eight families with different types of ichthyosis including four families with autosomal recessive congenital ichthyosis and four families with common ichthyosis. Whole exome sequencing and PCR based genotyping was carried out to find out the molecular basis of disease.RESULTS:In one family, a novel duplication sequence variant NM_002016.2:c.2767dupT; NP_002007.1:p.Ser923PhefsTer2 was identified in FLG gene; in four families a previously reported nonsense sequence variant NM_000359.3:c.232C>T; NP_002007.1:p.Arg78Ter was identified in TGM1 gene, while, in three families of X-linked recessive ichthyosis, the whole STS gene (NM_001320752.2; NP_001307681.2) regions were deleted.STUDY LIMITATION:Gene expression studies have not been performed that would have strengthened the findings of computational analysis.CONCLUSION:This study highlights the significance of the c.232C>T variant in the TGM1 gene as a possible founder mutation, complete STS gene deletion as reported previously in Pakistani population, while novel sequence variant in the FLG gene expands the spectrum of variations in this gene. These findings may be used for genetic counseling of the studied families.

Sequence variants causing SHFM. None. The peer review history for this article is available at https://www.webofscience.com/api/gateway/wos/peer-review/10.1111/cge.14430. Data will be available upon request.

Background: Nephrolithiasis is a common disease with a 10% lifetime risk in men and 5% in women. With the emergence of noninvasive and minimally invasive methods, the management of renal stones has vastly improved. Objective: Comparison of effectiveness of percutaneous nephrolithotomy vs retrograde intrarenal surgery for the treatment of renal pelvis stones. Methodology: This study was randomized controlled trial carried out at the Department of Urology and Renal Transplantation, Institute of Kidney Diseases Hayatabad Medical Complex,Peshawar for six months from 23-09-2018 to 22-03-2019. Total sample size was 70 patients. Patients in group A underwent Percutaneous Nephrolithotomy (PCNL) and Group B will be subjected to RIRS. All the patients will be advised for follow up visit at 2 weeks post operatively to determine intervention effectiveness in terms of complete stone clearance. Results: The mean size of the stone was 17.47mm ± 1.7SD, ranges 15 to 20 mm in both groups. In group A, PCNL Procedure was effective in 34(97.1%) patients at completion of study. While in group B, 28(80%) patients were effectively stone cleared. which is significant with p-value=0.027. Conclusion: Percutaneous Nephrolithotomy (PCNL) is more efficient and safe procedure for renal stone of size 1.5cm to 2 cm as compared to RIRS. Studies show that PCNL is more effective than retrograde intrarenal surgery in the treatment of renal pelvis stones. In the light of recent data, PCNL seems to be an ideal treatment modality in the management of patients. Nevertheless, these results must be confirmed by further prospective large randomized trials. Keywords: Percutaneous Nephrolithotomy, Retrograde Intrarenal Surgery, Renal Stones

An eco-friendly efficient supramolecular solvent-based method was developed for extraction and determination of selected non-steroidal anti-inflammatory drugs (NSAIDs) such as diclofenac sodium, caffeine and paracetamol in water samples followed by detection with high-performance liquid chromatography. Supramolecular solvent (SUPRAs) with composition of 400 mu L of 1-undecanol as reverse micelles in dispersing solvent of 15% tetrahydrofuran (THF) solution in water at pH 4 used as extracting solvent for selected NSAIDs. Various factors affecting the extraction efficiency of NSAIDs like amount of 1-undecanol, percentage of THF, composition of SUPRA, pH, vortex time and sample amount were studied. Limit of detection (S/N = 3) and quantification (S/N = 10) were 0.02 and 0.08 mu g mL(-1) for paracetamol, 0.006 and 0.02 mu g mL(-1) for caffeine, 0.06 and 0.2 mu g mL(-1) for diclofenac sodium with linear range of 0.1-12 mu g mL(-1). The inter-day relative standard deviation (RSD) values were 3.1%-5.2%, 3.3%-4.2% and 2.2%-3.6%, while for intra-day the RSD values obtained were 2.4%-4.1%, 1.4%-3.1% and 1.5%-4.1% for paracetamol, caffeine and diclofenac sodium, respectively. The proposed method has been applied successfully to the spiked water samples and recoveries were found in the range of 89.5%-94.6% for tape water, 88.5%-92.8% for canal water and 90.0%-95.2% for industrial wastewater samples was obtained.

Autosomal primary microcephaly (MCPH) is a heterogenetic disorder that affects brain's cerebral cortex size and leads to a reduction in the cranial vault. Along with the hallmark feature of reduced head circumference, microcephalic patients also exhibit a variable degree of intellectual disability as well. Genetic studies have reported 28 MCPH genes, most of which produce microtubule-associated proteins and are involved in cell division. Herein this study, 14 patients from seven Pashtun origin Pakistani families of primary microcephaly were analyzed. Mutation analysis was performed through targeted Sanger DNA sequencing on the basis of phenotype-linked genetic makeup. Genetic analysis in one family found a novel pathogenic DNA change in the abnormal spindle microtubule assembly (ASPM) gene (NM_018136.4:c.3871dupGA), while the rest of the families revealed recurrent nonsense mutation c.3978G>A (p.Trp1326*) in the same gene. The novel reported frameshift insertion presumably truncates the protein p.(Lys1291Glyfs*14) and deletes the N-terminus domains. Identification of novel ASPM-truncating mutation expands the mutational spectrum of the ASPM gene, while mapping of recurrent mutation c.3978G>A (p.Trp1326*) will aid in establishing its founder effect in the Khyber Pakhtunkhwa (KPK) inhabitant population of Pakistan and should be suggestively screened for premarital counseling of MCPH susceptible families. Most of the recruited families are related to first-degree consanguinity. Hence, all the family elders were counseled to avoid intrafamilial marriages.

AIM: To investigate the genetic basis of autosomal recessive retinitis pigmentosa (arRP) in two consanguineous/ endogamous Pakistani families. METHODS: Whole exome sequencing (WES) was performed on genomic DNA samples of patients with arRP to identify disease causing mutations. Sanger sequencing was performed to confirm familial segregation of identified mutations, and potential pathogenicity was determined by predictions of the mutations’ functions. RESULTS: A novel homozygous frameshift mutation [NM_000440.2:c.1054delG, p. (Gln352Argfs*4); Chr5:g.149286886del (GRCh37)] in the PDE6A gene in an endogamous family and a novel homozygous splice site mutation [NM_033100.3:c.1168-1G>A, Chr10:g.85968484G>A (GRCh37)] in the CDHR1 gene in a consanguineous family were identified. The PDE6A variant p. (Gln352Argfs*4) was predicted to be deleterious or pathogenic, whilst the CDHR1 variant c.1168-1G>A was predicted to result in potential alteration of splicing. CONCLUSION: This study expands the spectrum of genetic variants for arRP in Pakistani families.

Primitive epidermis develops the nail apparatus. Nails have a strong and inflexible nail plate at the end of each digit. Very few genes responsible for causing nonsyndromic form of nail dysplasia have been reported. In the current study, peripheral blood samples were collectedfrom three unaffected individuals and four affectedindividuals of Family A, while blood from two affected and three unaffected individuals were taken of Family B. Genotyping in both the families was performed using highly polymorphic short tandem repeat microsatellite markers. Sanger sequence of the FZD6 gene was performed and analysed for segregation analysis. A comparative modelling approach was used to predict the three-dimensional structures of FZD-6 protein using Modeller 4. Linkage analysis mapped a disease locus on chromosome 8q22.3, harbouring FZD6. Targeted Sanger sequencing of all the coding exons of FZD6 revealed a nonsense sequence variant in pedigree A, whereas a missense sequence variant in pedigree B. Finding and literature indicates the disease spectrum of Pakistani population with claw-shaped nail dysplasia, particularly in families of Pashtun origin.

To the Editor: Polydactyly is human autopod anomaly characterized by duplication of digits/phalanges in hands and/or feet. The disease is found as an isolated anomaly or associated with other autopod anomalies including syndactyly and split hand/foot malformation. Based on the location of an extra digit, polydactyly is subdivided into three types including post-axial, mesoaxial, and pre-axial polydactyly. Genetically, five genes including ZNF141, IQCE, ZRS/ SHH, GLI1, GLI3, FAM92A, and three other loci mapped on chromosome 13q21-32, 13q13.3-21.2, and 19p13.1-13.2 have been associated with nonsyndromic form of post-axial polydactyly. Clinically, pre-axial polydactyly is featured by duplication of thumb. Pre-axial polydactyly is caused by heterozygous variants in the GLI3 and ZRS/SHH.

BACKGROUND:Woodhouse-Sakati syndrome (WSS) is a rare neuroendocrine and ectodermal disorder inherited in an autosomal recessive pattern. The syndrome presents prominent clinical features, including alopecia, neuroendocrine defects, neurological findings and progressive hearing loss. The condition results from mutations in the DCAF17 gene.AIMS:To search for the underlying genetic defect in a Pakistani family with WSS phenotypes.METHODOLOGY:Whole exome sequencing was used to search for the disease-causing variant.RESULTS:Analysis of the exome data revealed a start loss sequence variant (c.1A>G, p.M1?) in DCAF17.CONCLUSION:This variant is predicted to abolish translation of the DCAF17 polypeptide. To our knowledge, this is the first start loss variant identified in the DCAF17.

Hereditary hearing impairment is a common sensory disorder that is genetically and phenotypically heterogeneous. In this study, we used a homozygosity mapping and exome sequencing strategy to study a consanguineous Pakistani family with autosomal recessive severe-to-profound hearing impairment. This led to the identification of a missense variant (p.Ile369Thr) in the LMX1A gene affecting a conserved residue in the C-terminus of the protein, which was predicted damaging by an in silico bioinformatics analysis. The p.Ile369Thr variant disrupts several C-terminal and homeodomain residue interactions, including an interaction with homeodomain residue p.Val241 that was previously found to be involved in autosomal dominant progressive HI. LIM-homeodomain factor Lmx1a is expressed in the inner ear through development, shows a progressive restriction to non-sensory epithelia, and is important in the separation of the sensory and non-sensory domains in the inner ear. Homozygous Lmx1a mutant mice (Dreher) are deaf with dysmorphic ears with an abnormal morphogenesis and fused and misshapen sensory organs; however, computed tomography performed on a hearing-impaired family member did not reveal any cochleovestibular malformations. Our results suggest that LMX1A is involved in both human autosomal recessive and dominant sensorineural hearing impairment.

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Pediatrics InternationalVolume 60, Issue 3 p. 304-306 Clinical Notes Sequence variants in GDF5 and TRPS1 underlie brachydactyly and tricho-rhino-phalangeal syndrome type III Asmat Ullah, Asmat Ullah Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, PakistanSearch for more papers by this authorMuhammad Umair, Muhammad Umair Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, PakistanSearch for more papers by this authorShabir Hussain, Shabir Hussain Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, PakistanSearch for more papers by this authorAbid Jan, Abid Jan Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, Pakistan Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, PakistanSearch for more papers by this authorWasim Ahmad, Corresponding Author Wasim Ahmad wahmad@qau.edu.pk orcid.org/0000-0003-1541-7258 Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, PakistanCorrespondence: Wasim Ahmad, PhD, Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan. Email: wahmad@qau.edu.pkSearch for more papers by this author Asmat Ullah, Asmat Ullah Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, PakistanSearch for more papers by this authorMuhammad Umair, Muhammad Umair Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, PakistanSearch for more papers by this authorShabir Hussain, Shabir Hussain Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, PakistanSearch for more papers by this authorAbid Jan, Abid Jan Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, Pakistan Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, PakistanSearch for more papers by this authorWasim Ahmad, Corresponding Author Wasim Ahmad wahmad@qau.edu.pk orcid.org/0000-0003-1541-7258 Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, PakistanCorrespondence: Wasim Ahmad, PhD, Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan. Email: wahmad@qau.edu.pkSearch for more papers by this author First published: 13 February 2018 https://doi.org/10.1111/ped.13473Citations: 4Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article.Citing Literature Volume60, Issue3March 2018Pages 304-306 RelatedInformation

BACKGROUND: Osteogenesis imperfecta (OI) is a heritable bone fragility disorder usually caused by dominant variants in COL1A1 or COL1A2 genes. Over the last few years, 17 genes including 12 autosomal recessive and five autosomal dominant forms of OI, involved in various aspects of bone formation, have been identified. METHODS: Whole-exome sequencing followed by conventional Sanger sequencing was performed in a single affected individual (IV-3) in a family. RESULTS: Here, we report the clinical and genetic characterization of OI type 3 in a consanguineous family with four affected members. Clinical examinations revealed low bone density, short stature, severe vertebral compression fractures, and multiple long bone fractures in the affected members. Exome sequencing revealed a biallelic pathogenic splice acceptor site variant (c. 359-3C>G) in a wingless-type mouse mammary tumor virus integration site family 1 (WNT1) gene located on chromosome 12q13.12. CONCLUSION: We report a biallelic splice site variant underlying OI type 3 and the first case from the Pakistani population.

Genodermatoses represent genetic anomalies of skin tissues including hair follicles, sebaceous glands, eccrine glands, nails, and teeth. Ten consanguineous families segregating various genodermatosis phenotypes were investigated in the present study.

Ellis–van Creveld syndrome is an autosomal recessive skeletal dysplasia primarily characterized by the features such as disproportionate dwarfism, short ribs, short limbs, dysplastic nails, cardiovascular malformations, post-axial polydactyly (PAP) (bilateral) of hands and feet. EVC/EVC2 located in head-to-head arrangement on chromosome 4p16 are the causative genes for EvC syndrome. In the study, we present two families, A and B, with Pakistani and Republic of Kosovo origin, respectively. They showed features of EvC syndrome and were clinically and genetically characterized. In family A, the affected members showed an additional feature of profound deafness. The whole exome sequencing (WES) in this family revealed two homozygous variants in EVC2 (c.30dupC; p.Thr11Hisfs*45) and TMC1 (\(\hbox {c}.1696\hbox {-}1\hbox {G}{>}\hbox {A}\)) genes. In family B, WES revealed novel compound heterozygous variants (p.Ser307Pro, \(\hbox {c}.2894{+}3\hbox {A}{>}\hbox {G}\)) in the EVC gene. This study reports first case of variants in the genes causing EvC syndrome and profound deafness in the same family.

Isolated congenital nail clubbing (ICNC; OMIM 119900) is a rare genodermatosis in which bilateral, symmetric enlargement of the nail plate and terminal segments of fingers and/or toes results from excessive proliferation of connective tissue between the nail matrix and distal phalanx. Loss of the normal angle between the nail and posterior nail fold is associated with a shiny, hypoplastic, thick-ended, long, broad nail. The thumbs are almost always involved, though some fingers or toes may be spared. Both autosomal dominant and autosomal recessive forms of ICNC have been described, sometimes associated with other systemic anomalies, which may include primary hypertrophic osteoarthropathy (PHO), the similar disorder pachydermoperiostitis (PDP), as well as cardiovascular, gastrointestinal, pulmonary and metabolic disorders.1,2 This article is protected by copyright. All rights reserved.

Purpose: To investigate the molecular basis of Bardet-Biedl syndrome (BBS) in five consanguineous families of Pakistani origin.Methods: Linkage in two families (A and B) was established to BBS7 on chromosome 4q27, in family C to BBS8 on chromosome 14q32.1, and in family D to BBS10 on chromosome 12q21.2. Family E was investigated directly with exome sequence analysis.Results: Sanger sequencing revealed two novel mutations and three previously reported mutations in the BBS genes. These mutations include two deletions (c.580_582delGCA, c.1592_1597delTTCCAG) in the BBS7 gene, a missense mutation (p.Gln449His) in the BBS8 gene, a frameshift mutation (c.271_272insT) in the BBS10 gene, and a nonsense mutation (p.Ser40*) in the MKKS (BBS6) gene.Conclusions: Two novel mutations and three previously reported variants, identified in the present study, further extend the body of evidence implicating BBS6, BBS7, BBS8, and BBS10 in causing BBS.