Musharraf Jelani

EDUCATION

PhD in Human Skin Disorders, MPhil in Human Ectodermal Dysplasias, Master in Biochemistry Molecular Biology.

RESEARCH INTERESTS

Human Genetics, Rare Mendelian Disorders, Exome Analysis, Bioinformatics.

Scopus Publications

Pathogenic variants identification in primary congenital glaucoma patients using whole exome sequencing
Shahzad Ahmad, Muhammad Saleem Gandapur, Musharraf Jelani, Anees Muhammad, Ihtisham Ul Haq, Yousaf Jamal Mahsood, Sajjad Ahmad, Wadi B. Alonazi, Nousheen Bibi, Muhammad Tahir Sarwar,et al.
Springer Science and Business Media LLC



A homozygous variant in ARHGAP39 is associated with lethal cerebellar vermis hypoplasia in a consanguineous Saudi family
Abdulfatah M. Alayoubi, Fatima Alfadhli, Mehnaz, Alia M. Albalawi, Khushnooda Ramzan, Musharraf Jelani, and Sulman Basit
Springer Science and Business Media LLC



Unveiling genetics of non-syndromic albinism using whole exome sequencing: A comprehensive study of TYR, TYRP1, OCA2 and MC1R genes in 17 families
Qaiser Zaman, Jamshid Khan, Mashal Ahmad, Hamza Khan, Hammad Tufail Chaudhary, Gauhar Rehman, Obaid Ur Rahman, Muhammad M. Shah, Javeria Hussain, Qaisar Jamal,et al.
Elsevier BV



Two novel homozygous variants of ATP6V0A2 and ALDH18A1 lead to autosomal recessive cutis laxa type 2 and 3 in two Pakistani families
Qaiser Zaman, Aiman Iftikhar, Gauhar Rehman, Qadeem Khan, Najumuddin, Amin Jan, Jamshid Khan, Muhammad Anas, Laiba, Muhammad Umair,et al.
Wiley
AbstractBackgroundAutosomal recessive cutis laxa type 2A (ARCL2A; OMIM: 219200) is characterized by neurovegetative, developmental and progeroid elastic skin anomalies. It is caused by biallelic variation in ATPase, H+ transporting V0 subunit A2 (ATP6V0A2; OMIM: 611716) located on chromosome 12q24.31. Autosomal recessive cutis laxa type 3A (ARCL3A; OMIM: 219150) is another subclinical type characterized by short stature, ophthalmological abnormalities and a progeria‐like appearance. The ARCL3A is caused by loss of function alterations in the aldehyde dehydrogenase 18 family member A1 (ALDH18A1; OMIM: 138250) gene located at chromosome 10q24.1.MethodsWhole‐exome sequencing (WES), and Sanger sequencing were performed for molecular diagnosis. 3D protein modeling was performed to investigate the deleterious effect of the variant on protein structure.ResultsIn this study, clinical and molecular diagnosis were performed for two families, ED‐01 and DWF‐41, which displayed hallmark features of ARCL2A and ARCL3A, respectively. Three affected individuals in the ED‐01 family (IV‐4, IV‐5 and V‐3) displayed sagging loose skin, down‐slanting palpebral fissures, excessive wrinkles on the abdomen, hands and feet, and prominent veins on the trunk. Meanwhile the affected individuals in the DWF‐41 family (V‐2 and V‐3) had progeroid skin, short stature, dysmorphology, low muscle tone, epilepsy, lordosis, scoliosis, delayed puberty and internal genitalia. WES in the index patient (ED‐01: IV‐4) identified a novel homozygous deletion (NM_012463.3: c.1977_1980del; p.[Val660LeufsTer23]) in exon 16 of the ATP6V0A2 while in DWF‐41 a novel homozygous missense variant (NM_001323413.1:c.1867G>A; p.[Asp623Asn]) in exon 15 of the ALDH18A1 was identified. Sanger validation in all available family members confirmed the autosomal recessive modes of inheritances in each family. Three dimensional in‐silico protein modeling suggested deleterious impact of the identified variants. Furthermore, these variants were assigned class 1 or “pathogenic” as per guidelines of American College of Medical Genetics 2015. Screening of ethnically matched healthy controls (n = 200 chromosomes), excluded the presence of these variations in general population.ConclusionsTo the best of our knowledge, this is the first report of ATP6V0A2 and ALDH18A1 variations in the Pakhtun ethnicity of Pakistani population. The study confirms that WES can be used as a first‐line diagnostic test in patients with cutis laxa, and provides basis for population screening and premarital testing to reduce the diseases burden in future generations.


Phenotypic Classification of Eye Colour and Developmental Validation of the Irisplex System on Population Living in Malakand Division, Pakistan
Murad Ali Rahat, Fazal Akbar, Akhtar Rasool, Muhammad Ilyas, Allah Rakha, Sulaiman Shams, Musharraf Jelani, Fehmida Bibi, Bader H. Shirah, Angham Abdulrhman Abdulkareem,et al.
MDPI AG
The core objective of forensic DNA typing is developing DNA profiles from biological evidence for personal identification. The present study was designed to check the validation of the IrisPlex system and the Prevalence of eye colour in the Pakhtoon population residing within the Malakand Division. Methods: Eye colour digital photographs and buccal swab samples of 893 individuals of different age groups were collected. Multiplexed SNaPshot single base extension chemistry was used, and the genotypic results were analysed. Snapshot data were used for eye colour prediction through the IrisPlex and FROG-kb tool. Results: The results of the present study found brown eye colour to be the most prevalent eye colour in comparison to intermediate and blue coloured. Overall, individuals with brown-coloured eyes possess CT (46.84%) and TT (53.16%) genotypes. Blue eye-coloured individuals are solely of the CC genotype, while individuals of intermediate eye colour carry CT (45.15%) and CC (53.85%) genotypes in rs12913832 SNP in the HERC2 gene. It was also revealed that brown-coloured eyes individuals were dominant among all age groups followed by intermediate and blue. Statistical analysis between particular variables and eye colour showed a significant p-value (<0.05) for rs16891982 SNP in SLC45A2 gene, rs12913832 SNP in HERC2 gene, rs1393350 SNP in SLC45A2, districts and gender. The rest of the SNPs were non-significant with eye colour, respectively. The rs12896399 SNP and SNP rs1800407 were found significant with rs16891982 SNP. The result also demonstrated that the study group differs from the world population based on eye colour. The two eye colour prediction results were compared, and it was discovered that IrisPlex and FROG-Kb had similar higher prediction ratios for Brown and Blue eye colour. Conclusions: The results of the current study revealed brown eye colour to be the most prevalent amongst members of the local population of Pakhtoon ethnicity in the Malakand Division of northern Pakistan. A set of contemporary human DNA samples with known phenotypes are used in this research to evaluate the custom panel’s prediction accuracy. With the aid of this forensic test, DNA typing can be supplemented with details about the appearance of the person from whom the sample was taken in cases involving missing persons, ancient human remains, and trace samples. This study may be helpful for future population genetics and forensics studies.


A Novel Homozygous Nonsense Variant in the DYM Underlies Dyggve-Melchior-Clausen Syndrome in Large Consanguineous Family
Abu Bakar, Sulaiman Shams, Nousheen Bibi, Asmat Ullah, Wasim Ahmad, Musharraf Jelani, Osama Yousef Muthaffar, Angham Abdulrhman Abdulkareem, Turki S. Abujamel, Absarul Haque,et al.
MDPI AG
(1) Background: Dyggve-Melchior-Clausen Syndrome is a skeletal dysplasia caused by a defect in the DYM gene (OMIM number 607461). Pathogenic variants in the gene have been reported to cause Dyggve-Melchior-Clausen (DMC; OMIM 223800) dysplasia and Smith-McCort (SMC; OMIM 607326) dysplasia. (2) Methods: In the present study, large consanguineous families with five affected individuals with osteochondrodysplasia phenotypes were recruited. The family members were analyzed by polymerase chain reaction for homozygosity mapping using highly polymorphic microsatellite markers. Subsequent to linkage analysis, the coding exons and exon intron border of the DYM gene were amplified. The amplified products were then sent for Sanger sequencing. The structural effect of the pathogenic variant was analyzed by different bioinformatics tools. (3) Results: Homozygosity mapping revealed a 9 Mb homozygous region on chromosome 18q21.1 harboring DYM shared by all available affected individuals. Sanger sequencing of the coding exons and exon intron borders of the DYM gene revealed a novel homozygous nonsense variant [DYM (NM_017653.6):c.1205T>A, p.(Leu402Ter)] in affected individuals. All the available unaffected individuals were either heterozygous or wild type for the identified variant. The identified mutation results in loss of protein stability and weekend interactions with other proteins making them pathogenic (4) Conclusions: This is the second nonsense mutation reported in a Pakistani population causing DMC. The study presented would be helpful in prenatal screening, genetic counseling, and carrier testing of other members in the Pakistani community.


Novel Variants in MPV17, PRX, GJB1, and SACS Cause Charcot–Marie–Tooth and Spastic Ataxia of Charlevoix–Saguenay Type Diseases
Qaiser Zaman, Muhammad Abbas Khan, Kalsoom Sahar, Gauhar Rehman, Hamza Khan, Mehwish Rehman, Najumuddin, Ilyas Ahmad, Muhmmad Tariq, Osama Yousef Muthaffar,et al.
MDPI AG
Charcot–Marie–Tooth disease (CMT) and autosomal recessive spastic ataxia of Charlevoix–Saguenay type (ARSACS) are large heterogeneous groups of sensory, neurological genetic disorders characterized by sensory neuropathies, muscular atrophies, abnormal sensory conduction velocities, and ataxia. CMT2EE (OMIM: 618400) is caused by mutations in MPV17 (OMIM: 137960), CMT4F (OMIM: 614895) is caused by PRX (OMIM: 605725), CMTX1 (OMIM: 302800) is caused by mutations in GJB1 (OMIM: 304040), and ARSACS (OMIM: 270550) is caused by mutations in SACS (OMIM: 604490). In this study, we enrolled four families: DG-01, BD-06, MR-01, and ICP-RD11, with 16 affected individuals, for clinical and molecular diagnoses. One patient from each family was analyzed for whole exome sequencing and Sanger sequencing was done for the rest of the family members. Affected individuals of families BD-06 and MR-01 show complete CMT phenotypes and family ICP-RD11 shows ARSACS type. Family DG-01 shows complete phenotypes for both CMT and ARSACS types. The affected individuals have walking difficulties, ataxia, distal limb weakness, axonal sensorimotor neuropathies, delayed motor development, pes cavus, and speech articulations with minor variations. The WES analysis in an indexed patient of family DG-01 identified two novel variants: c.83G>T (p.Gly28Val) in MPV17 and c.4934G>C (p.Arg1645Pro) in SACS. In family ICP-RD11, a recurrent mutation that causes ARSACS, c.262C>T (p.Arg88Ter) in SACS, was identified. Another novel variant, c.231C>A (p.Arg77Ter) in PRX, which causes CMT4F, was identified in family BD-06. In family MR-01, a hemizygous missense variant c.61G>C (p.Gly21Arg) in GJB1 was identified in the indexed patient. To the best of our knowledge, there are very few reports on MPV17, SACS, PRX, and GJB1 causing CMT and ARSACS phenotypes in the Pakistani population. Our study cohort suggests that whole exome sequencing can be a useful tool in diagnosing complex multigenic and phenotypically overlapping genetic disorders such as Charcot–Marie–Tooth disease (CMT) and spastic ataxia of Charlevoix–Saguenay type.


Whole exome sequencing identified five novel variants in CNTN2, CARS2, ARSA, and CLCN4 leading to epilepsy in consanguineous families
Angham Abdulrhman Abdulkareem, Qaiser Zaman, Hamza Khan, Sabar Khan, Gauhar Rehman, Nabeel Tariq, Mashal Ahmad, Muhammad Owais, Najumuddin, Osama Yousef Muthaffar,et al.
Frontiers Media SA
Introduction: Epilepsy is a group of neurological disorders characterized by recurring seizures and fits. The Epilepsy genes can be classified into four distinct groups, based on involvement of these genes in different pathways leading to Epilepsy as a phenotype. Genetically the disease has been associated with various pathways, leading to pure epilepsy-related disorders caused by CNTN2 variations, or involving physical or systemic issues along with epilepsy caused by CARS2 and ARSA, or developed by genes that are putatively involved in epilepsy lead by CLCN4 variations.Methods: In this study, five families of Pakistani origin (EP-01, EP-02, EP-04, EP-09, and EP-11) were included for molecular diagnosis.Results: Clinical presentations of these patients included neurological symptoms such as delayed development, seizures, regression, myoclonic epilepsy, progressive spastic tetraparesis, vision and hearing impairment, speech problems, muscle fibrillation, tremors, and cognitive decline. Whole exome sequencing in index patients and Sanger sequencing in all available individuals in each family identified four novel homozygous variants in genes CARS2: c.655G>A p.Ala219Thr (EP-01), ARSA: c.338T>C: p.Leu113Pro (EP-02), c.938G>T p.Arg313Leu (EP-11), CNTN2: c.1699G>T p.Glu567Ter (EP-04), and one novel hemizygous variant in gene CLCN4: c.2167C>T p.Arg723Trp (EP-09).Conclusion: To the best of our knowledge these variants were novel and had not been reported in familial epilepsy. These variants were absent in 200 ethnically matched healthy control chromosomes. Three dimensional protein analyses revealed drastic changes in the normal functions of the variant proteins. Furthermore, these variants were designated as “pathogenic” as per guidelines of American College of Medical Genetics 2015. Due to overlapping phenotypes, among the patients, clinical subtyping was not possible. However, whole exome sequencing successfully pinpointed the molecular diagnosis which could be helpful for better management of these patients. Therefore, we recommend that exome sequencing be performed as a first-line molecular diagnostic test in familial cases.


Report of Hermansky–Pudlak Syndrome in Two Families with Novel Variants in HPS3 and HPS4 Genes
Qaiser Zaman, Sadeeda, Muhammad Anas, Gauhar Rehman, Qadeem Khan, Aiman Iftikhar, Mashal Ahmad, Muhammad Owais, Ilyas Ahmad, Osama Muthaffar,et al.
MDPI AG
Background: Hermansky–Pudlak syndrome (HSP) was first reported in 1959 as oculocutaneous albinism with bleeding abnormalities, and now consists of 11 distinct heterogenic genetic disorders that are caused by mutations in four protein complexes: AP-3, BLOC1, BLOC2, and BLOC3. Most of the patients show albinism and a bleeding diathesis; additional features may present depending on the nature of a defective protein complex. The subtypes 3 and 4 have been known for mutations in HSP3 and HSP4 genes, respectively. Methods: In this study, two Pakhtun consanguineous families, ALB-09 and ALB-10, were enrolled for clinical and molecular diagnoses. Whole-exome sequencing (WES) of the index patient in each family followed by Sanger sequencing of all available samples was performed using 3Billion. Inc South Korea rare disease diagnostics services. Results: The affected individuals of families ALB-09 and ALB-10 showed typical phenotypes of HPS such as oculocutaneous albinism, poor vision, nystagmus, nystagmus-induced involuntary head nodding, bleeding diathesis, and enterocolitis; however, immune system weakness was not recorded. WES analyses of one index patient revealed a novel nonsense variant (NM_032383.4: HSP3; c.2766T > G) in family ALB-09 and a five bp deletion (NM_001349900.2: HSP4; c.1180_1184delGTTCC) variant in family ALB-10. Sanger sequencing confirmed homozygous segregation of the disease alleles in all affected individuals of the respective family. Conclusions: The substitution c.2766T > G creates a premature protein termination at codon 922 in HPS3, replacing tyrosine amino acid with a stop codon (p.Tyr922Ter), while the deletion mutation c.1180_1184delGTTCC leads to a reading frameshift and a premature termination codon adding 23 abnormal amino acids to HSP4 protein (p:Val394Pro395fsTer23). To the best of our knowledge, the two novel variants identified in HPS3 and HPS4 genes causing Hermansky–Pudlak syndrome are the first report from the Pakhtun Pakistani population. Our work expands the pathogenic spectrum of HPS3 and HPS4 genes, provides successful molecular diagnostics, and helps the families in genetic counselling and reducing the disease burden in their future generations.


Whole exome sequencing identifies a novel compound heterozygous GFM1 variant underlying developmental delay, dystonia, polymicrogyria, and severe intellectual disability in a Pakhtun family
Atta Ullah Khan, Ibrar Khan, Muhammad Ismail Khan, Muhammad Latif, Muhammad Imran Siddiqui, Shafi Ullah Khan, Thet Thet Htar, Ghazala Wahid, Ikram Ullah, Fehmida Bibi,et al.
Wiley
Mitochondrial protein synthesis requires three elongation factors including EF-Tu (TUFM; OMIM 602389), EF-Ts (TSFM; OMIM 604723), and EF-G1 (GFM1; OMIM 606639). Pathogenic variants in any of these three members result in defective mitochondrial translation which can impart an oxidative phosphorylation (OXPHOS) deficiency. In this study, we investigated a consanguineous Pakhtun Pakistani family. There were four affected siblings at the time of this study and one affected girl had died in infancy. The index patient had severe intellectual disability, global developmental delay, dystonia, no speech development, feeding difficulties, and nystagmus. MRI brain presented thinning of corpus callosum and polymicrogyria. Whole exome sequencing revealed a novel compound heterozygous variant in GFM1 located on chromosome 3q25.32. Sanger sequencing confirmed recessive segregation of the maternal (NM_001308164.1:c.409G > A; p.Val137Met) and paternal (NM_001308164.1:c.1880G > A; p.Arg627Gln) variants in all the four affected siblings. These variants are classified as "likely-pathogenic" according to the recommendation of ACMG/AMP guideline. GFM1 alterations mostly lead to severe phenotypes and the patients may die in early neonatal life; however, four of the affected siblings had survived till the ages of 10-17 years, without developing any life-threatening conditions. Mostly, in cousin marriages, the pathogenic variants are identical-by-descent, and affected siblings born to such parents are homozygous. Three homozygous variants were shortlisted in the analysis of the WES data, but Sanger sequencing did not confirm their segregation with the disease phenotype. This is the first report from Pakistan expanding pathogenicity of GFM1 gene.


Association of cytochromes P450 3A4*22 and 3A5*3 genotypes and polymorphism with response to simvastatin in hypercholesterolemia patients
Elbatool G. Elalem, Musharraf Jelani, Alaa Khedr, Aftab Ahmad, Tareef Y. Alaama, Mohamed Nabeel Alaama, Huda M. Al-Kreathy, and Zoheir A. Damanhouri
Public Library of Science (PLoS)
Backgrounds Inter-individual variability in response to statin was mainly due to genetic differences. This study aimed to investigate the association of CYP3A4*22 (rs35599367), CYP3A5*3 (rs776746) single nucleotide polymorphism (SNP) with response to simvastatin in hypercholesterolemia patients conducted at King Abdulaziz University hospital (KAUH) in Jeddah, Saudi Arabia. Patients and methods A total of 274 participants were registered in the current study. Hypercholesterolemic patients taking simvastatin 20 mg (n = 148) and control subjects (n = 126) were tested for rs35599367 and rs776746 genotypes using Custom Taqman ® Assay Probes. Response to simvastatin in these patients was assessed by determination of low density lipoprotein (LDL-C), total cholesterol (TC) and by measuring statin plasma levels using Liquid Chromatography-Mass Spectrometry (LC-MS). Results None of the participants carried a homozygous CYP3A4*22 mutant genotype, while 12 (4.4%) individuals had a heterozygous genotype and 262 (95.6%) had a wild homozygous genotype. The CYP3A5*3 allele was detected in the homozygous mutant form in 16 (5.8%) individuals, while 74 (27.0%) individuals carried the heterozygous genotype and 184 (67.2%) carried the wildtype homozygous genotype. Of the patient group, 15 (11%) were classified as intermediate metabolizers (IMs) and 133 (89%) as extensive metabolizers (EMs). Plasma simvastatin concentrations for the combined CYP3A4/5 genotypes were significantly (P<0.05) higher in the IMs group than in the EMs group. TC and plasma LDL-C levels were also significantly (P<0.05) higher in IMs than in EMs. Conclusion The present study showed associations between CYP3A4*22 (rs35599367) and CYP3A5*3 (rs776746) SNP combination genotypes with response to statins in hypercholesterolemia. Patients who had either a mutant homozygous allele for CYP3A5*3 or mutant homozygous and heterozygous alleles for CYP3A4*22 showed increased response to lower TC and LDL-C levels.


Biallelic inheritance in a single Pakistani family with intellectual disability implicates new candidate gene RDH14
S. Pastore, Tahir Muhammad, R. Harripaul, R. Lau, Muhammad Tariq Masood Khan, Muhammad Ismail Khan, O. Islam, Changsoo Kang, M. Ayub, M. Jelani and John B. Vincent

In a multi-branch family from Pakistan, individuals presenting with palmoplantar keratoderma segregate in autosomal dominant fashion, and individuals with intellectual disability (ID) segregate in apparent autosomal recessive fashion. Initial attempts to identify the ID locus using homozygosity-by-descent (HBD) mapping were unsuccessful. However, following an assumption of locus heterogeneity, a reiterative HBD approach in concert with whole exome sequencing (WES) was employed. We identified a known disease-linked mutation in the polymicrogyria gene, ADGRG1, in two affected members. In the remaining two (living) affected members, HBD mapping cross-referenced with WES data identified a single biallelic frameshifting variant in the gene encoding retinol dehydrogenase 14 (RDH14). Transcription data indicate that RDH14 is expressed in brain, but not in retina. Magnetic resonance imaging for the individuals with this RDH14 mutation show no signs of polymicrogyria, however cerebellar atrophy was a notable feature. RDH14 in HEK293 cells localized mainly in the nucleoplasm. Co-immunoprecipitation studies confirmed binding to the proton-activated chloride channel 1 (PACC1/TMEM206), which is greatly diminished by the mutation. Our studies suggest RDH14 as a candidate for autosomal recessive ID and cerebellar atrophy, implicating either disrupted retinoic acid signaling, or, through PACC1, disrupted chloride ion homeostasis in the brain as a putative disease mechanism.


Whole Exome Sequencing Confirms Molecular Diagnostics of Three Pakhtun Families With Autosomal Recessive Epidermolysis Bullosa
Fozia Fozia, Rubina Nazli, Nousheen Bibi, Sher Alam Khan, Noor Muhammad, Nafila Shakeeb, Saadullah Khan, Musharraf Jelani, and Naveed Wasif
Frontiers Media SA
Epidermolysis bullosa (EB) is a genetic skin disorder that shows heterogeneous clinical fragility. The patients develop skin blisters congenitally or in the early years of life at the dermo-epithelial junctions, including erosions, hyperkeratosis over the palms and soles. The other associated features are hypotrichosis on the scalp, absent or dystrophic nails, and dental anomalies. Molecular diagnosis through whole-exome sequencing (WES) has become one of the successful tool in clinical setups. In this study, three Pakhtun families from the Khyber Pakhtunkhwa province of Pakistan were ascertained. WES analysis of a proband in each family revealed two novel variants (COL17A1: NM_000494.4: c.4041T>G: p.Y1347* and PLEC: NM_201380.3: c.1283_1285delGCT: p.L426del) and one previously known COL17A1: NM_000494.4:c.3067C>T: p.Q1023*) variant in homozygous forms. Sanger sequencing of the identified variants confirmed that the heterozygous genotypes of the obligate carriers. The identified variants have not only increased the mutation spectrum of the COL17A1 and PLEC but also confirms their vital role in the morphogenesis of skin and its associated appendages. WES can be used as a first-line diagnostic tool in genetic testing and counselling families from Khyber Pakhtunkhwa, Pakistan.


Two missense mutations in GPNMB cause autosomal recessive amyloidosis cutis dyschromica in the consanguineous pakistani families
Obaid Ur Rahman, Jeena Kim, Caroline Mahon, Musharraf Jelani, and Changsoo Kang
Springer Science and Business Media LLC
BACKGROUND Amyloidosis cutis dyschromica (ACD) is a rare variant of cutaneous amyloidosis. This disorder often clusters in families, and it has been suggested that genetic factors might be involved in its development. OBJECTIVE To identify the genetic causes of ACD, we recruited a consanguineous Pakistani family with multiple cases of ACD that display a recessive mode of inheritance. METHODS We performed whole-exome sequencing of samples from 7 members of this family, followed by bioinformatic and in silico analyses to identify the causative variant. For the replication study, we recruited a British family with Pakistani ancestry, and sequenced all exons of glycoprotein non-metastatic melanoma protein b (GPNMB) to identify mutations. We also investigated effects of the mutations on the stability of the GPNMB protein using the I-TASSER three-dimensional modeling tool. RESULTS We found a novel homozygous mutation, p.Gly363Val (c.1088 G>T), in GPNMB in all affected cases. In a replication study, another homozygous missense mutation in GPNMB, pIle174Met (c.522 C>G), was carried by the affected son. The two mutations were not observed in our in-house data set comprising 217 healthy Pakistani individuals or in The Genome Aggregation Database. Our structural modeling of GPNMB suggested that p.Gly363Val enhanced its stability, whereas p.Ile174Met caused instability. CONCLUSIONS This study reports two novel missense mutations in two Pakistani families that cause ACD. The mutations appear to influence GPNMB stability, as revealed by protein modeling.


Whole exome sequencing reveals a homozygous SGCB variant in a Pakhtun family with limb girdle muscular dystrophy (LGMDR4) phenotype
Muhammad Tariq, Muhammad Latif, Memona Inam, Amin Jan, Nousheen Bibi, Hussein Sheikh Ali Mohamoud, Isse Ali, Habib Ahmad, Aziz Khan, Jamal Nasir,et al.
Elsevier BV



Whole exome sequencing identified a novel missense alteration in CC2D2A causing Joubert syndrome 9 in a Pakhtun family
Muhammad Ismail Khan, Muhammad Latif, Maria Saif, Hilal Ahmad, Atta Ullah Khan, Muhammad Imran Naseer, Hafiz Muhammad Jafar Hussain, and Musharraf Jelani
Wiley
BACKGROUND Joubert syndrome (JBTS) is a heterogenous disorder characterized by intellectual disability, developmental delays, molar tooth sign in brain imaging, hypotonia, ocular motor apraxia, and overlapping features of ciliopathies. There are 36 clinical subtypes of JBTS with an equal number of genes known so far for this phenotype. METHODS Whole exome sequencing (WES) and Sanger sequencing were performed for the molecular diagnosis of a Pakhtun family affected with Joubert syndrome type 9 (JBTS9). RESULTS A novel homozygous missense variant (c.4417C>G; Pro1473Ala) in exon 34 was identified in coiled-coil and C2 domains-containing protein 2A (CC2D2A; NM_001080522) gene. The variant co-segregated in autosomal recessive fashion within the family and was not found in 200 ethnically matched unaffected individuals. In-silico analyses supported the pathogenic effect of the altered CC2D2A protein. CONCLUSION To the best of our knowledge, this is the first report of CC2D2A alteration co-segragating with JBTS9 phenotype in a Pakhtun family from Pakistan. Our findings broaden the pathogenic spectrum of JBTS9, adding a novel variant to CC2D2A variations' pool. WES analysis is a successful molecular diagnostic tool for the rare genetic disorders specially in those populations where cousin marriages are more frequent. Efficient and accurate genetic testing and counselling of the affected families are helpful in patients' management and to reduce the disease burden in future generations.


Genetic variations in drug-metabolizing enzyme CYP2C9 among major ethnic groups of Pakistani population
Hizbullah, Sagheer Ahmed, Mah Noor Mumtaz, Zaira Zulfiqar, Sheikh Amir Hamza, Sami Siraj, Musharraf Jelani, Imran Imran, and Asifullah Khan
Elsevier BV
The genetic polymorphism of cytochrome P450 (CYPs)drug-metabolizing enzymes are well studied in human populations for drug safety and efficacy. CYP2C9 is a highly polymorphic CYP enzyme that oxidizing the indigenous compounds and xenobiotics. The present study was pursued to evaluate the genetic variation across the CYP2C9 gene among major groups of the Pakistani population. The CYP2C9 genomic region holding important warfarin drug-metabolizing SNPs was sequenced from 159 individuals belong from five major ethnic groups of Pakistani population. The population genetic analyses of the high-quality sequences data was performed using Arlequin v3.5, DnaSP v6.12 and Network 5 resources. The data analyses unveiled that genetic variance among samples mainly arose from population-scale differentiation among these ethnic groups with global Fst of 0.78, P-value < 0.0001. The highest pairwise population genetic variation observed between Saraiki and Baloch groups based on different statistical tests. Whereas, uniform genetic composition across CYP2C9 loci was inferred among Punjabi, Pathan and Sindhi groups with minimal genetic differentiation. Several SNPs, including the previously reported warfarin associated variants, i.e. rs2860905, rs1799853 (CYP2C9*2) and rs72558189 (CYP2C9*14) were detected in these population groups with diverse frequencies. Also, a novel intronic SNP, i.e. not available in dbSNP and Ensemble databases, was identified for a Sindhi individual sample. This novel SNP predicted to influence the CYP2C9 alternative transcript splicing. The pharmacogeneticsassessment of the CYP2C9 genetic variations identified in current study may important to test against the warfarin efficacy for different ethnicity of Pakistani population.


Identification of a recurrent nonsense mutation in HR gene responsible for atrichia with papular lesions in two Kashmiri families
Ghazanfar Ali, Naheed Bashir Awan, Sadia, Abdul Waheed Khawaja, Jia Nee Foo, Chiea Chuen Khor, Chu‐Hua Chang, Elaine GuoYan Chew, Farhat Rafique Kiani, and Musharraf Jelani
Wiley
Congenital atrichia (CA) is a rare form of irreversible alopecia with an autosomal recessive mode of inheritance. This form of hair loss is mainly associated with mutations in the human hairless (HR) gene located at chromosome 8p21.3. An additional unique feature atrichia with papular lesions (APL) comprises keratin‐filled cysts known as papules. The present study aimed to uncover the underlying genetic causes of APL in two consanguineous Kashmiri families.


Novel missense alteration in LRP4 gene underlies Cenani–Lenz syndactyly syndrome in a consanguineous family
Nuha Alrayes, Abdul Aziz, Farman Ullah, Muhammad Ishfaq, Musharraf Jelani, and Abdul Wali
Wiley
Syndactyly is a clinical feature of split‐hand foot malformation (SHFM), ectodermal‐dysplasia‐syndactyly (EDSS1) and Cenani–Lenz syndactyly syndromes (CLSS). In EDSS1, only cutaneous syndactyly is observed, with sparse hair, abnormal nails and dentition. In SHFM, bony syndactyly may vary from hypoplasia of one phalanx to aplasia of central digits, extending to complete fusion of all fingers and toes in CLSS. Several genes have been assigned to these syndromes. Performing a single step molecular diagnostics becomes a challenge when a phenotype has overlaps with several syndromes or when some of the clinical features are not fully expressed in patients.


A recurrent missense mutation in the EDAR gene causes severe autosomal recessive hypohidrotic ectodermal dysplasia in two consanguineous Kashmiri families
Sadia, Jia Nee Foo, Chiea Chuen Khor, Musharraf Jelani, and Ghazanfar Ali
Wiley
Hypohidrotic ectodermal dysplasia (HED) is a rare congenital disorder arising from the abnormal development of ectoderm derived structures, including skin, hair, nails, teeth and glands. These patients have sparse hair on the whole body, including the scalp, as well as hypoplastic teeth. They have no resistance to heat as a result of abnormal sweat glands. In total, four genes, namely ectodysplasin A (EDA), ectodysplasin A receptor (EDAR), EDAR‐associated death domain protein (EDARADD) and Wnt family member 10A (WNT10A), are known to be involved in the etiology of HED.


A mutation in the major autophagy gene, WIPI2, associated with global developmental abnormalities
Musharraf Jelani, Hannah C. Dooley, Andrea Gubas, Hussein Sheikh Ali Mohamoud, Muhammad Tariq Masood Khan, Zahir Ali, Changsoo Kang, Fazal Rahim, Amin Jan, Nirmal Vadgama,et al.
Oxford University Press (OUP)
Defects in autophagy are implicated in a growing number of diseases. Jelani et al. identify a mutation in WIPI2, a major autophagy gene, associated with a multisystemic global developmental disorder. Functional studies in cell lines derived from patients reveal significant reductions in the classic hallmarks of autophagy.


Exome analysis identifies a novel compound heterozygous alteration in tgm1 gene leading to lamellar ichthyosis in a child from Saudi Arabia: Case presentation
Sami Raja Alallasi, Amal A. Kokandi, Babajan Banagnapali, Noor Ahmad Shaik, Bandar Ali Al-Shehri, Nuha Mohammad Alrayes, Jumana Yousuf Al-Aama, and Musharraf Jelani
Frontiers Media SA
Background: Lamellar ichthyosis is an autosomal recessive type of rare skin disorders characterized with defective epidermis leading hyperkeratosis with brownish-gray scales over the body. These patients are born as collodion babies and may also exhibit additional features like erythema, ectropion, and eclabium. This disease is mainly caused by homozygous and compound heterozygous alterations in transglutaminase 1 encoding gene (TGM1), which is located on 14q12. Case presentation: This study reports the genetic analysis of a 4-year Saudi girl presenting lamellar ichthyosis. She was the first child of unrelated parents. The family had no previous history of the disease phenotype. She was born as a collodion baby without any prenatal complications. At the time of this study she had developed rough scaly skin on her legs, arms and trunk regions with thick palms and soles. Whole exome sequencing (WES) followed by Sanger sequence validation identified a novel compound heterozygous variant in TGM1 gene. The paternal variant was a missense transition (c.1141G>A; p.Ala381Thr) present at exon 7, while maternal variant (c.758-1G>C) was present at the intron4-exon5 boundary. To the best of our knowledge these variants had not been reported before in TGM1 gene. Conclusion: In isolated and inbred populations, homozygous variants are identified more frequently; however, our results suggest that compound heterozygous variants should also be considered especially when the marriages are not consanguineous.


A missense mutation in TRAPPC6A leads to build-up of the protein, in patients with a neurodevelopmental syndrome and dysmorphic features
Hussein Sheikh Mohamoud, Saleem Ahmed, Musharraf Jelani, Nuha Alrayes, Kay Childs, Nirmal Vadgama, Mona Mohammad Almramhi, Jumana Yousuf Al-Aama, Steve Goodbourn, and Jamal Nasir
Springer Science and Business Media LLC
Childhood onset clinical syndromes involving intellectual disability and dysmorphic features, such as polydactyly, suggest common developmental pathways link seemingly unrelated phenotypes. We identified a consanguineous family of Saudi origin with varying complex features including intellectual disability, speech delay, facial dysmorphism and polydactyly. Combining, microarray based comparative genomic hybridisation (CGH) to identify regions of homozygosity, with exome sequencing, led to the identification of homozygous mutations in five candidate genes (RSPH6A, ANKK1, AMOTL1, ALKBH8, TRAPPC6A), all of which appear to be pathogenic as predicted by Proven, SIFT and PolyPhen2 and segregate perfectly with the disease phenotype. We therefore looked for differences in expression levels of each protein in HEK293 cells, expressing either the wild-type or mutant full-length cDNA construct. Unexpectedly, wild-type TRAPPC6A appeared to be unstable, but addition of the proteasome inhibitor MG132 stabilised its expression. Mutations have previously been reported in several members of the TRAPP complex of proteins, including TRAPPC2, TRAPPC9 and TRAPPC11, resulting in disorders involving skeletal abnormalities, intellectual disability, speech impairment and developmental delay. TRAPPC6A joins a growing list of proteins belonging to the TRAPP complex, implicated in clinical syndromes with neurodevelopmental abnormalities.


The prevalence of APOL1 gene variants in a cohort of renal disease patients in Western Saudi Arabia
Soheir Adam, Maha Badawi, Galila Zaher, Bandar Alshehri, Ahmed Basaeed, Musharraf Jelani, and Abdullah Kashqari
Medknow
Two variants for APOL1; the gastrointestinal (G1) variant (S342G and 1384M substitutions) and the G2 variant (N388 and Y389 deletions) have been previously described to be associated with renal disease. The prevalence of APOL1 variants in Saudi Arabia is unknown. We aimed to determine the prevalence of APOL1 variants in a cohort of patients with renal disease in Saudi Arabia. Patients with renal disease followed up at King Abdulaziz University Hospital were approached consecutively at the out patient clinic, and unaffected controls were approached at the blood donation area. Clinical and laboratory data were collected from electronic medical records. Laboratory variables in controls were obtained on enrollment. This is a cross-sectional, cohort study. One hundred and one patients with a mean age of 54.5 (±19) years, and 119 unaffected controls with a mean age of 31.9 (±7.89) years, were enrolled. Seventy-four patients (68.5%) had hypertension and 62 (57.4%) had diabetes. The mean estimated glomerular filtration rate was 22.47 (± 27.6) mL/min. Two patients were heterozygous for G1 allele. Among the control group, two were heterozygous for G1 allele, and three were heterozygous for G2. All five controls had no evidence of renal disease and no family history of renal disease. The prevalence of APOL1 genetic risk variants in the study cohort was very low. Larger studies are needed to determine the prevalence among renal disease patients in Saudi Arabia.


Whole-exome sequencing analysis reveals co-segregation of a COL20A1 missense mutation in a Pakistani family with striate palmoplantar keratoderma
Muhammad Ismail Khan, Soyeon Choi, Muhammad Zahid, Habib Ahmad, Roshan Ali, Musharraf Jelani, and Changsoo Kang
Springer Science and Business Media LLC
Palmoplantar keratoderma (PPK) is a rare group of excessive skin disorder characterized by thickness over the palms and soles. The striate palmoplantar keratoderma (PPKS) is a form in which hyperkeratotic lesions are restricted to the pressure regions extending longitudinally in the length of each finger to the palm. Dominantly inherited mutations in genes including desmoglein 1, desmoplakin and keratin 1 have been suggested as genetic causes of PPKS. In this study, we investigated a three-generation Pakistani family segregating PPKS phenotype in autosomal dominant fashion to identify genetic cause in this family. We have performed whole-exome and Sanger sequencing followed by in silico bioinformatics analysis to pinpoint candidate mutation associated with PPK. Revealed a novel heterozygous mutation (NM_020882.2, COL20A1 c. 392C > G; p.Ser131Cys) in the loop region close to fibronectin type III-1 domain of the c ollagen 20 α1. This variant was not found in our in-house 219 ethnically matched Pakistani unaffected controls and showed minor allele frequency of 3.4 × 10−5 in Exome Aggregation Consortium database containing exome data of 59,464 worldwide individuals. It was assigned as “pathogenic” by in silico prediction tools. Previously, association of mutation in the COL14A1, one of the paralogous gene of COL20A1, with PPK was reported in the study with a Chinese family. Our study proposes COL20A1 gene as another potential candidate gene for PPKS which expand the spectrum of collagen proteins in the pathogenicity of PPK.