Biallelic KITLG variants lead to a distinct spectrum of hypomelanosis and sensorineural hearing loss.

BACKGROUND: Pathogenic variants in KITLG, a crucial protein involved in pigmentation and neural crest cell migration, cause non-syndromic hearing loss, Waardenburg syndrome type 2, familial progressive hyperpigmentation and familial progressive hyper- and hypopigmentation, all of which are inherited in an autosomal dominant manner. OBJECTIVES: To describe the genotypic and clinical spectrum of biallelic KITLG-variants. METHODS: We used a genotype-first approach through the GeneMatcher data sharing platform to collect individuals with biallelic KITLG variants and reviewed the literature for overlapping reports. RESULTS: We describe the first case series with biallelic KITLG variants; we expand the known hypomelanosis spectrum to include a 'sock-and-glove-like', symmetric distribution, progressive repigmentation and generalized hypomelanosis. We speculate that KITLG biallelic loss-of-function variants cause generalized hypomelanosis, whilst variants with residual function lead to a variable auditory-pigmentary disorder mostly reminiscent of Waardenburg syndrome type 2 or piebaldism. CONCLUSIONS: We provide consolidating evidence that biallelic KITLG variants cause a distinct auditory-pigmentary disorder. We evidence a significant clinical variability, similar to the one previously observed in KIT-related piebaldism.

Diagnosis and Management of Global Development Delay: Consensus Guidelines of Growth, Development and Behavioral Pediatrics Chapter, Neurology Chapter and Neurodevelopment Pediatrics Chapter of the Indian Academy of Pediatrics.

JUSTIFICATION: Global developmental delay (GDD) is a relatively common neurodevelopmental disorder; however, paucity of published literature and absence of uniform guidelines increases the complexity of clinical management of this condition. Hence, there is a need of practical guidelines for the pediatrician on the diagnosis and management of GDD, summarizing the available evidence, and filling in the gaps in existing knowledge and practices. PROCESS: Seven subcommittees of subject experts comprising of writing and expert group from among members of Indian Academy of Pediatrics (IAP) and its chapters of Neurology, Neurodevelopment Pediatrics and Growth Development and Behavioral Pediatrics were constituted, who reviewed literature, developed key questions and prepared the first draft on guidelines after multiple rounds of discussion. The guidelines were then discussed by the whole group in an online meeting. The points of contention were discussed and a general consensus was arrived at, after which final guidelines were drafted by the writing group and approved by all contributors. The guidelines were then approved by the Executive Board of IAP. Guidelines: GDD is defined as significant delay (at least 2 standard deviations below the mean with standardized developmental tests) in at least two developmental domains in children under 5 years of age; however, children whose delay can be explained primarily by motor issues or severe uncorrected visual/hearing impairment are excluded. Severity of GDD can be classified as mild, moderate, severe and profound on adaptive functioning. For all children, in addition to routine surveillance, developmental screening using standardized tools should be done at 9-12 months,18-24 months, and at school entry; whereas, for high risk infants, it should be done 6-monthly till 24 months and yearly till 5 years of age; in addition to once at school entry. All children, especially those diagnosed with GDD, should be screened for ASD at 18-24 months, and if screen negative, again at 3 years of age. It is recommended that investigations should always follow a careful history and examination to plan targeted testing and, vision and hearing screening should be done in all cases prior to standardized tests of development. Neuro-imaging, preferably magnetic resonance imaging of the brain, should be obtained when specific clinical indicators are present. Biochemical and metabolic investigations should be targeted towards identifying treatable conditions and genetic tests are recommended in presence of clinical suspicion of a genetic syndrome and/or in the absence of a clear etiology. Multidisciplinary intervention should be initiated soon after the delay is recognized even before a formal diagnosis is made, and early intervention for high risk infants should start in the nursery with developmentally supportive care. Detailed structured counselling of family regarding the diagnosis, etiology, comorbidities, investigations, management, prognosis and follow-up is recommended. Regular targeted follow-up should be done, preferably in consultation with a team of experts led by a developmental pediatrician/ pediatric neurologist.

Whole exome sequencing identifies a novel pathogenic variation [p.(Gly194valfs*7)] in SLC45A2 in the homozygous state in multiple members of a family with oculocutaneous albinism in southern India.

Deleterious mutations within the SLC45A2 gene, encoding membrane-associated transporter protein (MATP), are responsible for type 4 oculocutaneous albinism. The cytogenetic location of SLC45A2 is 5p13.2 and it comprises seven exons located over around 40 kb. Its encoded protein, MATP, is 530 amino acids long and has 12 putative transmembrane domains. MATP is synthesized within melanocytes. It is in these cells that melanogenesis takes place and the melanin is contained within specialized organelles called melanosomes. Previous studies have shown that when MATP expression was reduced using small interfering RNA in MNT-1 melanoma cells, pH was lowered within melanosomes, they became poorly melanized and tyrosinase activity within melanocytes was also reduced. This type of albinism produces a broad spectrum of phenotypes, ranging from complete absence of melanin to brown hair and brown irides. In the current study, blood was collected from a family in which four members had oculocutaneous albinism, showing a complete absence of melanin in skin, hair and eyes. Screening of the TYR gene using the extracted DNA showed no mutation and therefore whole exome sequencing analysis was performed. A novel deletion mutation c.579delG [p.(Gly194Valfs*7)] in the SLC45A2 gene, predicted to be pathogenic and to result in both frameshift and premature termination of the MATP chain, was identified. These data add to the information pertaining to the mutation spectrum of OCA4.

Report of second case and clinical and molecular characterization of Eiken syndrome.

We report a boy with Eiken syndrome caused by a homozygous missense variant in Parathyroid hormone 1 receptor (PTH1R) c.103G > A [p.(Glu35Lys)]. Eiken syndrome is a very rare skeletal dysplasia due to bi-allelic variants in PTH1R. Only one affected family has been known to-date. The hallmarks include delayed ossification of bone including the epiphyses, pubic symphysis, and primary ossification centers of the short tubular bones, coarse bone trabeculae, and modeling abnormalities. The phenotype being described here recapitulates the delayed ossification and modeling abnormalities of Eiken syndrome. In addition, supernumerary epiphyses of the tubular bones of the hands and primary failure of eruption of teeth were observed in our proband. This report characterizes Eiken syndrome and confirms that bi-allelic hypomorphic variants in PTH1R are probably to cause this condition.

A review of skeletal dysplasia research in India.

We aimed to review the contributions by Indian researchers to the subspecialty of skeletal dysplasias (SDs). Literature search using specific keywords in PubMed was performed to retrieve all the published literature on SDs as on July 6, 2017. All published literature on SDs wherein at least one author was from an Indian institute was included. Publications were grouped into different categories based on the major emphasis of the research paper. Five hundred and forty publications in English language were retrieved and categorized into five different groups. The publications were categorized as reports based on: (i) phenotypes (n = 437), (ii) mutations (n = 51), (iii) novel genes (n = 9), (iv) therapeutic interventions (n = 31), and (v) reviews (n = 12). Most of the publications were single-patient case reports describing the clinical and radiological features of the patients affected with SDs (n = 352). We enlisted all the significant Indian contributions. We have also highlighted the reports in which Indians have contributed to discovery of new genes and phenotypes. This review highlights the substantial Indian contributions to SD research, which is poised to reach even greater heights given the size and structure of our population, technological advances, and expanding national and international collaborations.

Seven additional families with spondylocarpotarsal synostosis syndrome with novel biallelic deleterious variants in FLNB.

The location and/or type of variants in FLNB result in a spectrum of osteochondrodysplasias ranging from mild forms, like spondylocarpotarsal synostosis syndrome and Larsen syndrome, to severe perinatal lethal forms, such as atelosteogenesis I and III and Boomerang dysplasia. Spondylocarpotarsal synostosis syndrome is characterized by disproportionate short stature, vertebral anomalies and fusion of carpal and tarsal bones. Biallelic loss-of-function variants in FLNB are known to cause spondylocarpotarsal synostosis syndrome and 9 families and 9 pathogenic variants have been reported so far. We report clinical features of 10 additional patients from 7 families with spondylocarpotarsal synostosis syndrome due to 7 novel deleterious variants in FLNB, thus expanding the clinical and molecular repertoire of spondylocarpotarsal synostosis syndrome. Our report validates key clinical (fused thoracic vertebrae and carpal and tarsal coalition) and molecular (truncating variants in FLNB) characteristics of this condition.

Novel KIAA0753 mutations extend the phenotype of skeletal ciliopathies.

The skeletal ciliopathies are a heterogeneous group of disorders with a significant clinical and genetic variability and the main clinical features are thoracic hypoplasia and short tubular bones. To date, 25 genes have been identified in association with skeletal ciliopathies. Mutations in the KIAA0753 gene have recently been associated with Joubert syndrome (JBTS) and orofaciodigital (OFD) syndrome. We report biallelic pathogenic variants in KIAA0753 in four patients with short-rib type skeletal dysplasia. The manifestations in our patients are variable and ranging from fetal lethal to viable and moderate skeletal dysplasia with narrow thorax and abnormal metaphyses. We demonstrate that KIAA0753 is expressed in normal fetal human growth plate and show that the affected fetus, with a compound heterozygous frameshift and a nonsense mutation in KIAA0753, has an abnormal proliferative zone and a broad hypertrophic zone. The importance of KIAA0753 for normal skeletal development is further confirmed by our findings that zebrafish embryos homozygous for a nonsense mutation in kiaa0753 display altered cartilage patterning.

Second family provides further evidence for causation of Steel syndrome by biallelic mutations in COL27A1.

Steel syndrome is a rare disorder of the skeleton characterized by facial dysmorphism, short stature, carpal coalition, dislocated radial heads, bilateral hip dislocation and vertical talus. Homozygous variants in COL27A1 were reported in an extending family from Puerto Rico. Here, we report a 5-year-old girl from a non-consanguineous family with facial dysmorphism, short stature, carpal coalition, dislocation of radial heads, bilateral hip dislocation, scoliosis and vertical talus. Exome sequencing identified 2 novel compound heterozygous variants c.521_528del (p.(Cys174Serfs*34)) and c.2119C>T (p.(Arg707*)) in COL27A1 in this child and the parents were heterozygous carriers. We hence report the second molecularly proven case of Steel syndrome and the first case to be reported among non-Puerto Rican population. Our report further validates the role of COL27A1 mutations in causation of Steel syndrome.

Autosomal recessive spinocerebellar ataxia 20: Report of a new patient and review of literature.

Inherited ataxias are an extremely heterogeneous group of disorders. Autosomal recessive spinocerebellar ataxia 20 (SCAR20) is a recently described disorder characterized by intellectual disability, ataxia, coarse facial features, progressive loss of Purkinje cells in the cerebellum and often hearing loss and skeletal abnormalities. Mutations in the gene SNX14, which plays an important role in autophagy, have been found to cause SCAR20. The unique clinical findings of progressive coarsening of facial features makes the clinical phenotype recognizable among the various hereditary ataxias. Here we report on a child with a novel missense mutation in the SNX14 gene that appears to be debilitating for protein conformation, function and review the previously reported cases from 15 families.

Identification and characterization of 20 novel pathogenic variants in 60 unrelated Indian patients with mucopolysaccharidoses type I and type II.

Mucopolysaccharidoses (MPS), a subgroup of lysosomal storage disorders, are caused due to deficiency of specific lysosomal enzyme involved in catabolism of glycosaminoglycans. To date more than 200 pathogenic variants in the alpha-l-iduronidase (IDUA) for MPS I and ∼500 pathogenic variants in the iduronate-2-sulphatase (IDS) for MPS II have been reported worldwide. The mutation spectrum of MPS type I and MPS type II disorders in Indian population is not characterized yet. In this study, we carried out clinical, biochemical, molecular and in silico analyses to establish the mutation spectrum of MPS I and MPS II in the Indian population. We conducted molecular analysis for 60 MPS-affected patients [MPS I (n = 30) (Hurler syndrome = 17, Hurler-Scheie syndrome = 13), and MPS II (n = 30) (severe = 18, attenuated = 12)] and identified a total of 44 [MPS I (n = 22) and MPS II (n = 22)] different pathogenic variants comprising missense, nonsense, frameshift, gross deletions and splice site variants. A total of 20 [MPS I (n = 14), and MPS II (n = 6)] novel pathogenic sequence variants were identified in our patient cohort. We found that 32% of pathogenic variants detected in IDUA were recurrent and 25% in MPS II. This is the first study revealing the mutation spectrum of MPS I and MPS II patients in the Indian population.

A homozygous nonsense variant in IFT52 is associated with a human skeletal ciliopathy.

Intraflagellar transport (IFT) is vital for the functioning of primary cilia. Defects in several components of IFT complexes cause a spectrum of ciliopathies with variable involvement of skeleton, brain, eyes, ectoderm and kidneys. We examined a child from a consanguineous family who had short stature, narrow thorax, short hands and feet, postaxial polydactyly of hands, pigmentary retinopathy, small teeth and skeletal dysplasia. The clinical phenotype of the child shows significant overlap with cranioectodermal dysplasia type I (Sensenbrenner syndrome). Whole-exome sequencing revealed a homozygous nonsense variant p.R142* in IFT52 encoding an IFT-B core complex protein as the probable cause of her condition. This is the first report of a human disease associated with IFT52.

EVALUATION OF MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION AS A TOOL FOR DIAGNOSIS AND CARRIER DETECTION IN FAMILIES WITH A DYSTROPHINOPATHY.

We set out to evaluate multiplex ligation dependent probe amplification (MLPA) as a tool for diagnosis and carrier detection in families with a dystrophinopathy. Fifty three Indian families with provisional diagnosis of Duchene muscular dystrophy or Becker muscular dystrophy were evaluated by MLPA and multiplex polymerase chain reaction (PCR). Sanger sequencing was used to analyze the entire gene in one patient. Mothers were tested for carrier status whenever possible. Molecular analysis of DMD gene by combining MLPA and multiplex PCR yielded a mutation detection rate of 62% (33/53). Deletions were detected in 27/53 (51%) cases, duplications in 5/53 (9%) cases, a small deletion one case and Sanger sequencing detected a nonsense mutation in one case. Mutation was not detected in 36% (19/53) cases. Fifty six percent of mothers (9/16) were found to be carriers. MLPA helped to refine the results of multiplex PCR testing in 22 patients (5 duplications, 16 deletions and one small deletion). We also describe a situation where a deletion of single exon on MLPA (but not detected by multiplex PCR) was actually due to a deletion of two nucleotides in the probe ligation site. MLPA appears to score over multiplex PCR in diagnosis and carrier detection, specifically by detecting deletions and duplications that are not detected by traditional multiplex PCR.

ALOBAR HOLOPROSENCEPHALY, CLEFT LIP/PALATE, URORECTAL SEPTUM MALFORMATION SEQUENCE AND CONGENITAL PERINEAL HERNIA IN A FETUS.

We report on a fetus with alobar holoprosencephaly, complete cleft lip and palate, urorectal septum malformation sequence and perineal hernia. To our knowledge this appears to be a novel fetal malformation syndrome.

Microduplications encompassing the Sonic hedgehog limb enhancer ZRS are associated with Haas-type polysyndactyly and Laurin-Sandrow syndrome.

Laurin-Sandrow syndrome (LSS) is a rare autosomal dominant disorder characterized by polysyndactyly of hands and/or feet, mirror image duplication of the feet, nasal defects, and loss of identity between fibula and tibia. The genetic basis of LSS is currently unknown. LSS shows phenotypic overlap with Haas-type polysyndactyly (HTS) regarding the digital phenotype. Here we report on five unrelated families with overlapping microduplications encompassing the Sonic hedgehog (SHH) limb enhancer ZPA regulatory sequence (ZRS) on chromosome 7q36. Clinically, the patients show polysyndactyly phenotypes and various types of lower limb malformations ranging from syndactyly to mirror image polydactyly with duplications of the fibulae. We show that larger duplications of the ZRS region (>80 kb) are associated with HTS, whereas smaller duplications (<80 kb) result in the LSS phenotype. On the basis of our data, the latter can be clearly distinguished from HTS by the presence of mirror image polysyndactyly of the feet with duplication of the fibula. Our results expand the clinical phenotype of the ZRS-associated syndromes and suggest that smaller duplications (<80 kb) are associated with a more severe phenotype. In addition, we show that these small microduplications within the ZRS region are the underlying genetic cause of Laurin-Sandrow syndrome.

Pfeiffer Syndrome with Extreme Proptosis, Hypothyroidism and Tail like Appendage.

Pfeiffer syndrome is a rare genetic disorder with combination of bicoronal craniosynostosis, broad thumbs, broad great toes, ankylosis of elbow and partial variable syndactyly of the hands and feet. Since the disorder was reported by Pfeiffer in 1964, new associations have been added on. Authors report a newborn with features of Pfeiffer syndrome type 3 with hypothyroidism, tail like appendage and extremely anteriorly placed anus as new associations.

Prenatal diagnosis of absent pulmonary valve confirmed by autopsy.

Absent pulmonary valve syndrome (APVS) is a rare congenital cardiac anomaly. This syndrome is comprised of subtotal or total absence of pulmonary valve leaflets, stenosis of the pulmonary artery orifice, aneurysmal dilation of the main pulmonary artery and ventricular septal defect. We report a case of APVS with neural tube defect detected prenatally at 22 weeks of gestation by echocardiography, and subsequently confirmed by autopsy of the still born fetus. The common presentations, means of diagnosis and variants of APVS are discussed in brief.

Analysis of the WISP3 gene in Indian families with progressive pseudorheumatoid dysplasia.

Progressive pseudorheumatoid dysplasia (PPD) is a progressive skeletal syndrome characterized by stiffness, swelling and pain in multiple joints with associated osteoporosis in affected patients. Radiographically, the predominant features resemble a spondyloepiphyseal dysplasia. Mutations in the WISP3 gene are known to cause this autosomal recessive condition. To date, only a limited number of studies have looked into the spectrum of mutations causing PPD. We report on clinical features and WISP3 mutations in a large series of Indian patients with this rare skeletal dysplasia. Families with at least one member showing clinical and radiologic features of PPD were recruited for the study. Symptoms, signs and radiographic findings were documented in 35 patients from 25 unrelated families. Swelling of small joints of hands and contractures are the most common presenting features. Mutation analysis was carried out by bidirectional sequencing of the WISP3 gene in all 35 patients. We summarize the clinical features of 35 patients with PPD and report on 11 different homozygous mutations and one instance of compound heterozygosity. Eight (c.233G>A, c.340T>C, c.348C>A, c.433T>C, c.682T>C, c.802T>G, c.947_951delAATTT, and c.1010G>A) are novel mutations and three (c.156C>A, c.248G>A, and c.739_740delTG) have been reported previously. One missense mutation (c.1010G>A; p.Cys337Tyr) appears to be the most common in our population being seen in 10 unrelated families. This is the largest cohort of patients with PPD in the literature and the first report from India on mutation analysis of WISP3. We also review all the mutations reported in WISP3 till date.

Placental Teratoma Presenting as a Lobulated Mass behind the Neck of Fetus: A Case Report.

Placental teratoma is a rare nontrophoblastic benign tumour, which is thought to arise from germ cells. These tumours contain elements derived from multiple germ cell layers. We report a case of teratoma, where on ultrasound; there were two echogenic masses of 4 cm × 5 cm and 3 cm × 4 cm, arising from the placenta. Elective lower segment cesarean section was done in view of breech presentation at 38 weeks of gestation. Gross examination of the placenta showed two lobulated masses of 5 cm × 5 cm and 4 cm × 4.5 cm, respectively. Histopathological examination of the placenta was suggestive of teratoma of the placenta. The fetus was normal.The maternal and fetal outcome was good.

Profile of patients with Von Gierke disease from India.

Molecular diagnosis of Von Gierke disease is possible by mutation analysis of G6PC gene. GSD type 1a cases account for 20 % of glycogenoses in our center. We diagnosed ten unrelated patients with glycogen storage disease based on clinical, biochemical and histopathology investigations. Mutation analysis was done by sequencing the G6PC gene. Two unrelated patients were found to be homozygous for a novel mutation c.355 C >; G (p.H119D). They were born to non-consanguineous parents from Karnataka. This suggests founder effect. Mutation detection confirms the diagnosis and assists in counseling and prenatal diagnosis.