In silico structural, functional and pathogenicity evaluation of a novel mutation: An overview of HSD3B2 gene mutations

Gene

Volumn 503, Issue 2, 2012, Pages 215-221

  Rabbani, Bahareh ^a,b   Mahdieh, Nejat ^b,c,d   Haghi Ashtiani, Mohammad Taghi ^b   Setoodeh, Aria ^b   Rabbani, Ali ^a,b  

^a TEHRAN UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^b TEHRAN UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^c ILAM UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^d NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

Endocrine disorder; HSD3B2 gene; Mutation

Indexed keywords

3(OR 17)BETA HYDROXYSTEROID DEHYDROGENASE; 3(OR 17)BETA HYDROXYSTEROID DEHYDROGENASE TYPE II; ALANINE; ANDROSTENEDIONE; CORTICOTROPIN; FLUDROCORTISONE; HYDROCORTISONE; HYDROXYPROGESTERONE; POTASSIUM; PRASTERONE; PROLINE; SODIUM; STEROID; TESTOSTERONE; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; 3(OR 17)BETA HYDROXYSTEROID DEHYDROGENASE DEFICIENCY; 5' UNTRANSLATED REGION; AMBIGUOUS GENITALIA; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BIOINFORMATICS; BLOOD SAMPLING; BODY HEIGHT; BODY WEIGHT; CASE REPORT; CHORDEE; COMPUTER PROGRAM; DEHYDRATION; DNA EXTRACTION; ENZYME DEFICIENCY; EXON; FLUID THERAPY; GENE FUNCTION; GENE SEQUENCE; GENE STRUCTURE; GENERAL PRACTITIONER; GENETIC ANALYSIS; GENETIC COUNSELING; GENOTYPE; HEAD CIRCUMFERENCE; HOMOZYGOSITY; HORMONE SUBSTITUTION; HUMAN; HYPERKALEMIA; HYPERPIGMENTATION; HYPONATREMIA; HYPOSPADIAS; INFANCY; INFANT; INGUINAL HERNIA; IRAN; KARYOTYPE 46,XY; MALE; MEMBRANE BINDING; MICROPENIS; MISSENSE MUTATION; NEWBORN; PATHOGENICITY; PLASMA RENIN ACTIVITY; POLYMERASE CHAIN REACTION; POTASSIUM BLOOD LEVEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; PULSE RATE; SALT WASTING; SCROTUM DISORDER; SEGREGATION ANALYSIS; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; SODIUM BLOOD LEVEL; TACHYCARDIA;

ADRENAL HYPERPLASIA, CONGENITAL; AMINO ACID SEQUENCE; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DISORDERS OF SEX DEVELOPMENT; GENOTYPE; HUMANS; INFANT, NEWBORN; MALE; MOLECULAR SEQUENCE DATA; MUTATION, MISSENSE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROGESTERONE REDUCTASE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84861814613     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.04.080     Document Type: Article

References (53)

1. Alos N., et al. A novel A10E homozygous mutation in the HSD3B2 gene causing severe salt-wasting 3beta-hydroxysteroid dehydrogenase deficiency in 46,XX and 46,XY French-Canadians: evaluation of gonadal function after puberty. J. Clin. Endocrinol. Metab. 2000, 85(5):1968-1974.
2. Berube D., et al. The gene encoding human 3-beta hydroxysteroid dehydrogenase/isomerase mapped to the p13 band of chromosome 1. Cytogenet. Cell Genet. 1989, 51:962-963.
3. Bromberg Y., Rost B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res. 2007, 35(11):3823-3835.
4. Calabrese R., et al. Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum. Mutat. 2009, 30(8):1237-1244.
5. Capriotti E., Fariselli P., Casadio R. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res. 2005, 33. ((Web Server issue):W306-10).
6. Capriotti E., Calabrese R., Casadio R. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics 2006, 22(22):2729-2734.
7. Codner E., et al. Molecular study of the 3 beta-hydroxysteroid dehydrogenase gene type II in patients with hypospadias. J. Clin. Endocrinol. Metab. 2004, 89(2):957-964.
8. Cordes F.S., et al. Proline-induced distortions of transmembrane helices. J. Mol. Biol. 2002, 323:951-960.
9. Headon D.R., Hsiao J., Ungar F. The intracellular localization of adrenal 3beta-hydroxysteroid dehydrogenase/delta5-isomerase by density gradient perturbation. Biochem. Biophys. Res. Commun. 1978, 82(3):1006-1012.
10. Katsumata N., et al. A novel missense mutation in the type II 3 beta-hydroxysteroid dehydrogenase gene in a family with classical salt-wasting congenital adrenal hyperplasia due to 3 beta-hydroxysteroid dehydrogenase deficiency. Hum. Mol. Genet. 1995, 4(4):745-746.
11. Kelley L.A., Sternberg M.J. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 2009, 4(3):363-371.
12. Kiefer F., et al. The SWISS-MODEL Repository and associated resources. Nucleic Acids Res. 2009, 37:D387-D392.
13. Kopp J., Schwede T. The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res. 2004, 32:D230-D234.
14. Lachance Y., et al. Structure of the human type II 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4 isomerase (3 beta-HSD) gene: adrenal and gonadal specificity. DNA Cell Biol. 1991, 10(10):701-711.
15. Marui S., et al. A novel homozygous nonsense mutations E135* in the type II 3beta-hydroxysteroid dehydrogenase gene in a girl with salt-losing congenital adrenal hyperplasia. Mutations in brief no. 168. Online. Hum. Mutat. 1998, 12(2):139.
16. McCartin S., et al. Phenotypic variability and origins of mutations in the gene encoding 3beta-hydroxysteroid dehydrogenase type II. J. Mol. Endocrinol. 2000, 24(1):75-82.
17. Mébarki F., et al. Nonsalt-losing male pseudohermaphroditism due to the novel homozygous N100S mutation in the type II 3 beta-hydroxysteroid dehydrogenase gene. J. Clin. Endocrinol. Metab. 1995, 80(7):2127-2134.
18. Mendonça B.B., et al. Mutation in 3 beta-hydroxysteroid dehydrogenase type II associated with pseudohermaphroditism in males and premature pubarche or cryptic expression in females. J. Mol. Endocrinol. 1994, 12(1):119-122.
19. Miller S.A., Dykes D.D., Polesky H.F. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 1988, 16(3):1215.
20. Moisan A.M., et al. New insight into the molecular basis of 3beta-hydroxysteroid dehydrogenase deficiency: identification of eight mutations in the HSD3B2 gene eleven patients from seven new families and comparison of the functional properties of twenty-five mutant enzymes. J. Clin. Endocrinol. Metab. 1999, 84(12):4410-4425.
21. Nayak S., Lee P.A., Witchel S.F. Variants of the type II 3beta-hydroxysteroid dehydrogenase gene in children with premature pubic hair and hyperandrogenic adolescents. Mol. Genet. Metab. 1998, 64(3):184-192.
22. Ng P.C., Henikoff S. Predicting deleterious amino acid substitutions. Genome Res. 2001, 11(5):863-874.
23. Pang S. The molecular and clinical spectrum of 3beta-hydroxysteroid dehydrogenase deficiency disorder. Trends Endocrinol. Metab. 1998, 9:82-86.
24. Pang S., et al. A novel nonstop mutation in the stop codon and a novel missense mutation in the type II 3beta-hydroxysteroid dehydrogenase (3beta-HSD) gene causing, respectively, nonclassic and classic 3beta-HSD deficiency congenital adrenal hyperplasia. J. Clin. Endocrinol. Metab. 2002, 87(6):2556-2563.
25. Pawlak K.J., et al. Inner mitochondrial translocase Tim50 interacts with 3β-hydroxysteroid dehydrogenase type 2 to regulate adrenal and gonadal steroidogenesis. J. Biol. Chem. 2011, 286(45):39130-39140.
26. Penning T.M. Molecular endocrinology of hydroxysteroid dehydrogenases. Endocr. Rev. 1997, 18:281-305.
27. Rabbani B., et al. Mutation analysis of CYP21A2 gene in the Iranian population. Genet. Test. Mol. Biomarkers 2011, 16(2):82-90.
28. Rabbani B., et al. Molecular diagnosis of congenital adrenal hyperplasia in Iran: focusing on CYP21A2 gene. Iran. J. Pediatr. 2011, 21(2):139-149.
29. Ramazani A., et al. The frequency of eight common point mutations in CYP21 gene in Iranian patients with congenital adrenal hyperplasia. Iran. Biomed. J. 2008, 12(1):49-53.
30. Ramensky V., Bork P., Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 2002, 30(17):3894-3900.
31. Rheaume E., et al. Congenital adrenal hyperplasia due to point mutations in the type II 3 beta-hydroxysteroid dehydrogenase gene. Nat. Genet. 1992, 1(4):239-245.
32. Rheaume E., et al. Molecular basis of congenital adrenal hyperplasia in two siblings with classical nonsalt-losing 3-B hydroxysteroid dehydrogenase deficiency. J. Clin. Endocrinol. Metab. 1994, 79:1012-1018.
33. Rhéaume E., et al. Identification and characterization of the G15D mutation found in a male patient with 3 beta-hydroxysteroid dehydrogenase (3 beta-HSD) deficiency: alteration of the putative NAD-binding domain of type II 3 beta-HSD. Biochemistry 1995, 34(9):2893-2900.
34. Roy A., Kucukural A., Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 2010, 5(4):725-738.
35. Russell A.J., et al. Mutation in the human gene for 3 beta-hydroxysteroid dehydrogenase type II leading to male pseudohermaphroditism without salt loss. J. Mol. Endocrinol. 1994, 12(2):225-237.
36. Sanchez R., et al. Functional characterization of the novel L108W and P186L mutations detected in the type II 3 beta-hydroxysteroid dehydrogenase gene of a male pseudohermaphrodite with congenital adrenal hyperplasia. Hum. Mol. Genet. 1994, 3(9):1639-1645.
37. Scrutton N.S., Berry A., Perham R.N. Redesign of the coenzyme specificity of a dehydrogenase by protein engineering. Nature 1990, 343(6253):38-43.
38. Simard J., de Launoit Y., Labrie F. Characterization of the structure-activity relationships of rat types I and II 3 beta-hydroxysteroid dehydrogenase/delta 5 -delta 4 isomerase by site-directed mutagenesis and expression in HeLa cells. J. Biol. Chem. 1991, 266(23):14842-14845.
39. Simard J., et al. Molecular basis of congenital adrenal hyperplasia due to 3 beta-hydroxysteroid dehydrogenase deficiency. Mol. Endocrinol. 1993, 7(5):716-728.
40. Simard J., et al. Molecular biology of the 3beta-hydroxysteroid dehydrogenase/delta5-delta4 isomerase gene family. Endocr. Rev. 2005, 26(4):525-582.
41. Szklarczyk D., et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011, 39. ((Database issue):D561-8).
42. Tajima T., et al. Molecular analysis of type II 3 beta-hydroxysteroid dehydrogenase gene in Japanese patients with classical 3 beta-hydroxysteroid dehydrogenase deficiency. Hum. Mol. Genet. 1995, 4(5):969-971.
43. Thilen A., Larsson A. Congenital adrenal hyperplasia in Sweden 1969-1986. Prevalence, symptoms and age at diagnosis. Acta Paediatr. Scand. 1990, 79(2):168-175.
44. Thomas J.L., et al. Creation of a fully active, cytosolic form of human type I 3beta-hydroxysteroid dehydrogenase/isomerase by the deletion of a membrane-spanning domain. J. Mol. Endocrinol. 1999, 23(2):231-239.
45. Thomas J.L., et al. Structure/function relationships responsible for the kinetic differences between human type 1 and type 2 3beta-hydroxysteroid dehydrogenase and for the catalysis of the type 1 activity. J. Biol. Chem. 2002, 277:42795-42801.
46. Thomas J.L., et al. Structure/function relationships responsible for coenzyme specificity and the isomerase activity of human type 1 3 beta-hydroxysteroid dehydrogenase/isomerase. J. Biol. Chem. 2003, 278(37):35483-35490.
47. Thusberg J., Vihinen M. Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods. Hum. Mutat. 2009, 30(5):703-714.
48. Vakili R., et al. Molecular analysis of the CYP21 gene and prenatal diagnosis in families with 21-hydroxylase deficiency in northeastern Iran. Horm. Res. 2005, 63(3):119-124.
49. Wass M.N., Kelley L.A., Sternberg M.J. 3DLigandSite: predicting ligand-binding sites using similar structures. Nucleic Acids Res. 2010, 38. ((Web Server issue):W469-73).
50. Welzel M., et al. Carboxyl-terminal mutations in 3beta-hydroxysteroid dehydrogenase type II cause severe salt-wasting congenital adrenal hyperplasia. J. Clin. Endocrinol. Metab. 2008, 93(4):1418-1425.
51. Yohannan S., et al. Proline substitutions are not easily accommodated in a membrane protein. J. Mol. Biol. 2004, 341:1-6.
52. Zhang Y., et al. Human ovarian expression of 17 beta-hydroxysteroid dehydrogenase types 1, 2, and 3. J. Clin. Endocrinol. Metab. 1996, 81(10):3594-3598.
53. Zhang L., et al. Characterization of two novel homozygous missense mutations involving codon 6 and 259 of type II 3beta-hydroxysteroid dehydrogenase (3betaHSD) gene causing, respectively, nonsalt-wasting and salt-wasting 3betaHSD deficiency disorder. J. Clin. Endocrinol. Metab. 2000, 85(4):1678-1685.