Mapping the NPHP-JBTS-MKS protein network reveals ciliopathy disease genes and pathways.

Nephronophthisis (NPHP), Joubert (JBTS), and Meckel-Gruber (MKS) syndromes are autosomal-recessive ciliopathies presenting with cystic kidneys, retinal degeneration, and cerebellar/neural tube malformation. Whether defects in kidney, retinal, or neural disease primarily involve ciliary, Hedgehog, or cell polarity pathways remains unclear. Using high-confidence proteomics, we identified 850 interactors copurifying with nine NPHP/JBTS/MKS proteins and discovered three connected modules: "NPHP1-4-8" functioning at the apical surface, "NPHP5-6" at centrosomes, and "MKS" linked to Hedgehog signaling. Assays for ciliogenesis and epithelial morphogenesis in 3D renal cultures link renal cystic disease to apical organization defects, whereas ciliary and Hedgehog pathway defects lead to retinal or neural deficits. Using 38 interactors as candidates, linkage and sequencing analysis of 250 patients identified ATXN10 and TCTN2 as new NPHP-JBTS genes, and our Tctn2 mouse knockout shows neural tube and Hedgehog signaling defects. Our study further illustrates the power of linking proteomic networks and human genetics to uncover critical disease pathways.

Genetics aspect of vitamin C (Ascorbic Acid) biosynthesis and signaling pathways in fruits and vegetables crops.

Vitamin C, also known as ascorbic acid, is an essential nutrient that plays a critical role in many physiological processes in plants and animals. In humans, vitamin C is an antioxidant, reducing agent, and cofactor in diverse chemical processes. The established role of vitamin C as an antioxidant in plants is well recognized. It neutralizes reactive oxygen species (ROS) that can cause damage to cells. Also, it plays an important role in recycling other antioxidants, such as vitamin E, which helps maintain the overall balance of the plant's antioxidant system. However, unlike plants, humans cannot synthesize ascorbic acid or vitamin C in their bodies due to the absence of an enzyme called gulonolactone oxidase. This is why humans need to obtain vitamin C through their diet. Different fruits and vegetables contain varying levels of vitamin C. The biosynthesis of vitamin C in plants occurs primarily in the chloroplasts and the endoplasmic reticulum (ER). The biosynthesis of vitamin C is a complex process regulated by various factors such as light, temperature, and plant hormones. Recent research has identified several key genes that regulate vitamin C biosynthesis, including the GLDH and GLDH genes. The expression of these genes is known to be regulated by various factors such as light, temperature, and plant hormones. Recent studies highlight vitamin C's crucial role in regulating plant stress response pathways, encompassing drought, high salinity, and oxidative stress. The key enzymes in vitamin C biosynthesis are L-galactose dehydrogenase (GLDH) and L-galactono-1, 4-lactone dehydrogenase (GLDH). Genetic studies reveal key genes like GLDH and GLDH in Vitamin C biosynthesis, offering potential for crop improvement. Genetic variations influence nutritional content through their impact on vitamin C levels. Investigating the roles of genes in stress responses provides insights for developing resilient techniques in crop growth. Some fruits and vegetables, such as oranges, lemons, and grapefruits, along with strawberries and kiwi, are rich in vitamin C. Guava. Papaya provides a boost of vitamin C and dietary fiber. At the same time, red and yellow bell peppers, broccoli, pineapple, mangoes, and kale are additional sources of this essential nutrient, promoting overall health. In this review, we will discuss a brief history of Vitamin C and its signaling and biosynthesis pathway and summarize the regulation of its content in various fruits and vegetables.

Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity.

The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments.

Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana.

Carotenoid cleavage oxygenase (CCO) is an enzyme capable of converting carotenoids into volatile, aromatic compounds and it plays an important role in the production of two significant plant hormones, i.e., abscisic acid (ABA) and strigolactone (SL). The cucumber plant genome has not been mined for genomewide identification of the CCO gene family. In the present study, we conducted a comprehensive genome-wide analysis to identify and thoroughly examine the CCO gene family within the genomic sequence of Cucumis sativus L. A Total of 10 CCO genes were identified and mostly localized in the cytoplasm and chloroplast. The CCO gene is divided into seven subfamilies i.e. 3 NCED, 3 CCD, and 1 CCD-like (CCDL) subfamily according to phylogenetic analysis. Cis-regulatory elements (CREs) analysis revealed the elements associated with growth and development as well as reactions to phytohormonal, biotic, and abiotic stress conditions. CCOs were involved in a variety of physiological and metabolic processes, according to Gene Ontology annotation. Additionally, 10 CCO genes were regulated by 84 miRNA. The CsCCO genes had substantial purifying selection acting upon them, according to the synteny block. In addition, RNAseq analysis indicated that CsCCO genes were expressed in response to phloem transportation and treatment of chitosan oligosaccharides. CsCCD7 and CsNCED2 showed the highest gene expression in response to the exogenous application of chitosan oligosaccharides to improve cold stress in cucumbers. We also found that these genes CsCCD4a and CsCCDL-a showed the highest expression in different plant organs with respect to phloem content. The cucumber CCO gene family was the subject of the first genome-wide report in this study, which may help us better understand cucumber CCO proteins and lay the groundwork for the gene family's future cloning and functional investigations.

Physical vapor deposition-free scalable high-efficiency electrical contacts to MoS2.

Fermi-level pinning caused by the kinetic damage during metallization has been recognized as one of the major reasons for the non-ideal behavior of electrical contacts, forbidding reaching the Schottky-Mott limit. In this manuscript, we present a scalable technique wherein Indium, a low-work-function metal, is diffused to contact a few-layered MoS2flake. The technique exploits a smooth outflow of Indium over gold electrodes to make edge contacts to pre-transferred MoS2flakes. We compare the performance of three pairs of contacts made onto the same MoS2flake, the bottom-gold, top-gold, and Indium contacts, and find that the Indium contacts are superior to other contacts. The Indium contacts maintain linearI-Vcharacteristics down to cryogenic temperatures with an extracted Schottky barrier height of ∼2.1 meV. First-principle calculations show the induced in-gap states close to the Fermi level, and the damage-free contact interface could be the reason for the nearly Ohmic behavior of the Indium/MoS2interface.

Genome wide association mapping of yield and various desirable agronomic traits in Rice.

BACKGROUND: Rice (Oryza sativa L.) is one of the staple foods worldwide. To feed the growing population, the improvement of rice cultivars is important. To make the improvement in the rice breeding program, it is imperative to understand the similarities and differences of the existing rice accessions to find out the genetic diversity. Previous studies demonstrated the existence of abundant elite genes in rice landraces. A genome-wide association study (GWAS) was performed for yield and yield related traits to find the genetic diversity. DESIGN: Experimental study. METHODS AND RESULTS: A total of 204 SSRs markers were used among 17 SSRs found to be located on each chromosome in the rice genome. The diversity was analyzed using different genetic characters i.e., the total number of alleles (TNA), polymorphic information content (PIC), and gene diversity by Power markers, and the values for each genetic character per marker ranged from 2 to 9, 0.332 to 0.887 and 0.423 to 0.900 respectively across the whole genome. The results of population structure identified four main groups. MTA identified several markers associated with many agronomically important traits. These results will be very useful for the selection of potential parents, recombinants, and MTAs that govern the improvements and developments of new high yielding rice varieties. CONCLUSIONS: Analysis of diversity in germplasm is important for the improvement of cultivars in the breeding program. In the present study, the diversity was analyzed with different methods and found that enormous diversity was present in the studied rice germplasm. The structure analysis found the presence of 4 genetic groups in the existing germplasm. A total of 129 marker-trait associations (MTAs) have been found in this study.

KIF1A novel frameshift variant p.(Ser887Profs*64) exhibits clinical heterogeneity in a Pakistani family with hereditary sensory and autonomic neuropathy type IIC.

Background: Hereditary sensory and autonomic neuropathies (HSANs) are rare heterogeneous group of neurological disorders caused by peripheral nerve deterioration. The HSANs sub-clinical classes have clinical and genetic overlap which often lead to misdiagnosis. In the present study a Pakistani family with five affected members suffering from severe neuropathy were genetically analyzed to identify the disease causative element in the family.Methods: Genome wide high-density single nucleotide polymorphism (SNP) microarray analysis was carried out followed by whole exome sequencing of the affected proband and another affected sibling. Shared homozygous regions in all severely affected members were identified through homozygosity mapping approach.Results: The largest homozygous region of 14.1 Mb shared by the five severely affected members of the family was identified on chromosome 2. Subsequent exome sequencing identified a novel single nucleotide deletion c.2658del; p.(Ser887Profs*64) in KIF1A. Segregation analysis revealed that this mutation was homozygous in all five affected individuals of the family with severe clinical manifestation, while members of the family that were heterozygous carriers shared abnormal skin features (scaly skin) only with the homozygous affected members.Conclusions: A novel frameshift mutation p.(Ser887Profs*64) in KIF1A is the potential cause of severe HSANIIC in a Pakistani family along with incomplete penetrance in mutation carriers. We demonstrate that using a combination of different techniques not only strengthens the gene finding approach but also helps in proper sub-clinical characterization along with identification of mutated alleles exhibiting incomplete penetrance leading to intrafamilial clinical variability in HSAN group of inherited diseases.

Machine vision-based Statistical texture analysis techniques for characterization of liver tissues using CT images.

OBJECTIVE: To characterize human liver tissues by demonstrating the ability of machine vision, and to propose a new auto-generated report based on texture analysis that may work with co-occurrence matrix statistics. METHODS: The retrospective study was conducted at Bahawal Victoria Hospital (BVH), Bahawalpur, Pakistan, and comprised clinically verified computed tomography imaging data between October 2018 and September 2020. The image samples and related data were used to segregate classes 1-4. Appropriate image classes belonging to the same disease were trained to confirm the abnormalities in liver tissues using supervised learning methods, principal component analysis, linear discriminant analysis, and non-linear discriminant analysis. Robust and reliable texture features were investigated by generating testing classes. Overall performance of the presented machine vision approach was analyzed using four parameters; precision, recall/sensitivity, F1-score, and accuracy. Statistical analysis was done using B11 software. RESULTS: There were 312 image samples from 71 patients; 51(71.8%) males and 20(28.2%) females. Among the patients, 19(26.7%) had abscess, 15(21.1%) had metastatic disease, 23(32.4%) had tumour necrosis, 6(8.5%) had vascular disorder, and 8(11.3%) were normal. Principal component analysis, linear discriminant analysis, and non-linear discriminant analysis showed high >97.86% values, but the discrimination rate was 100% for class 4. CONCLUSIONS: Abnormalities in the human liver could be discriminated and diagnosed by texture analysis techniques using second-order statistics that may assist the radiologist and medical physicists in predicting the severity and proliferation of abnormalities in liver diseases.

Prevalence of antibiotic resistance pattern in shigella isolates procured from pediatric patients at Faisalabad - Pakistan.

Shigella infection (shigellosis) is an intestinal disease caused by a shigella isolates belongs to a family Enterobacteriacea. Watery diarrhea, abdominal pain and tenesmus are the prominent symptoms of shigella infection. The present study was designed to determine period prevalence and antimicrobial susceptibility of Shigella species recovered from stool specimens obtained from diarrheal paediatric patients under 5 years of age. This cross-sectional study was carried out for a period of six months (Jan to June, 2016). All Shigella isolates were identified based on colony morphology, microscopic characteristics, and biochemical characteristics. After applying Kirby Baur disc diffusion method only 22 (18.96%) stool specimens were found positive for Shigella isolates among the 116 stool specimens. The isolates were also found susceptible to Levofloxacin (72.72%), Azithromycin (59.09%), and Cefotaxime (40.90%). However, the said isolates were resistant to Lincomycin (100%) and Penicillin-G (100%), followed by Amoxicillin (95.45%) and Oxacillin (95.45%). The chi-square test was used to check the close association among antimicrobial agents used and as highly significant (p-value < 2.2e-16). Based on antimicrobial susceptibility findings, Levofloxacin, Azithromycin and Cefotoxime were found effective for the control of shigellosis.

Greig Cephalopolysyndactyly Syndrome: Phenotypic Variability Associated with Variants in Two Different Domains of GLI3.

BACKGROUND: GLI3 is a transcriptional regulator of several genes involved in mammalian skeletal development. Mutations in the pleiotropic gene GLI3 may result in different inherited disorders including Greig cephalopolysyndactyly syndrome (GCPS). GCPS is characterized by mild to severe craniofacial and limb malformations. METHODS AND RESULTS: Here, we report clinical and molecular study of 3 families with GCPS originated in different regions of Pakistan. Sanger sequencing revealed two novel variants including a frameshift [c. 3790_3791InsC, p.(Gly1236Argfs*11)] and a missense [c.1692A>G, p.(His536Arg)], and one previously reported variant [c.1965_1966delAT, p.(His627Glufs*48)] located in 2 different domains of the GLI3. CONCLUSION: This study not only expanded spectrum of the mutations in the GLI3 but also highlighted phenotypic variability in the GCPS patients. This will facilitate diagnosis and genetic counseling of families with same and related disorders in the Pakistani population.

Genetic architecture of Al3+ toxicity tolerance in rice F2:3 populations determined through QTL mapping.

Aluminum (Al3+) toxicity is one of the factors limiting crop production in acidic soils. Identifying quantitative trait loci (QTLs)/genes for tolerance to Al3+ toxicity at seed germination can aid the development of new tolerant cultivars. The segregating population derived from Pak Basmati (Indica) × Pokkali (Indica) was used for mapping QTLs linked with tolerance to Al3+ toxicity ranging from 0 to 20 mM at pH 4 ± 0.2 at germination. The favorable alleles for all new QTLs were analyzed based on germination traits, i.e., final germination percentage (FG%), germination energy (GE), germination speed (GS), germination index (GI), mean germination time (MGT), germination value (GV), germination velocity (GVe), peak value of germination (GPV), and germination capacity (GC), and growth traits, such as root length (RL), shoot length (SL), total dry biomass (TDB) and germination vigor index (GVI). The phenotypic evolution showed transgressive variations. For genome-wide mapping, 90 polymorphic SSRs with 4 gene-specific markers and Win QTL Cart were used for QTL analysis. In all, 35 QTLs for germination and 11 QTLs for seedling growth were detected in distinct chromosomal regions by composite interval mapping (CIM), and multiple interval mapping (MIM) confirmed the pleiotropy at region RM128 on chromosome 1. Based on our genetic mapping studies, the genes/QTLs underlying tolerance to Al3+ toxicity could differ for both the germination and seedling stages in segregated populations. The QTLs identified in this study could be a source of new alleles for improving tolerance to Al3+ toxicity in rice.

Microbiological and antimicrobial pattern of diabetic foot ulcers (DFUs) at a tertiary care center in North East, Punjab.

OBJECTIVE: To determine the pattern of antimicrobial sensitivity of common microorganisms isolated from diabetic foot infections. METHODS: The cross-sectional study was conducted from January to August 2019 at the Diabetes and Footcare Clinic, Mayo Hospital, Lahore, Pakistan, and comprised deep-seated tissue samples from the ulcer bed that were tested for culture and sensitivity. Antimicrobial susceptibility was determined in accordance with Clinical and Laboratory Standards Institute guidelines. Data was analysed using SPSS 26. RESULTS: There were 389 bacterial isolates collected from 201 patients who had a mean age of 53.05±10.70 years. . Of the isolates, 238(61.11%) were gram-negative and 151(38.89%) were gram-positive organisms. Methicillin-resistant Staphylococcus aureuswas found in 62(64.58%) isolates. CONCLUSIONS: Early identification of diabetic foot infections can help in timely initiation of empirical treatment and prevention of unwanted amputations.

Very early onset inflammatory bowel disease: Spectrum of clinical presentation, diagnostic tools and outcome in children.

OBJECTIVE: To explore the spectrum of presentation, underlying monogenetic defects and outcome in very early onset inflammatory bowel disease (VEO-IBD). METHOD: The prospective, observational study was conducted at the Children's Hospital, Lahore, Pakistan, from January 2017 to December 2018, and comprised children developing features of inflammatory bowel disease aged <6 years. Data included demography, clinical presentation, diagnostic tools and outcome. Data was analysed using SPSS 21. RESULTS: Of the 60 children with relevant symptoms, 26(43.3%) were diagnosed as having very early onset inflammatory bowel disease. Of them, 13(50%) had underlying monogenic defect, and 16(61.5%) had ulcerative colitis. There were 22(84.6%) males with median age of 1.5(11) months in monogenic inflammatory bowel disease versus 24(43) months for non-monogenic inflammatory bowel disease (p<0.05). In the monogenic group, isolated rectal bleeding was the major presentation 13(100%) versus non-monogenic who presented mainly with failure to thrive 13(100%). Upper and lower endoscopies with histopathology had good diagnostic yield and inflammatory infiltrates on the biopsied tissues were the major findings. Mutations detected among the subjects were XIAP, PRKDC, PIK3CD, RAG-1, LRBA, DOCK8, TTC7, MEFV and EPCAM. Mortality was significantly higher in the monogenic group 7(54%) than in the non-monogenic group 2(15%) (p<0.05). CONCLUSIONS: Very early onset inflammatory bowel disease should be suspected when conventional management fails to rectify common disease mimickers. Testing for underlying immunological defect and genetic mutation would be helpful for managing these rare disorders.

Clinical Practice Guidelines For The Management Of Colorectal Cancer, A Consensus Statement By The Society Of Surgeons® And Surgical Oncology Society Of Pakistan®.

A joint effort by the Society of Surgeons Pakistan and Society of Surgical Oncology Pakistan, these guidelines provide a framework for the practicing surgeons involved in care and management of patients with colorectal cancer. The guidelines take into account the issues related to our local circumstances and provide a minimum standard of care that must be given to these patients. The Guideline Committee had members from all disciplines, including surgery, surgical oncology, medical oncology and radiation oncology. The guidelines have attempted to simplify things to understand and follow for the practicing surgeons. With these guidelines we wish to eliminate disparities in treatment among institutions and prevent any under treatment of patients.

Empathy levels among undergraduate medical students in Pakistan, a cross sectional study using Jefferson scale of physician empathy.

OBJECTIVE: To determine empathy level among undergraduate medical students with respect to gender and the year of study. METHODS: The cross-sectional study was conducted at the University College of Medicine and Dentistry, Lahore, Pakistan, from December, 2015, to January, 2016, and comprised undergraduate medical students of either gender in all the five years of their course. Data was collected using the student version of the Jefferson Scale of Physician Empathy. Data was analysed using SPSS 20. RESULTS: Of the 260 students, 153(58.9%) were females and 107(41.1%) were males. Overall mean empathy level was 90.63±11.55. Females scored higher than males (p<0.05). The highest empathy level was seen among the First Year medical students 93.39±9.11, while the lowest was seen in Third Year students 87.71±13.94. CONCLUSIONS: Overall empathy level was seriously low, indicating the need for curricular reforms.

Presentation of pleural effusion and dilated cardiomyopathy in a case of dystrophic epidermolysis bullosa.

Epidermolysis Bullosa (EB), a genetic disorder of the skin that presents with eruptive lesions accompanied by blistering has multiple types. We present a case of dystrophic and epidermolysis bullosa (DEB), a rare variant of the disease with the underlying pathophysiology involving a mutation of type VII collagen that serves as an anchoring protein for basement membrane to the dermis. The patient presented with palmoplantar hyperkeratosis with blistering extending on multiple sites of the body, bilateral pleural effusion and an ejection fraction of 23% with moderate mitral regurgitation. The patient was treated symptomatically with diuretics and inotropic medication for the dilated heart, along with draining of pleural spaces. No case of DEB with pleural effusion has been reported prior to this one. We believe this is the first case that presented with both pleural effusion and dilated cardiomyopathy.

Pharmaceutical evaluation of Graphirine syrup formulated from some common indigenous herbs of Pakistan.

Since ancient times humans have relied on traditional medicine and herbal formulation for the cure of various diseases and disorders. Globally, interest in use of herbal medicine has increased; as drawbacks of modern medicine and have started getting more prominent. Most of the traditional system of medicine; all in their formulations depends on plants. Traditional herbal cough products have considered to be mild, nontoxic, non-sedative and even harmless. As Syrup is commonly taken for the relief of cough; we aimed to formulate a cough syrup (Graphirine) from some common indigenous herbs; Adhatoda vasica, Piper longum and Rosa Damasena and evaluate its physicochemical parameters along with the changes in accelerated stability testing. Preformulation studies, i.e. moisture content, ash, water and ethanol extractive values of all three herbs were defined. Physicochemical factors, quantitative spectral measurement, FTIR spectrum for identification of compounds; along with accelerated stability and possible microbial fungal growth; were also checked for the formulated syrup. Each and every parameter complied with the specifications.

Mn(II) Ions Assisted Near-Infrared Single-Mode Lasing from an Individual Mn-Doped CdS Nanobelts.

Tunable single-mode lasers are attractive for their potential applications in signal processing, optical communication, and displays. Here we present the Mn(II) ions assisted single-mode lasing occurring at near-infrared (NIR) band instead of the green emission band of CdS nanobelts (NBs) for the first time. Successful substation of Mn(II) ions at the tetrahedral Cd2+ cites in the CdS matrix were confirmed by EPR. Light Mn(II) doping (≤1%) in CdS belts not only red-shifted the Raman modes but also increased crystallinity compared to pure CdS NBs due to strong excitons-phonon couplings. Up to 3 µJ · cm-2 pumping fluence of ns laser, lightly doped CdS:Mn NBs show two photoluminescence (PL) emissions. First emission centered at 514.2 nm (green) corresponds to band-edge of CdS and an in-gap emission centered at 771.4 nm (NIR) corresponds to Mn(II) ions aggregates. After using intense excitation pulse, these NBs exhibited lasing at 791.4 nm with the lowest laser thresholds at 4.2 µJ · cm-2 in the CdS system. This lasing action is further confirmed by lifetime kinetics. The results indicated that the lasing in these NBs involves the localised excitons magnetic polarons and Farby-Perot (F-P) optical resonant processes at room temperature.

Type 1 gallbladder perforation: A rare cause of acute abdomen.

Gallbladder perforation is rare. Diagnosis is usually made during operative intervention. Delay in recognition is associated with high morbidity and mortality. We report a case of type 1 gall bladder perforation in a male patient with no previous complaints related to gallstones.

Identification of Novel Mutation in CNGA3 gene by Whole-Exome Sequencing and In-Silico Analyses for Genotype-Phenotype Assessment with Autosomal Recessive Achromatopsia in Pakistani families.

OBJECTIVE: To identify the underlying genetic anomalies in two consanguineous Pakistani families with autosomal recessive achromatopsia. METHODS: The exploratory study was conducted under the patronage of International Islamic University, Islamabad, Pakistan, and Sungshin Women University, Seoul, South Korea, after two families coded PKCN-02 and PKCN-07 belonging to different ethnic groups were recruited from different areas of Khyber Pakhtunkhawa province of Pakistan in July 2016. The families were originally diagnosed with nystagmus upon medical examination. Exome sequencing was performed to identify the possible causative gene which was found to be cyclic nucleotide-gated channel alpha-3. Sanger sequencing was performed to confirm the mutations. After genetic analysis, clinical analysis was re-evaluated for colour vision using Ishihara 26 plates. Pathogenic potential of these mutations was evaluated using algorithmic mutation prediction tools. In-silico analysis was performed to predict effect of these mutations on protein structure of the gene in question. RESULTS: Exome sequencing revealed a reported missense mutation c .1306C>T (p.R436W) in family PKCN-02 and a novel missense mutation c.1540G>A (p.D514N) in family PKCN-07. After mutational analysis, clinical re-evaluation revealed that both families were segregating autosomal recessive achromatopsia. Further, the topological model of the cyclic nucleotide-gated channel alpha-3 polypeptide describes these missense mutations primarily affecting the C-linker and cyclic guanosine monophosphate-binding sites, respectively. Protein structure modelling of cyclic nucleotide-gated channel alpha-3 protein revealed abnormal structure produced by p.R436W and p.D514N.. CONCLUSIONS: Exome sequencing approach was used to first identify the genetic alteration in families with nystagmus. Two mutations in cyclic nucleotide-gated channel alpha-3gene were uncovered, including one novel mutation. Clinical re-evaluation uncovered that both families had achromatopsia.