SMPD1 mutation update: Database and comprehensive analysis of published and novel variants

Human Mutation

Volumn 37, Issue 2, 2016, Pages 139-147

  Zampieri, Stefania ^a   Filocamo, Mirella ^b   Pianta, Annalisa ^a   Lualdi, Susanna ^b   Gort, Laura ^c   Coll, Maria Jose ^c   Sinnott, Richard ^d   Geberhiwot, Tarekegn ^e   Bembi, Bruno ^a   Dardis, Andrea ^a  

^a SANTA MARIA DELLA MISERICORDIA UNIVERSITY HOSPITAL   (Italy)

^b G GASLINI INSTITUTE   (Italy)

^c INSTITUT D INVESTIGACIONS BIOMÈDIQUES AUGUST PI I SUNYER IDIBAPS   (Spain)

^d UNIVERSITY OF MELBOURNE   (Australia)

^e UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

Acid sphingomyelinase; Lysosomal storage disorder; Niemann pick; SMPD1

Indexed keywords

MESSENGER RNA; SPHINGOMYELIN PHOSPHODIESTERASE; SPHINGOMYELIN PHOSPHODIESTERASE 1, HUMAN;

ARTICLE; DNA POLYMORPHISM; ENZYME ACTIVITY; FRAMESHIFT MUTATION; GENE; GENE DELETION; GENE MUTATION; GENE NOMENCLATURE; GENETIC COUNSELING; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; HUMAN; INTRON; MISSENSE MUTATION; NIEMANN PICK DISEASE; NONHUMAN; PARKINSON DISEASE; PRIORITY JOURNAL; PROTEIN FUNCTION; RNA SPLICING; SMPD1 GENE; EXON; GENE EXPRESSION; GENETIC ASSOCIATION STUDY; GENETIC DATABASE; GENETICS; GENOTYPE; MUTATION; NIEMANN-PICK DISEASE, TYPE A; NIEMANN-PICK DISEASE, TYPE B; OPEN READING FRAME; PATHOLOGY; PHENOTYPE; RECESSIVE GENE;

DATABASES, GENETIC; EXONS; GENE EXPRESSION; GENES, RECESSIVE; GENETIC ASSOCIATION STUDIES; GENOTYPE; HUMANS; INTRONS; MUTATION; NIEMANN-PICK DISEASE, TYPE A; NIEMANN-PICK DISEASE, TYPE B; OPEN READING FRAMES; PHENOTYPE; RNA SPLICING; RNA, MESSENGER; SPHINGOMYELIN PHOSPHODIESTERASE;

EID: 84949844559     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22923     Document Type: Article

References (78)

1. Acuna M, Martinez P, Moraga C, He X, Moraga M, Hunter B, Nuernberg P, Gutierrez RA, Gonzalez M, Schuchman EH, Luis Santos J, Miguel JF, et al. 2015. Epidemiological, clinical and biochemical characterization of the p. (Ala359Asp) SMPD1 variant causing Niemann-Pick disease type B. Eur J Hum Genet Apr 29. doi: 10.1038/ejhg.2015.89.
2. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. 2010. A method and server for predicting damaging missense mutations. Nat Methods 7:248-249.
3. Aneja A, Sharma A, Dalal A, Sondhi V. 2012. R542X mutation in SMPD1 gene: genetically novel mutation with phenotypic features intermediate between type A and type B Niemann-Pick disease. BMJ Case Rep 27. doi: 10.1136/bcr-2012-006959.
4. Aykut A, Karaca E, Onay H, Ucar SK, Coker M, Cogulu O, Ozkinay F. 2013. Analysis of the sphingomyelin phosphodiesterase 1 gene (SMPD1) in Turkish Niemann- Pick disease patients: mutation profile and description of a novel mutation. Gene 526:484-486.
5. Cho YU, Chae JD, Lee WM, Woo JJ, Lee HB, Gong SJ, Park CJ, Kim GH, Yoo HW. 2009. A case of a Korean adult affected by type B Niemann-Pick disease: secondary seablue histiocytosis and molecular characterization. Korean J Lab Med 29:97-103
6. da Veiga Pereira L, Desnick RJ, Adler DA, Disteche CM, Schuchman EH. 1991. Regional assignment of the human acid sphingomyelinase gene (SMPD1) by PCR analysis of somatic cell hybrids and in situ hybridization to 11p15.1-p15.4. Genomics 9:229-234.
7. Dardis A, Zampieri S, Filocamo M, Burlina A, Bembi B, Pittis MG. 2005. Functional in vitro characterization of 14 SMPD1 mutations identified in Italian patients affected by Niemann Pick Type B disease. Hum Mutat 26:164.
8. den Dunnen JT, Antonarakis SE. 2000.Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat 15:7-12.
9. den Dunnen JT, Antonarakis SE. 2001. Nomenclature for the description of human sequence variations. Hum Genet 109:121-124.
10. Desnick JP, Kim J, He X, Wasserstein MP, Simonaro CM, Schuchman EH. 2010. Identification and characterization of eight novel SMPD1mutations causing types A and B Niemann-Pick disease. Mol Med 16:316-321.
11. Ferlinz K, Hurwitz R, Sandhoff K. 1991. Molecular basis of acid sphingomyelinase deficiency in a patient with Niemann-Pick disease type A. Biochem Biophys Res Commun 179:1187-1191.
12. Ferlinz K, Hurwitz R, Vielhaber G, Suzuki K, Sandhoff K. 1994. Occurrence of two molecular forms of human acid sphingomyelinase. Biochem J 301:855-862.
13. Ferlinz K, Hurwitz R, Weiler M, Suzuki K, Sandhoff K, Vanier MT. 1995. Molecular analysis of the acid sphingomyelinase deficiency in a family with an intermediate form of Niemann-Pick disease. Am J Hum Genet 56:1343-1349.
14. Ferlinz K, Hurwitz R, Moczall H, Lansmann S, Schuchman EH, Sandhoff K. 1997. Functional characterization of the N-glycosylation sites of human acid sphingomyelinase by site-directed mutagenesis. Eur J Biochem 243:511-511.
15. Fernández-Burriel M, Peña L, Ramos JC, Cabrera JC, Marti M, Rodríguez-Quiñones F, Chabás A. 2003. The R608del mutation in the acid sphingomyelinase gene (SMPD1) is the most prevalent among patients from Gran Canaria Island with Niemann-Pick disease type B. Clin Genet 63:235-236.
16. Foo JN, Liany H, Bei JX, Yu XQ, Liu J, Au WL, Prakash KM, Tan LC, Tan EK. 2013. Rare lysosomal enzyme gene SMPD1 variant (p.R591C) associates with Parkinson’s disease. Neurobiol Aging 34: 2890.
17. Galehdari H, Tangestani R, Ghasemian S. 2013. New single nucleotide deletion in the SMPD1 gene causes niemann pick disease type A in a child from Southwest Iran: a case report. Iran J Pediatr 23:233-236.
18. Gan-Or Z, Ozelius LJ, Bar-Shira A, Saunders-Pullman R, Mirelman A, Kornreich R, Gana-Weisz M, Raymond D, Rozenkrantz L, Deik A, Gurevich T, Gross SJ, et al. 2013. The p.L302Pmutation in the lysosomal enzyme gene SMPD1 is a risk factor for Parkinson disease. Neurology 80:1606-1610.
19. Gluck I, Zeigler M, Bargal R, Schiff E, Bach G. 1998. Niemann Pick Disease type A in Israeli Arabs: 677delT, a common novel single mutation. Mutat Brief 12:136.
20. Grasko Y, Hooper AJ, Burnett JR, Watts GF. 2014. A novel missense SMPD1 gene mutation, T460P, and clinical findings in a patient with Niemann-Pick disease type B presenting to a lipid disorders clinic. Ann Clin Biochem 51:615-618.
21. Gucev Z, Tasic V, Pop-Jordanova N, Jancevska A, Simonaro CM, Schuchmann EH. 2013. Two siblings with Niemann-Pick disease (NPD) type B: clinical findings and novel mutations of the acid sphingomyelinase gene. Indian J Pediatr 80:163-164.
22. He X, Miranda SR, Xiong X, Dagan A, Gatt S, Schuchman EH. 1999. Characterization of human acid sphingomyelinase purified fromthe media of over expressing Chinese hamster ovary cells. Biochim Biophys Acta 1432:251-264.
23. Hollak CE, de Sonnaville ES, Cassiman D, Linthorst GE, Groener JE, Morava E, Wevers RA, Mannens M, Aerts JM, Meersseman W, Akkerman E, Niezen-Koning KE, et al. 2012. Acid sphingomyelinase (Asm) deficiency patients in The Netherlands and Belgium: disease spectrum and natural course in attenuated patients. Mol Genet Metab 107:526-533.
24. Horinouchi K, Erlich S, Perl DP, Ferlinz K, Bisgaier CL, Sandhoff K, Desnick RJ, Stewart CL, Schuchman EH. 1995. Acid sphingomyelinase deficient mice: a model of types A and B Niemann-Pick disease. Nat Genet 10:288-293.
25. Hua R, Wu H, Cui Z, Chen JX, Wang Z. 2012. A novel SMPD1mutation in two Chinese sibling patients with type B Niemann-Pick disease. Chin Med J 125:1511-1512.
26. Ida H, Rennert OM, Eto Y, Chan WY. 1993. Cloning of a human acid sphingomyelinase cDNAwith a newmutation that renders the enzymeinactive. J Biochem 114:15-20.
27. Ida H, Rennert OM, Maekawa K, Eto Y. 1996. Identification of three novelmutations in the acid sphinogomyelinase gene of Japanese patients with Niemann-Pick disease type A and B. Hum Mutat 7:65-67.
28. Irun P, Mallén M, Dominguez C, Rodriguez-Sureda V, Alvarez-Sala LA, Arslan N, Bermejo N, Guerrero C, Perez de Soto I, Villalón L, Giraldo P, Pocovi M. 2013. Identification of seven novel SMPD1 mutations causing Niemann-Pick disease types A and B. Clin Genet 84:356-361.
29. Jenkins RW, Idkowiak-Baldys J, Simbari F, Canals D, Roddy P, Riner CD, Clarke CJ, Hannun YA. 2011. A novel mechanism of lysosomal acid sphingomyelinase maturation: requirement for carboxyl-terminal proteolytic processing. J Biol Chem 286:3777-3788.
30. Jones I, He X, Katouzian F, Darroch PI, Schuchman EH. 2008. Characterization of common SMPD1 mutations causing types A and B Niemann-Pick disease and generation of mutation-specific mouse models. Mol Genet Metab 95:152-162.
31. Kumar P, Henikoff S, Ng PC. 2009. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4:1073-1081.
32. Lan MY, Lin SJ, Chen YF, Peng CH, Liu YF. 2009. A novel missense mutation of the SMPD1 gene in a Taiwanese patient with type B Niemann-Pick disease. Ann Hematol 88:695-697.
33. Lansmann S, Schuette CG, Bartelsen O, Hoernschemeyer J, Linke T, Weisgerber J, Sandhoff K. 2003. Human acid sphingomyelinase. Eur J Biochem 270:1076-1088.
34. Lee CY, Tamura T, Rabah N, Lee DY, Ruel I, Hafiane A, Iatan I, Nyholt D, Laporte F, Lazure C, Wada I, Krimbou L, Genest J. 2007. Carboxyl-terminal disulfide bond of acid sphingomyelinase is critical for its secretion and enzymatic function. Biochemistry 46:14969-14978.
35. Levran O, Desnick RJ, Schuchman EH. 1991a. Niemann-Pick disease: a frequent missensemutation in the acid sphingomyelinase gene of Ashkenazi Jewish type A and B patients. Proc Natl Acad Sci USA 88:3748-3752.
36. Levran O, Desnick RJ, Schuchman EH. 1991b. Niemann-Pick type B disease. Identification of a single codon deletion in the acid sphingomyelinase gene and genotype/ phenotype correlations in type A and B patients. J Clin Invest 88:806-810.
37. Levran O, Desnick RJ, Schuchman EH. 1992. Identification and expression of a common missensemutation (L302P) in the acid sphingomyelinase gene ofAshkenazi Jewish type A Niemann-Pick disease patients. Blood 80:2081-2087.
38. Levran O, Desnick RJ, Schuchman EH. 1993a. Identification of a 3’ acceptor splice site mutation (g2610c) in the acid sphingomyelinase gene of patients with Niemann- Pick disease. Hum Mol Genet- 2:205-206.
39. Levran O, Desnick RJ, Schuchman EH. 1993b. Type A Niemann-Pick disease: a frameshift mutation in the acid sphingomyelinase gene (fsP330) occurs in Ashkenazi Jewish patients. Hum Mutat 2:317-319.
40. Lidove O, Sedel F, Charlotte F, Froissart R, Vanier MT. 2015. Cirrhosis and liver failure: expanding phenotype of Acid sphingomyelinase-deficient niemann-pick disease in adulthood. JIMD Rep 15:117-121.
41. Manshadi MD, Kamalidehghan B, Keshavarzi F, Aryani O, Dadgar S, Arastehkani A, Tondar M, Ahmadipour F, Meng GY, Houshmand M. 2015. Four novel p.N385K, p.V36A, c.1033-1034insT and c.1417-1418delCT mutations in the sphingomyelin phosphodiesterase 1 (SMPD1) gene in patients with types A and B Niemann-Pick disease (NPD). Int J Mol Sci 16:6668-6676.
42. McGovern MM, Schuchman EH. 2006. Acid sphingomyelinase deficiency. In: Pagon RA, Adam MP, Ardinger HH, Wallace SE, Amemiya A, Bean LJH, Bird TD, Dolan CR, Fong CT, Smith RJH, Stephens K, editors. Gene Reviews. Seattle (WA): University of Washington, Seattle.
43. Meersseman W, Verschueren P, Tousseyn T, De Vos R, Cassiman D. 2011. PAS-positive macrophages-not always infection. Lancet 377:1890.
44. Mihaylova V, Hantke J, Sinigerska I, Cherninkova S, Raicheva M, Bouwer S, Tincheva R, Khuyomdziev D, Bertranpetit J, Chandler D, Angelicheva D, Kremensky I, et al. 2007. Highly variable neural involvement in sphingomyelinase-deficient Niemann-Pick disease caused by an ancestral Gypsy mutation. Brain 130:1050-1061.
45. Miranda SR, Erlich S, Friedrich VL Jr, Haskins ME, Gatt S, Schuchman EH. 1998. Biochemical, pathological, and clinical response to transplantation of normal bone marrow cells into acid sphingomyelinase-deficient mice. Transplantation 65:884-892.
46. Miranda SR, Erlich S, Friedrich VL Jr., Gatt S, Schuchman EH. 2000. Hematopoietic stem cell gene therapy leads to marked visceral organ improvements and a delayed onset of neurological abnormalities in the acid sphingomyelinase deficient mouse model of Niemann-Pick disease. Gene Ther 7:1768-1776.
47. Mukherjee SB, Pandey M, Kapoor S, Priya TP. 2012. Infant with type A Niemann Pick disease and undetectable Niemann Pick cells in bone marrow. Indian Pediatr 49:490-492.
48. Müssig K, Harzer K, Mayrhofer H, Krägeloh-Mann I, Häring HU, Machicao F. 2006. Clinical findings in Niemann-Pick disease type B. Intern Med J 36:135-136.
49. Passini MA, Macauley SL, Huff MR, Taksir TV, Bu J, Wu IH, Piepenhagen PA, Dodge JC, Shihabuddin LS, O’Riordan CR, Schuchman EH, Stewart GR. 2005. AAV vectormediated correction of brain pathology in a mouse model of Niemann-Pick A disease. Mol Ther 11:754-762.
50. Pavlů H, Elleder M. 1997. Two novel mutations in patients with atypical phenotypes of acid sphingomyelinase deficiency. J Inherit Metab Dis 20:615-616.
51. Pavlů-Pereira H, Asfaw B, Poupctová H, Ledvinová J, Sikora J, Vanier MT, Sandhoff K, Zeman J, Novotná Z, Chudoba D, Elleder M. 2005. Acid sphingomyelinase deficiency. Phenotype variability with prevalence of intermediate phenotype in a series of twenty-five Czech and Slovak patients. A multi-approach study. J Inherit Metab Dis 28:203-227.
52. Pittis MG, Ricci V, Guerci VI, Marçais C, Ciana G, Dardis A, Gerin F, Stroppiano M, Vanier MT, Filocamo M, Bembi B. 2004. Acid sphingomyelinase: identification of nine novel mutations among Italian Niemann Pick type B patients and characterization of in vivo functional in-frame start codon. Hum Mutat 24:186-187.
53. Ponting CP. 1994. Acid sphingomyelinase possesses a domain homologous to its activator proteins: saposins B and D. Protein Sci 3:359-361.
54. Qiu H, Edmunds T, Baker-Malcolm J, Karey KP, Estes S, Schwarz C, Hughes H, Van Patten SM. 2003. Activation of human acid sphingomyelinase through modification or deletion of C-terminal cysteine. J Biol Chem 278:32744-32752.
55. Quintern LE, Schuchman EH, Levran O, Suchi M, Ferlinz K, Reinke H, Sandhoff K, Desnick RJ. 1989. Isolation of cDNA clones encoding human acid sphingomyelinase: occurrence of alternatively processed transcripts. EMBO J 8:2469-2473.
56. Rhein C, Naumann J, Mühle C, Zill P, Adli M, Hegerl U, Hiemke C, Mergl R, Möller HJ, Reichel M, Kornhuber J. 2013. The Acid Sphingomyelinase Sequence Variant p.A487V Is Not Associated With Decreased Levels of Enzymatic Activity. JIMD Rep 8:1-6.
57. Ricci V, Stroppiano M, Corsolini F, Di Rocco M, Parenti G, Regis S, Grossi S, Biancheri R, Mazzotti R, Filocamo M. 2004. Screening of 25 Italian patients with Niemann- Pick A reveals fourteen new mutations, one common and thirteen private, in SMPD1. Hum Mutat 24:105.
58. Rodríguez-Pascau L, Gort L, Schuchman EH, Vilageliu L, Grinberg D, Chabás A. 2009. Identification and characterization of SMPD1 mutations causing Niemann-Pick types A and B in Spanish patients. Hum Mutat 30:1117-1122.
59. Schuchman EH, Desnick RJ. 2001. Niemann Pick Disease type A and B: acid sphingomylinases deficiencies. In: Scriver CR, Beaudet AL, Sly WS, Valle D, editors. The metabolic and molecular basis of inherited disease. New York: McGraw-Hill. p 3589-3610.
60. Schuchman EH, Wasserstein MP. 2015. Types A and B Niemann-Pick disease. Best Pract Res Clin Endocrinol Metab 29:237-247
61. Schuchman EH, Levran O, Pereira LV, Desnick RJ. 1992. Structural organization and complete nucleotide sequence of the gene encoding human acid sphingomyelinase (SMPD1). Genomics 12:197-205.
62. Schuchman EH, Miranda SR. 1997. Niemann-Pick disease: mutation update, genotype/phenotype correlations, and prospects for genetic testing. Genet Test 1:13-19.
63. Schuchman EH, Suchi M, Takahashi T, Sandhoff K, Desnick RJ. 1991. Human acid sphingomyelinase. Isolation, nucleotide sequence and expression of the full-length and alternatively spliced cDNAs. J Biol Chem 266:8531-8539.
64. Schuchman EH. 1995. Two new mutations in the acid sphingomyelinase gene causing type a Niemann-pick disease: N389T and R441X. Hum Mutat 6:352-354.
65. Schwartz S, Hall E, Ast G. 2009. SROOGLE: web server for integrative, user-friendly visualization of splicing signals. Nucleic Acids Res 37:W189-92.
66. Seto M, Whitlow M, McCarrick MA, Srinivasan S, Zhu Y, Pagila R, Mintzer R, Light D, Johns A, Meurer-Ogden JA. 2004. A model of the acid sphingomyelinase phosphoesterase domain based on its remote structural homolog purple acid phosphatase. Protein Sci 13:3172-3186.
67. Sikora J, Pavlu-Pereira H, Elleder M, Roelofs H, Wevers RA. 2003. Seven novel acid sphingomyelinase gene mutations in Niemann-Pick type A and B patients. Ann Hum Genet 67:63-70.
68. Simonaro CM, Desnick RJ, McGovern MM, Wasserstein MP, Schuchman EH. 2002. The demographics and distribution of type B Niemann-Pick disease: novel mutations lead to new genotype/phenotype correlations. Am J Hum Genet 71:1413-1419.
69. Shah AJ, Kapoor N, Crooks GM, Parkman R, Weinberg KI, Wilson K, Kohn DB. 2005. Successful hematopoietic stemcell transplantation for Niemann-Pick disease type B. Pediatrics 116:1022-1025.
70. Takahashi T, Desnick RJ, Takada G, Schuchman EH. 1992. Identification of a missense mutation (S436R) in the acid sphingomyelinase gene from a Japanese patient with type B Niemann-Pick disease. Hum Mutat 1:70-71.
71. Takahashi T, Suchi M, Desnick RJ, Takada G, Schuchman EH. 1992. Identification and expression of five mutations in the human acid sphingomyelinase gene causing types A and B Niemann-Pick disease. Molecular evidence for genetic heterogeneity in the neuronopathic and non-neuronopathic forms. J Biol Chem 267:12552-12558.
72. Takahashi T, Suchi M, Sato W, Ten SB, Sakuragawa N, Desnick RJ, Schuchman EH, Takada G. 1995. Identification and expression of a missense mutation (Y446C) in the acid sphingomyelinase gene froma Japanese patient with type A Niemann-Pick disease. Tohoku J Exp Med 177:117-123.
73. Toth B, Erdøs M, Székely A, Ritli L, Bagossi P, Sümegi J, Maródi L. 2012. Molecular genetic characterization of novel sphingomyelin phosphodiesterase 1 mutations causing niemann-pick disease. JIMD Rep 3:125-129.
74. van Diggelen OP, Voznyi YV, Keulemans JL, Schoonderwoerd K, Ledvinova J, Mengel E, Zschiesche M, Santer R, Harzer K. 2005. A new fluorimetric enzyme assay for the diagnosis of Niemann-Pick A/B, with specificity of natural sphingomyelinase substrate. J Inherit Metab Dis 28:733-741.
75. Victor S, Coulter JB, Besley GT, Ellis I, Desnick RJ, Schuchman EH, Vellodi A. 2003. Niemann-Pick disease: sixteen-year follow-up of allogeneic bone marrow transplantation in a type B variant. J Inherit Metab Dis 26:775-785.
76. Vanier MT, Ferlinz K, Rousson R, Duthel S, Louisot P, Sandhoff K, Suzuki K. 1993. Deletion of arginine (608) in acid sphingomyelinase is the prevalent mutation among Niemann-Pick disease type B patients from northern Africa. Hum Genet 92:325-330.
77. Wan Q, Schuchman EH. 1995. A novel polymorphism in the human acid sphingomyelinase gene due to size variation of the signal peptide region. Biochim Biophys Acta 1270:207-210.
78. Zhang H, Wang Y, Gong Z, Li X, Qiu W, Han L, Ye J, Gu X. 2013. Identification of a distinct mutation spectrum in the SMPD1 gene of Chinese patients with acid sphingomyelinase-deficient Niemann-Pick disease. Orphanet J Rare Dis 8:15.