Muscle spasms as presenting feature of Nivelon-Nivelon-Mabile syndrome.

Hedgehog acyltransferase gene (HHAT)-associated Nivelon-Nivelon-Mabile syndrome (NNMS) is a rare genetic disorder of multiple system involvement with microcephaly, central nervous system malformations, skeletal dysplasia, and 46,XY sex reversal. Other variable and inconsistent features reported in this disorder are muscle spasms, facial dysmorphism, prenatal onset growth restriction, microphthalmia, and holoprosencephaly. This is the sixth postnatal reported patient with biallelic variants in HHAT gene, who presented with microcephaly, short stature, muscle hypertrophy, muscle spasms, and facial dysmorphism. The most prominent and presenting finding in this patient were muscle hypertrophy and muscle spasms which had a clinical response to phenytoin and acetazolamide treatment. Our report emphasizes the phenotypic variability of NNMS and further reiterates muscle spasms as an important clinical manifestation of this extremely rare condition.

A data set of variants derived from 1455 clinical and research exomes is efficient in variant prioritization for early-onset monogenic disorders in Indians.

Given the genomic uniqueness, a local data set is most desired for Indians, who are underrepresented in existing public databases. We hypothesize patients with rare monogenic disorders and their family members can provide a reliable source of common variants in the population. Exome sequencing (ES) data from families with rare Mendelian disorders was aggregated from five centers in India. The dataset was refined by excluding related individuals and removing the disease-causing variants (refined cohort). The efficiency of these data sets was assessed in a new set of 50 exomes against gnomAD and GenomeAsia. Our original cohort comprised 1455 individuals from 1203 families. The refined cohort had 836 unrelated individuals that retained 1,251,064 variants with 181,125 population-specific and 489,618 common variants. The allele frequencies from our cohort helped to define 97,609 rare variants in gnomAD and 44,520 rare variants in GenomeAsia as common variants in our population. Our variant dataset provided an additional 1.7% and 0.1% efficiency for prioritizing heterozygous and homozygous variants respectively for rare monogenic disorders. We observed additional 19 genes/human knockouts. We list carrier frequency for 142 recessive disorders. This is a large and useful resource of exonic variants for Indians. Despite limitations, datasets from patients are efficient tools for variant prioritization in a resource-limited setting.

Exome sequencing for perinatal phenotypes: The significance of deep phenotyping.

OBJECTIVE: To ascertain the performance of exome sequencing (ES) technology for determining the etiological basis of abnormal perinatal phenotypes and to study the impact of comprehensive phenotyping on variant prioritization. METHODS: A carefully selected cohort of 32/204 fetuses with abnormal perinatal phenotypes following postmortem/postnatal deep phenotyping underwent ES to identify a causative variant for the fetal phenotype. A retrospective comparative analysis of the prenatal versus postmortem/postnatal phenotype-based variant prioritization was performed with aid of Phenolyzer software. A review of selected literature reports was done to examine the completeness of phenotypic information for cases in those reports and how it impacted the performance of fetal ES. RESULTS: In 18/32 (56%) fetuses, a pathogenic/likely pathogenic variant was identified. This included novel genotype-phenotype associations, expanded prenatal phenotypes of known Mendelian disorders and dual Mendelian diagnoses. The retrospective analysis revealed that the putative diagnostic variant could not be identified on basis of prenatal findings alone in 15/22 (68%) cases, indicating the importance of comprehensive postmortem/postnatal phenotype information. Literature review was supportive of these findings but could not be conclusive due to marked heterogeneity of involved studies. CONCLUSION: Comprehensive phenotyping is essential for improving diagnostic performance and facilitating identification of novel genotype-phenotype associations in perinatal cohorts undergoing ES.

Homozygous PCDH12 variants result in phenotype of cerebellar ataxia, dystonia, retinopathy, and dysmorphism.

We report on a sib pair of Indian origin born of a consanguineous parentage with a novel phenotype of distinct facial dysmorphism, cerebellar ataxia, dystonia, and exudative retinopathy due to homozygous PCDH12 nonsense variations. cDNA studies showed >90% reduction in transcript levels in both patients, indicating nonsense-mediated decay and loss of function as the probable causative molecular mechanism of the phenotype.

Novel splice-site variant of UCHL1 in an Indian family with autosomal recessive spastic paraplegia-79.

Spastic Paraplegia-79 (SPG79) is an autosomal recessive type of childhood onset complicated by hereditary spastic paraplegia. SPG79 is characterized by spasticity, paraplegia, optic atrophy, cerebellar signs, and other variable clinical features. Recessive, disease causing variants in Ubiquitin C-terminal hydrolase-L1 (UCHL1) gene have been implicated as a cause for SPG79 in two families till now. In this study, we report on a third family of SPG79 with two similarly affected siblings, harboring a novel homozygous splice-site variant in the UCHL1 gene (NM_004181.4: c.459+2T>C). The variant was identified by whole-exome sequencing and validated by Sanger sequencing in the family.

Homozygosity for a nonsense variant in AIMP2 is associated with a progressive neurodevelopmental disorder with microcephaly, seizures, and spastic quadriparesis.

We ascertained two unrelated consanguineous families with two affected children each having microcephaly, refractory seizures, intellectual disability, and spastic quadriparesis. Magnetic resonance imaging showed atrophy of cerebrum, cerebellum and spinal cord, prominent cisterna magna, symmetric T2 hypo-intensities in the bilateral basal ganglia and thinning of corpus callosum. Whole-exome sequencing of three affected individuals revealed c.105C>A [p.(Tyr35Ter)] variant in AIMP2. The variant lies in a common homozygous region of 940 kb on chromosome 7 and is likely to have been inherited from a common ancestor. The phenotype noted in our subjects' shares marked similarity with that of hypomyelinating leukodystrophy-3 caused by mutations in closely related gene AIMP1. We hereby report the first human disease associated with deleterious mutations in AIMP2.

Tarsal-carpal coalition syndrome: Report of a novel missense mutation in NOG gene and phenotypic delineation.

We report a family of Indian origin presenting with Tarsal-carpal coalition syndrome (TCC), which is a rare genetic disorder of skeletal abnormalities, inherited in autosomal dominant manner. In this family, three individuals (mother and two children) were found to be similarly affected with slight intrafamilial individual variability in the phenotype. Sanger sequencing revealed a novel heterozygous missense mutation in NOG gene (NM_005450.4:c.611G>A) in all the affected individuals of the family. Until now only six mutations have been reported in different families affected with TCC syndrome worldwide. This report further delineates the phenotypic spectrum of this rare disorder with the addition of a new variant to the mutation spectrum.

Whole exome sequencing reveals a mutation in ARMC9 as a cause of mental retardation, ptosis, and polydactyly.

Intellectual disability (ID) refers to deficits in mental abilities, social behavior, and motor skills to perform activities of daily living as compared to peers. Numerous genetic and environmental factors may be responsible for ID. We report on elucidation of molecular basis for syndromic ID associated with ptosis, polydactyly, and MRI features suggestive of Joubert syndrome using homozygosity mapping followed by exome sequencing. The analysis revealed a novel synonymous variation p.T293T (c.879G>A) which leads to a splicing defect in ARMC9 gene. The variant is present in conserved region of ARM domain of ARMC9 protein, which is predicted to form a platform for protein interaction. This domain is likely to be altered in patient due to splicing defect caused by this synonymous variation. Our report of variant in ARMC9 Leading to Joubert syndrome phenotype (JS30), elucidates the genetic heterogeneity of Joubert syndrome, and expands the gene list for ciliopathies.

Familial choreoathetosis due to novel heterozygous mutation in PDE10A.

PDE10A encodes a dual cAMP-cGMP phosphodiesterase that is enriched in the medium spiny neurons of the corpus striatum in the brain and plays an important role in basal ganglia circuitry. Three unrelated patients with childhood onset chorea and striatal abnormalities on MRI brain with heterozygous de novo variants in PDE10A have been described previously. Two families with eight affected individuals with biallelic mutations in PDE10A have also been described previously. We report a family with multiple affected individuals with childhood onset chorea, striatal abnormalities, and a novel heterozygous mutation, c.1001T>G(p.F334C) in PDE10A which was identified by exome sequencing.

Autosomal recessive otofaciocervical syndrome type 2 with novel homozygous small insertion in PAX1 gene.

Otofaciocervical syndrome (OTFCS) is described as a single gene disorder of both autosomal dominant and autosomal recessive inheritance. The major clinical features of OTFCS include ear malformations (external/middle/inner ear), facial dysmorphism, shoulder girdle abnormalities, vertebral anomalies, and mild intellectual disability. The autosomal recessive form of OTFCS syndrome (OTFCS2) has been recently reported to be caused due to homozygous mutations in PAX1 gene. Here we report a third family of OTFCS2 phenotype wherein whole exome sequencing identified a novel homozygous small insertion in PAX1 as the underlying genetic cause.

Exome sequencing identifies novel ACE splice-site variant in a fetus with renal tubular dysgenesis.

We report a 32-week fetus conceived of consanguineous parentage which presented with severe early onset oligohydramnios and history of a similarly affected sibling in previous pregnancy. Ultrasonography and autopsy were inconclusive, prompting exome sequencing on fetal DNA. This resulted in identification of a homozygous novel 3' splice-site variation in intron 17 of the ACE gene (NM_000789.3:c.2642-1G>A), confirming diagnosis of autosomal recessive renal tubular dysgenesis, and facilitating prenatal diagnosis in subsequent pregnancy.

A Dysmorphology Based Systematic Approach Toward Perinatal Genetic Diagnosis in a Fetal Autopsy Series.

BACKGROUND: This retrospective study assesses the contribution of genetic disorders in fetuses undergoing postmortem evaluation and the performance of a clinical dysmorphology based systematic approach toward genetic diagnosis. MATERIALS AND METHODS: Ninety fetuses, including spontaneous losses and terminated pregnancies, underwent a postmortem evaluation including dysmorphological examination, radiological studies, and histopathological examination. Genetic testing including karyotyping, biochemical testing, Sanger sequencing, and exome sequencing were performed selectively. RESULTS: A genetic etiology was concluded in 48 fetuses (55%). As a standalone test, dysmorphological examination was able to ascertain a definite genetic diagnosis in sixteen cases, histopathology in six; and karyotyping, biochemical testing and exome sequencing in two cases each (Total 28). Additionally, dysmorphology findings indicated possible genetic disorder in 20 cases. CONCLUSION: Genetic etiologies contribute significantly to fetuses undergoing autopsy in this series. A systematic approach to postmortem fetal evaluation guided by dysmorphological examination provides high diagnostic yield toward perinatal genetic diagnosis.

Co-Occurrence of Leber Congenital Amaurosis and Meckel Syndrome Type 1 in a Fetus: Is There a Lesson to Be Learned?

A patient referred for prenatal diagnostics, after first-trimester ultrasound due to a previous child with Leber congenital amaurosis, was suggestive of a Meckel syndrome-like phenotype. Fetal autopsy confirmed the multiple anomalies, and whole-exome sequencing of the fetal DNA identified a pathogenic variant in the RPGRIP1 gene, previously identified in the elder sibling, and a variant causative of Meckel syndrome 1 in the MKS1 gene. Reporting the MKS1 mutation, which was present in heterozygous state in the elder sibling, as a secondary finding would have enabled the parents to be tested for carrier status of the same variant and appropriate counseling could have been provided prior to the onset of the pregnancy. Although the information may not be of great benefit in cases where the ultrasonographic changes can be recognized early, it would be of definitive help where diagnostic imaging in early pregnancy is not possible.

Screening for methylenetetrahydrofolate reductase C677T and A1298C polymorphisms in Indian patients with idiopathic mental retardation.

Although genetic, nutritional, and environmental factors have been found to aggravate mental retardation in approximately 1% of individuals, no cause is known till date. In this study, two genetic polymorphisms in methylenetetrahydrofolate reductase (MTHFR), C677T (rs#1801133) and A1298C (rs#1801131), have been investigated in idiopathic mental retardation (IMR) subjects. Significantly higher frequency of the C677 allele was observed in IMR (n = 155; chi(2) = 5.5; P = 0.019) and moderate IMR (n = 67; chi(2) = 6.16; P = 0.013) groups as compared to controls (n = 126); for A1298C, no significant difference was noticed. TDT analysis revealed preferential transmission of C677 allele to a small group of mild IMR probands (chi(2) = 5.545; P = 0.018). Higher frequency of CA haplotype was also noticed in IMR cases as compared to controls (chi(2) = 6.28; P = 0.012). We infer from the present investigation that these polymorphisms are not contributing to the aetiology of IMR in this population since both case-control and family-based analysis revealed no significant transmission of the mutated allele.

Exome sequencing reveals blended phenotype of double heterozygous FBN1 and FBN2 variants in a fetus.

We report a 29 week fetus with arthrogryposis multiplex congenita, multiple joint dislocations, scoliosis and dysmorphism who was detected to be double heterozygote for putatively pathogenic FBN1 (NM_000138.4:c.6004C > T; p.Pro2002Ser) and FBN2 (NM_001999.3:c.2945G > T; p.Cys982Phe) variants on exome sequencing. The de-novo status of these variants is not confirmed as parental genotypes could not be ascertained. A comparison of the post-mortem findings of the fetus with reported phenotypes of Beals and Marfan syndromes indicated overlapping clinical features suggestive of a blended phenotype.

Whole exome sequencing identifies a novel 5 Mb deletion at 14q12 region in a patient with global developmental delay, microcephaly and seizures.

Rett syndrome is a neurodevelopmental disorder affecting the nervous, musculoskeletal and gastroenteric systems. Affected individuals show normal neonatal development for 6-18 months followed by sudden growth arrest, psychomotor retardation and a broad spectrum of clinical features. Sequence variants in MECP2 gene have been identified as the major genetic etiology accounting for 90-95% of patients. Apart from MECP2, pathogenic sequence variants and copy number variants of FOXG1 gene lead to congenital type of Rett syndrome which is a more severe form and characterised by absence of early normal development as seen in classical Rett syndrome. In this report we describe a female child with global developmental delay, microcephaly and myoclonic seizures harbouring a 5 Mb deletion in 14q12 locus resulting in deletion of single copy of brain specific genes FOXG1, PRKD1 and NOVA1. Whole exome sequencing ruled out any possible role of other pathogenic single nucleotide variants and/or indels as the etiology for the observed phenotype. However, copy number variation analysis from the whole exome data detected a ~ 5 Mb microdeletion at the long arm of chromosome 14q12 region. The deletion was confirmed through array Comparative Genomic Hybridization and validated by quantitative PCR. Further, parents were analysed for mosaicism through metaphase Fluorescence in-situ Hybridisation. Our report broadens the phenotype of atypical Rett syndrome and reiterates the role of exome sequencing not only in detection of point mutation/small indels but also for detection of large deletions/duplication in coding regions.

Whole exome sequencing identifies a homozygous nonsense variation in ALMS1 gene in a patient with syndromic obesity.

In the present study we report on genetic analysis in a patient with developmental delay, truncal obesity and vision problem, to find the causative mutation. Whole exome sequencing was performed on genomic DNA extracted from whole blood of the patient which revealed a homozygous nonsense variant (c.2816T>A) in exon 8 of ALMS1 gene that results in a stop codon and premature truncation at codon 939 (p.L939Ter) of the protein. The mutation was confirmed by Sanger sequencing. Exome sequencing was helpful in establishing diagnosis of Alstrom syndrome in this patient. This case highlights the utility of exome sequencing in clinical practice.

Significance of Dopaminergic Gene Variants in the Male Biasness of ADHD.

OBJECTIVE: ADHD is frequently detected in boys though there is no established cause. One possibility is that genes predisposing to ADHD have sexually dimorphic effects. With an aim to find out the reason for this male biasness, contribution of 14 functional polymorphisms was investigated in ADHD subjects. METHOD: Genomic DNA of probands, their parents, and ethnically matched controls was subjected to analysis of single-nucleotide polymorphisms and variable number of tandem repeats (VNTRs). RESULTS: Case-control analysis revealed significant higher occurrence of DAT1 intron 8 VNTR "5R" allele ( p = .028), DBH rs1108580 "A" allele ( p = .027), and MAOA-u VNTR-rs6323 3R-T haplotype ( p = .007) in male probands. Family-based analysis showed significant preferential transmission of Dopamine receptor D4 exon 3 VNTR-rs1800955 7R-T haplotype from parents to male probands ( p = .008). Interaction between DBH gene variants and low enzymatic activity was also noticed, especially in male probands. CONCLUSION: Data obtained may partly answer the male biasness of ADHD.