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Orphanet Journal of Rare Diseases
Published in: Orphanet Journal of Rare Diseases 1/2018

Open Access 01-12-2018 | Research

Improving the diagnosis of cobalamin and related defects by genomic analysis, plus functional and structural assessment of novel variants

Authors: Sandra Brasil, Fátima Leal, Ana Vega, Rosa Navarrete, María Jesús Ecay, Lourdes R. Desviat, Casandra Riera, Natàlia Padilla, Xavier de la Cruz, Mari Luz Couce, Elena Martin-Hernández, Ana Morais, Consuelo Pedrón, Luis Peña-Quintana, Miriam Rigoldi, Norma Specola, Isabel Tavares de Almeida, Inmaculada Vives, Raquel Yahyaoui, Pilar Rodríguez-Pombo, Magdalena Ugarte, Celia Pérez-Cerda, Begoña Merinero, Belén Pérez

Published in: Orphanet Journal of Rare Diseases | Issue 1/2018

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Abstract

Background

Cellular cobalamin defects are a locus and allelic heterogeneous disorder. The gold standard for coming to genetic diagnoses of cobalamin defects has for some time been gene-by-gene Sanger sequencing of individual DNA fragments. Enzymatic and cellular methods are employed before such sequencing to help in the selection of the gene defects to be sought, but this is time-consuming and laborious. Furthermore some cases remain undiagnosed because no biochemical methods have been available to test for cobalamin absorption and transport defects.

Results

This paper reports the use of massive parallel sequencing of DNA (exome analysis) for the accurate and rapid genetic diagnosis of cobalamin-related defects in a cohort of affected patients. The method was first validated in an initial cohort with different cobalamin defects. Mendelian segregation, the frequency of mutations, and the comprehensive structural and functional analysis of gene variants, identified disease-causing mutations in 12 genes involved in the absorption and synthesis of active cofactors of vitamin B12 (22 cases), and in the non-cobalamin metabolism-related genes ACSF3 (in four biochemically misdiagnosed patients) and SUCLA2 (in one patient with an unusual presentation). We have identified thirteen new variants all classified as pathogenic according to the ACGM recommendation but four were classified as variant likely pathogenic in MUT and SUCLA2. Functional and structural analysis provided evidences to classify them as pathogenic variants.

Conclusions

The present findings suggest that the technology used is sufficiently sensitive and specific, and the results it provides sufficiently reproducible, to recommend its use as a second-tier test after the biochemical detection of cobalamin disorder markers in the first days of life. However, for accurate diagnoses to be made, biochemical and functional tests that allow comprehensive clinical phenotyping are also needed.
Appendix
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Literature
1.
Baumgartner MR, Fowler B. Vitamin B12 Disorders. In: Nenad Blau MD, Michael Gibson K, Dionisi-Vici C, editors. Physicians’s guide to the diagnosis, treatment and follow-up of inherited metabolic diseases; 2014. p. 205–17.
2.
Banerjee R. B12 trafficking in mammals: a for coenzyme escort service. ACS Chem Biol. 2006;1:149–59.CrossRefPubMed
3.
Carmel R, Parker J, Kelman Z. Genomic mutations associated with mild and severe deficiencies of transcobalamin I (haptocorrin) that cause mildly and severely low serum cobalamin levels. Br J Haematol. 2009;147:386–91.CrossRefPubMed
4.
Carmel R, Green R, Rosenblatt DS, Watkins D. Update on cobalamin, folate, and homocysteine. Hematology Am Soc Hematol Educ Program. 2003;62–81.
5.
Banerjee R, Gherasim C, Padovani D. The tinker, tailor, soldier in intracellular B12 trafficking. Curr Opin Chem Biol. 2009;13:477–84.CrossRef
6.
Watkins D, Rosenblatt DS. Update and new concepts in vitamin responsive disorders of folate transport and metabolism. J Inherit Metab Dis. 2012;35:665–70.CrossRefPubMed
7.
Quadros EV, Lai SC, Nakayama Y, Sequeira JM, Hannibal L, et al. Positive newborn screen for methylmalonic aciduria identifies the first mutation in TCblR/CD320, the gene for cellular uptake of transcobalamin-bound vitamin B(12). Hum Mutat. 2010;31:924–9.CrossRefPubMedPubMedCentral
8.
Rutsch F, Gailus S, Suormala T, Fowler B. LMBRD1: the gene for the cblF defect of vitamin B(1)(2) metabolism. J Inherit Metab Dis. 2011;34:121–6.CrossRefPubMed
9.
Coelho D, Kim JC, Miousse IR, Fung S, du Moulin M, et al. Mutations in ABCD4 cause a new inborn error of vitamin B12 metabolism. Nat Genet. 2012;44:1152–5.CrossRefPubMed
10.
Lerner-Ellis JP, Tirone JC, Pawelek PD, Dore C, Atkinson JL, et al. Identification of the gene responsible for methylmalonic aciduria and homocystinuria, cblC type. Nat Genet. 2006;38:93–100.CrossRefPubMed
11.
Yu HC, Sloan JL, Scharer G, Brebner A, Quintana AM, et al. An X-linked cobalamin disorder caused by mutations in transcriptional coregulator HCFC1. Am J Hum Genet. 2013;93:506–14.CrossRefPubMedPubMedCentral
12.
Pupavac M, Watkins D, Petrella F, Fahiminiya S, Janer A, et al. (2016) Inborn error of Cobalamin metabolism associated with the intracellular accumulation of Transcobalamin-bound Cobalamin and mutations in ZNF143, which codes for a transcriptional activator. Hum Mutat. 2016;37(9):976–82.
13.
Quintana AM, Yu HC, Brebner A, Pupavac M, Geiger EA, et al. Mutations in THAP11 cause an inborn error of cobalamin metabolism and developmental abnormalities. Hum Mol Genet. 2017;26:2838–49.CrossRefPubMedPubMedCentral
14.
Gueant JL, Chery C, Oussalah A, Nadaf J, Coelho D, et al. A PRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients. Nat Commun. 2018;9:67.CrossRefPubMedPubMedCentral
15.
Stucki M, Coelho D, Suormala T, Burda P, Fowler B, et al. Molecular mechanisms leading to three different phenotypes in the cblD defect of intracellular cobalamin metabolism. Hum Mol Genet. 2012;21:1410–8.CrossRefPubMed
16.
Dobson CM, Wai T, Leclerc D, Kadir H, Narang M, et al. Identification of the gene responsible for the cblB complementation group of vitamin B12-dependent methylmalonic aciduria. Hum Mol Genet. 2002;11:3361–9.CrossRefPubMed
17.
Froese DS, Kochan G, Muniz JR, Wu X, Gileadi C, et al. Structures of the human GTPase MMAA and vitamin B12-dependent methylmalonyl-CoA mutase and insight into their complex formation. J Biol Chem. 2010;285:38204–13.CrossRefPubMedPubMedCentral
18.
Maas RR, Marina AD, de Brouwer AP, Wevers RA, Rodenburg RJ, et al. SUCLA2 deficiency: a deafness-dystonia syndrome with distinctive metabolic findings (report of a new patient and review of the literature). JIMD Rep. 2016;27:27–32.CrossRefPubMed
19.
Pupavac M, Tian X, Chu J, Wang G, Feng Y, et al. Added value of next generation gene panel analysis for patients with elevated methylmalonic acid and no clinical diagnosis following functional studies of vitamin B12 metabolism. Mol Genet Metab. 2016;117:363–8.CrossRefPubMed
20.
Sloan JL, Johnston JJ, Manoli I, Chandler RJ, Krause C, et al. Exome sequencing identifies ACSF3 as a cause of combined malonic and methylmalonic aciduria. Nat Genet. 2011;43:883–6.CrossRefPubMedPubMedCentral
21.
Fowler B, Leonard JV, Baumgartner MR. Causes of and diagnostic approach to methylmalonic acidurias. J Inherit Metab Dis. 2008;31:350–60.CrossRefPubMed
22.
Malvagia S, Haynes CA, Grisotto L, Ombrone D, Funghini S, et al. Heptadecanoylcarnitine (C17) a novel candidate biomarker for newborn screening of propionic and methylmalonic acidemias. Clin Chim Acta. 2015;450:342–8.CrossRefPubMedPubMedCentral
23.
Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, et al. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet. 2010;42:30–5.CrossRefPubMed
24.
Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011;12:745–55.CrossRefPubMed
25.
Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, et al. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med. 2013;369:1502–11.CrossRefPubMedPubMedCentral
26.
Vega AI, Medrano C, Navarrete R, Desviat LR, Merinero B, et al. Molecular diagnosis of glycogen storage disease and disorders with overlapping clinical symptoms by massive parallel sequencing. Genet Med. 2016;18:1037–43.CrossRefPubMed
27.
Richards S, Aziz N, Bale S, Bick D, Das S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405–24.CrossRefPubMedPubMedCentral
28.
Kleinberger J, Maloney KA, Pollin TI, Jeng LJ. An openly available online tool for implementing the ACMG/AMP standards and guidelines for the interpretation of sequence variants. Genet Med. 2016;18:1165.CrossRefPubMedPubMedCentral
29.
Forny P, Schnellmann AS, Buerer C, Lutz S, Fowler B, et al. Molecular genetic characterization of 151 Mut-type Methylmalonic Aciduria patients and identification of 41 novel mutations in MUT. Hum Mutat. 2016;37:745–54.CrossRefPubMed
30.
Perez B, Rincon A, Jorge-Finnigan A, Richard E, Merinero B, et al. Pseudoexon exclusion by antisense therapy in methylmalonic aciduria (MMAuria). Hum Mutat. 2009;30:1676–82.CrossRefPubMed
31.
Brasil S, Richard E, Jorge-Finnigan A, Leal F, Merinero B, et al. Methylmalonic aciduria cblB type: characterization of two novel mutations and mitochondrial dysfunction studies. Clin Genet. 2015;87:576–81.CrossRefPubMed
32.
Fraser ME, Hayakawa K, Hume MS, Ryan DG, Brownie ER. Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase. J Biol Chem. 2006;281:11058–65.CrossRefPubMed
33.
Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, et al. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 2014;42:W252–8.CrossRefPubMedPubMedCentral
34.
Tanner SM, Sturm AC, Baack EC, Liyanarachchi S, de la Chapelle A. Inherited cobalamin malabsorption. Mutations in three genes reveal functional and ethnic patterns. Orphanet J Rare Dis. 2012;7:56.CrossRefPubMedPubMedCentral
35.
Xue Y, Ankala A, Wilcox WR, Hegde MR. Solving the molecular diagnostic testing conundrum for Mendelian disorders in the era of next-generation sequencing: single-gene, gene panel, or exome/genome sequencing. Genet Med. 2015;17:444–51.CrossRefPubMed
36.
Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, et al. ACMG clinical laboratory standards for next-generation sequencing. Genet Med. 2013;15:733–47.CrossRefPubMedPubMedCentral
37.
Rincon A, Aguado C, Desviat LR, Sanchez-Alcudia R, Ugarte M, et al. Propionic and Methylmalonic Acidemia: antisense therapeutics for Intronic variations causing aberrantly spliced messenger RNA. Am J Hum Genet. 2007;81:1262–70.CrossRefPubMedPubMedCentral
38.
Carrozzo R, Verrigni D, Rasmussen M, de Coo R, Amartino H, et al. Succinate-CoA ligase deficiency due to mutations in SUCLA2 and SUCLG1: phenotype and genotype correlations in 71 patients. J Inherit Metab Dis. 2016;39:243–52.CrossRefPubMed
39.
de Sain-van der Velden MG, van der Ham M, Jans JJ, Visser G, Prinsen HC, et al. A new approach for fast metabolic diagnostics in CMAMMA. JIMD Rep. 2016;30:15–22.CrossRefPubMedPubMedCentral
40.
Chu J, Pupavac M, Watkins D, Tian X, Feng Y, et al. Next generation sequencing of patients with Mut methylmalonic aciduria: validation of somatic cell studies and identification of 16 novel mutations. Mol Genet Metab. 2016;118:264–71.CrossRefPubMed
41.
Pedersen CB, Kolvraa S, Kolvraa A, Stenbroen V, Kjeldsen M, et al. The ACADS gene variation spectrum in 114 patients with short-chain acyl-CoA dehydrogenase (SCAD) deficiency is dominated by missense variations leading to protein misfolding at the cellular level. Hum Genet. 2008;124:43–56.CrossRefPubMed
42.
Lam C, Carter JM, Cederbaum SD, Neidich J, Gallant NM, et al. Analysis of cases of 3-methylcrotonyl CoA carboxylase deficiency (3-MCCD) in the California newborn screening program reported in the state database. Mol Genet Metab. 2013;110:477–83.CrossRefPubMed
43.
Alfares A, Nunez LD, Al-Thihli K, Mitchell J, Melancon S, et al. Combined malonic and methylmalonic aciduria: exome sequencing reveals mutations in the ACSF3 gene in patients with a non-classic phenotype. J Med Genet. 2011;48:602–5.CrossRefPubMed
44.
Matilainen S, Isohanni P, Euro L, Lonnqvist T, Pihko H, et al. Mitochondrial encephalomyopathy and retinoblastoma explained by compound heterozygosity of SUCLA2 point mutation and 13q14 deletion. Eur J Hum Genet. 2015;23:325–30.CrossRefPubMed
Metadata
Title
Improving the diagnosis of cobalamin and related defects by genomic analysis, plus functional and structural assessment of novel variants
Authors
Sandra Brasil
Fátima Leal
Ana Vega
Rosa Navarrete
María Jesús Ecay
Lourdes R. Desviat
Casandra Riera
Natàlia Padilla
Xavier de la Cruz
Mari Luz Couce
Elena Martin-Hernández
Ana Morais
Consuelo Pedrón
Luis Peña-Quintana
Miriam Rigoldi
Norma Specola
Isabel Tavares de Almeida
Inmaculada Vives
Raquel Yahyaoui
Pilar Rodríguez-Pombo
Magdalena Ugarte
Celia Pérez-Cerda
Begoña Merinero
Belén Pérez
Publication date
01-12-2018
Publisher
BioMed Central
Published in
Orphanet Journal of Rare Diseases / Issue 1/2018
Electronic ISSN: 1750-1172
DOI
https://doi.org/10.1186/s13023-018-0862-y

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