European Journal of Human Genetics (2016) 24, doi:10.1038/ejhg.2016.53 & 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved 1018-4813/16 www.nature.com/ejhg CLINICAL UTILITY GENE CARD Clinical Utility Gene Card for: Congenital Generalized Lipodystrophy Isabelle Jéru*,1,2,3, Camille Vatier2,3,4, David Araujo-Vilar5, Corinne Vigouroux1,2,3,4 and Olivier Lascols1,2,3 European Journal of Human Genetics (2016) 24, doi:10.1038/ejhg.2016.53; published online 18 May 2016 1. DISEASE CHARACTERISTICS molecular defects have been reported: nonsense, missense, splice-site 1.1 Name of the disease (synonyms) variants, deletions and insertions.3 Most of them result in frameshift There are four subclasses of Congenital Generalized Lipodystrophy and/or truncated proteins, which are likely to lead to the complete loss (CGL), also named Berardinelli–Seip Congenital Lipodystrophy (BSCL): of AGPAT2 function. This can be demonstrated in vitro by measure- Type 1 CGL (CGL1). ment of AGPAT2 enzymatic activity.4 Type 2 CGL (CGL2). BSCL2—CGL2 is an autosomal recessive disorder. Several dozen Type 3 CGL (CGL3). disease-causing variants have been described. The following molecular Type 4 CGL (CGL4). defects have been reported: nonsense, missense, splice-site variants, It is important to underline that CGL is an expanding group of deletions and insertions.3,5 Most of them result in frameshift and/or fi disorders, whose classi cation is still underway. In addition to the truncated proteins, which are likely to lead to complete loss of BSCL2 diseases known as CGL in OMIM, generalized lipodystrophies can be function (for more details, see http://databases.lovd.nl/shared/variants/ encountered in other Mendelian disorders including severe insulin- BSCL2/unique). Notably, disease-causing variants in this gene have resistance syndromes, complex progeroid syndromes, as well as also been identified in patients with distal hereditary motor neuro- autoinflammatory diseases. A de novo variant in the promoter of the 6 FOS pathies or neurodegenerative syndromes. gene has also been reported in a generalized lipodystrophy, CAV1—disease-causing variants in this gene are very rare. A though this disease has not entered the CGL classification so far.1 The homozygous nonsense variant was identified in a patient with CGL.7 description of all these rare entities is beyond the scope of this clinical In addition, a nonsense variant, two deletions leading to frameshifts utility gene card, which will focus on the so-called CGL. and a variant located within the 5′-untranslated region of the gene were reported in the heterozygous state in patients with atypical forms 1.2 OMIM# of the disease of lipodystrophies, either partial or generalized.8–10 Notably, disease- CGL1: #608594. fi CGL2: #269700. causing variants in this gene have also been identi ed in patients 11 CGL3: #612526. described with isolated pulmonary hypertension. PTRF— CGL4: #613327. CGL4 is an autosomal recessive disorder associating generalized lipodystrophy and muscular dystrophy. A bit more than 1.3 Name of the analysed genes or dna/chromosome segments 10 disease-causing variants have been described to date. The following CGL1: AGPAT2. molecular defects have been reported: nonsense, splice-site variants, CGL2: BSCL2. deletions and insertions.12 All of them result in frameshift and/or CGL3: CAV1. truncated proteins, which are likely to lead to complete loss of PTRF CGL4: PTRF. function. Individuals carrying disease-causing variants in the hetero- zygous state can present minor signs of the disease. 1.4 OMIM# of the gene(s) Except for BSCL2, there is no specific database listing molecular AGPAT2:*603100. defects implicated in CGL. BSCL2: *606158. CAV1: *601047. PTRF:*603198. 1.6 Analytical methods Sanger sequencing of PCR products corresponding to the coding 1.5 Mutational spectrum regions and conserved splice sites is performed on a routine basis. AGPAT2—CGL1 is an autosomal recessive disorder. Several dozen Next-generation sequencing, including gene-targeted and whole- disease-causing variants have been described.2 The following exome sequencing approaches, is also used. 1AP-HP, Hôpital Saint-Antoine, Laboratoire Commun de Biologie et Génétique Moléculaires, Paris, France; 2Sorbonne Universités, UPMC Univ Paris 06, INSERM, UMR_S938, Centre de Recherche Saint-Antoine, Paris, France; 3ICAN, Institute of Cardiometabolism and Nutrition, Paris, France; 4AP-HP, Hôpital Saint-Antoine, Service d'Endocrinologie, Diabétologie et Endocrinologie de la Reproduction, Paris, France; 5CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain *Correspondence: Dr I Jéru, AP-HP, Hôpital Saint-Antoine, Laboratoire Commun de Biologie et Génétique Moléculaires, 184 rue du Faubourg Saint-Antoine, Paris 75012, France. Tel: +33 1 4928 2809; Fax: +33 1 4928 2206; E-mail: [email protected] Received 23 November 2015; revised 4 April 2016; accepted 21 April 2016; published online 18 May 2016 Clinical Utility Gene Card e2 1.7 Analytical validation regions and flanking intronic sequences. Single-nucleotide polymorph- There are several steps in the analytical validation process. isms (SNPs) within PCR primer-binding sites can result in preferential amplification of a single allele and constitute a rare cause of missed Sequencing of both DNA strands (forward and reverse) is variant, so that careful checking of primer-binding sites for SNPs is performed. essential. Notably, potential deep-intronic variants, variants in pro- When two heterozygous variants or a homozygous variant are moters, large deletions and duplications would not be detected by found, testing of the patients’ parents is recommended to confirm Sanger sequencing performed on a routine basis. Next-generation that the defect is biallelic. More generally, identification of the same sequencing allows the detection of copy-number variations. variant in the affected proband’s relatives provides additional confirmation of the result. When the genetic test is positive, a 2.2 Analytical specificity search of the molecular defects is also recommended on a second (proportion of negative tests if the genotype is not present) independent sample from the patient. 100%. The analytical validation described above should avoid false- Newly discovered variants may be searched for in databases positive tests. As CGL are recessive disorders, false-positive results with listing benign and pathogenic variants. Pathogenicity of variants two unknown sequence variations are not expected. can also be tested by in silico prediction methods and functional studies. 2.3 Clinical sensitivity (proportion of positive tests if the disease is present) Notably, there is to date no external quality assessment dedicated to The clinical sensitivity can be dependent on variable factors such as this specific set of genes proposed by the European Molecular Genetics age, sex or family history. In such cases a general statement should be Quality Network. given, even if a quantification can only be made case by case. When the diagnosis has been properly established based on clinical 1.8 Estimated frequency of the disease (Incidence at birth (‘birth investigation, family history, imaging and biochemical results, very few prevalence’) or population prevalence. If known to be variable negative tests are expected. Molecular testing of AGPAT2 and BSCL2 between ethnic groups, please report): explain more than 95% of cases,3 whereas CAV1 and PTRF explain Less than 500 patients have been reported worldwide. The popula- very few of them. When genetic testing is negative in a patient with tion prevalence has been estimated to be about 1 in 10 million.13 symptoms evocative of CGL, differential diagnoses can be considered (please see section 3.1). 1.9 Diagnostic setting 2.4 Clinical specificity Yes No (proportion of negative tests if the disease is present) fi A. (Differential) diagnostics ⊠ □ The clinical speci city can be dependent on variable factors such as B. Predictive testing □ ⊠ age or family history. In such cases a general statement should be C. Risk assessment in relatives ⊠ □ given, even if a quantification can only be made case by case. D. Prenatal ⊠ □ Close to 100%. A precise quantification is difficult, since molecular testing of CGL genes is not performed on a routine basis in asymptomatic individuals. Comment: CGL is characterized by a loss of nearly all the body fat with 2.5 Positive clinical predictive value extreme muscularity. Manifestations appear at birth or during early (life time risk to develop the disease if the test is positive) infancy and are associated with metabolic complications (insulin The positive clinical predictive value is 100%. Incomplete pene- resistance with acanthosis nigricans and alterations of glucose home- trance is extremely rare in autosomal recessive disorders and has not ostasis, hypertriglyceridaemia and hepatic steatosis). been reported in CGL. As mentioned previously, disease onset is at birth or during early childhood. 2. TEST CHARACTERISTICS 2.6 Negative clinical predictive value (probability of not developing the disease if the test is negative) Genotype or disease A: True positives C: False negative Assume an increased risk based on family history for a non-affected B: False positives D: True negative person. Allelic and locus heterogeneity may need to be considered. Present Absent Index case in that family had been tested: The negative clinical predictive value is nearly 100%, although a Test negative test does