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Classic Cornelia De Lange Syndrome with Variant of Unknown Significance Detected in NIPBL Gene Mutation: a Case Report Jay J

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Classic Cornelia De Lange Syndrome with Variant of Unknown Significance Detected in NIPBL Gene Mutation: a Case Report Jay J Desai et al. Egyptian Journal of Medical Human Genetics (2021) 22:28 Egyptian Journal of Medical https://doi.org/10.1186/s43042-021-00142-3 Human Genetics CASE REPORT Open Access Classic Cornelia de Lange syndrome with variant of unknown significance detected in NIPBL gene mutation: a case report Jay J. Desai1, Sreelata B. Nair1* and S. Pappachan2 Abstract Background: Cornelia de Lange syndrome is a relatively uncommon disorder associated with multiple congenital anomalies/mental retardation of unknown etiology with its incidence varying from 1:10,000 to 1:50,000 live births in different population groups without any known racial predilections. Main clinical features of this syndrome consist of distinctive dysmorphic facial appearance, growth retardation, developmental delay, mental retardation, hirsutism, and skeletal formation anomaly. Case presentation: This case presents a variation of unknown significance in the NIPBL gene-exon 39, chr5: 37048649T>A c.6635T>A (p.Val2212Glu) with clinical phenotype of Cornelia de Lange syndrome. Our patient belonged to South Indian origin with clinical features of synophrys, micrognathia, long smooth philtrum, and clinodactyly with bilateral simian crease. Conclusion: Cornelia de Lange syndrome is a rare but well-characterized disorder, in which multiple systems of the body are affected. It is important that the treating physician ensures coordination of the diversiform aspects of care in both childhood and adulthood. Proper and timely diagnosis using next generation sequencing helps in management and possibility of prenatal diagnosis. Keywords: Cornelia de Lange syndrome, Developmental delay, Dysmorphism, NIPBL, Missense mutation Background abnormalities is the main cause of death in these In 1916, Dr. W. Brachmann described the first case patients [2]. of this syndrome but in 1933 Cornelia de Lange, a Cornelia de Lange syndrome (CDLS) is a multisys- Dutch pediatrician from Amsterdam was the first to tem developmental disorder with dysmorphic faces report about two cases of this syndrome [1]. It is also being the most diagnostic feature characterized by called Brachmann de Lange syndrome, Amsterdam microcephaly, bushy eyebrows with synophrys, long dwarfism, Bushy syndrome. There is variable inci- eyelashes, hirsutism, smooth long philtrum, low set dence of this syndrome ranging from 1:10,000 to 1: ears, thin lips, carp shaped mouth, and flared nostrils. 50,000 live births with no racial predilection [2]. It is Other clinical features are low birth weight, failure to slightly more commonly seen in females when com- thrive, prenatal and postnatal growth, mental and de- pared to males (F/M: 1.3/1). Most children with this velopmental retardation, learning difficulties, and fail- syndrome cannot survive beyond 2 years. Pneumonia uretothrive[3, 4]. along with cardiac, respiratory, and gastrointestinal The overall CDLS phenotype involves a spectrum which includes the classic CDLS, non-classic CDLS * Correspondence: [email protected] as well as other syndromes phenotype (Coffin-Siris 1Department of Medical Genetics, Lifeline Super Specialty Hospital, 14th Mile syndrome, Rubinstein-Taybi syndrome, Nicolaides– Melood PO, Adoor, Pathanamthitta, Kerala 691523, India Baraitser syndrome) with almost identical clinical Full list of author information is available at the end of the article © The Author(s). 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Desai et al. Egyptian Journal of Medical Human Genetics (2021) 22:28 Page 2 of 6 Fig. 1 Clinical findings of the patient features [5]. CDLS is caused by pathogenic variants in genes involved in cohesion functioning. As per Kline et al. [5], till date, there is no individual with a classic CDLS phenotype in whom a variant gene without cohesion function has been definitely shown Table 1 Clinical features of Cornelia de Lange syndrome and our to be causative. All recognized, established, and obvi- case based on First International Consensus Statement, 2018 [5] ous causes of CDLS can thus be labeled as cohesino- Our case pathies but not all cohesinopathies result in CDLS [5]. Most of the cases with CDLS are usually spor- Cardinal features (2 points each if present) adic and 10% of total cases have chromosomal alter- • Synophrys and/or thick eyebrows + ations like unbalanced chromosomal rearrangements • Short nose, concave nasal ridge, and/or upturned + [6], duplications, or partial trisomy of chromosome nasal tip 3q26-27 [7]. Mutation in the Nipped-B-Like (NIPBL) • Long and/or smooth philtrum + gene is the most common and has been diagnosed • Thin upper lip vermilion and/or downturned corners + in 26 to 56% cases as an etiological factor [8]. How- of mouth ever, as per the first international consensus state- • Hand oligodactyly and/or adactyly − ment, first-line molecular diagnostic approach should • Congenital diaphragmatic hernia − be next-generation sequencing (NGS)-based screen- Suggestive features (1 point each if present) ing—either gene panel, whole-exome sequencing • Global developmental delay and/or intellectual disability + (WES) or whole-genome sequencing (WGS)—includ- • ing currently known CDLS genes (NIPBL, structural Prenatal growth retardation (< 2 SD) + maintenance of chromosomes 1A (SMC1A), struc- • Postnatal growth retardation (< 2 SD) + tural maintenance of chromosomes 3 (SMC3), • Microcephaly (prenatally and/or postnatally) + RAD21 cohesin complex component (RAD21), • Small hands and/or feet + (BRD4 Bromodomain-containing protein 4, ), histone • Short fifth finger + deacetylase 8 (HDAC8), and ankyrin repeat domain • Hirsutism + 11 (ANKRD11)[5]. Here, we present a case of sporadic CDLS and its gen- Clinical score etic workup. • ≥ 11 points, of which at least 3 are cardinal: classic CdLs 15 • 9 or 10 points, of which at least 2 are cardinal: Case presentation non- classic CdLs A 2-year-old male child of South Indian origin (Ker- • 4–8 points, of which at least 1 is cardinal: molecular ala) was brought to the Department of Medical Gen- testing for CdLs indicated eticsbytheparents(Father—32 years/ Mother—28 • < 4 points: insufficient to indicate molecular testing for CdLs years) for having progressive growth deficiency, Desai et al. Egyptian Journal of Medical Human Genetics (2021) 22:28 Page 3 of 6 Fig. 2 Integrated genome viewer snapshot showing heterozygous mutation in NIPBL gene-EXON 39, chr5:37048649 T>A childhood developmental delay, and mental retard- Child had the following clinical features on examination: ation. He was the second male child born of a non- Global developmental delay, mental retardation, consanguineous marriage with uneventful antenatal growth retardation, dysmorphic face characterized by period. He was born after pre-term caesarean section bushy eyebrows, dystichiasis, synophrys, long curly eye- done at 33 weeks of gestation in view of previous lashes, broad nasal root with flared nostrils, upturned caesarean section in labor (as per the hospital re- nose, carp shaped mouth, thin bow-shaped lips with cords and the discharge summary) with birth weight downturned corners, and long smooth philtrum was of 1.29 kg (small for gestational age) and cried im- noted (Fig. 1a, b). The child also had short stubby fin- mediately after birth. Their first child was a 5-years- gers, bilateral simian crease, bilateral short 5th finger old boy who appeared clinically normal. Both the with clinodactyly (Fig. 1c), bilateral partial cutaneous parents also appeared clinically normal, and there syndactyly of 2nd and 3rd toe fingers, unilateral crypt- three generations pedigree did not reveal any history orchidism, hirsutism, and craniosynostosis. Parents gave of deformity/mental retardation. Anthropometric history of epilepsy and the child was on multiple antiepi- measurements of the child at presentation were as leptic medications. Child had not attained walking and follows: sitting and milestones were delayed and mental retard- ation was seen. Weight: 7.6 kg (below 3rd percentile) As per the consensus, classic CDLS should have the Height: 79 cm (below 3rd percentile) score of 11 and above with presence of at least 3 car- Head circumference: 43 cm (below 3rd percentile) dinal features [5]. Our patient had cardinal features such Desai et al. Egyptian Journal of Medical Human Genetics Table 2 In-silico predictions (variant analysis report)* S.No Variant Annotation Tools Categorical Description Database Result 1. Sort Intolerated From Tolerated (SIFT) D: Deleterious (SIFT score ≤ 0.05); DbSNP Deleterious (SIFT score = 0.01) T: Tolerated (SIFT score >0.05) 2. Polymorphism Phenotyping v2 (Poly Phen v2) D: Probably damaging (pp2_score ≥ 0.957), PDB, DSSP, HumDiv, HumVar Possibly damaging (pp2_score = 0.92) P: Possibly damaging (0.453 ≤
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  • KBG Syndrome Involving a Single Nucleotide Duplication in ANKRD11
    Downloaded from molecularcasestudies.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Molecular Case Study Research Report Title: KBG syndrome involving a single nucleotide duplication in ANKRD11 Authors: Robert Kleyner1*, Janet Malcolmson1,2*, David Tegay1, Kenneth Ward3, Annette Maughan4, Glenn Maughan5, Lesa Nelson3, Kai Wang6,7,8, Reid Robison8, Gholson J. Lyon1,8,# 1Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; 2Genetic Counseling Graduate Program, Long Island University (LIU), 720 Northern Boulevard, Brookville, NY 11548; 3Affiliated Genetics, Inc. 2749 East Parleys Way Suite 100 Salt Lake City, UT 84109; 4Epilepsy Association of Utah, 8539 So. Redwood Rd., West Jordan, UT. 84088; 5KBG Syndrome Foundation, 8539 So. Redwood Rd., West Jordan, UT. 84088; 6Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90089, US; 7Department of Psychiatry & Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; 8Utah Foundation for Biomedical Research, Salt Lake City, UT *These authors contributed equally to this work. #To whom correspondence should be addressed: Email: [email protected] Downloaded from molecularcasestudies.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press ABSTRACT KBG syndrome is a rare autosomal dominant genetic condition characterized by neurological involvement and distinct facial, hand and skeletal features. Over 70 cases have been reported; however, it is likely that KBG syndrome is underdiagnosed due to lack of comprehensive characterization of the heterogeneous phenotypic features. We describe the clinical manifestations in a male currently at 13 years of age, who exhibited symptoms including epilepsy, severe developmental delay, distinct facial features and hand anomalies, without a positive genetic diagnosis.
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