Gene-based burden testing implicates four novel susceptibility genes associated with isolated short stature in pediatric patients

Song KC, Jin SL, Kwon AR, Chae HW, Ahn JM, Kim DH, et al. Etiologies and characteristics of children with chief complaint of short stature. Ann Pediatr Endocrinol Metab. 2015;20:34–9. https://doi.org/10.6065/apem.2015.20.1.34.

Article  PubMed  PubMed Central  Google Scholar 

Marchini A, Ogata T, Rappold GA. A track record on SHOX: from basic research to complex models and therapy. Endocr Rev. 2016;37:417–48. https://doi.org/10.1210/er.2016-1036.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rao E, Weiss B, Fukami M, Rump A, Niesler B, Mertz A, et al. Pseudoautosomal deletions encompassing a novel homeobox gene cause growth failure in idiopathic short stature and Turner syndrome. Nat Genet. 1997;16:54–63. https://doi.org/10.1038/ng0597-54.

Article  CAS  PubMed  Google Scholar 

Wang SR, Jacobsen CM, Carmichael H, Edmund AB, Robinson JW, Olney RC, et al. Heterozygous mutations in natriuretic peptide receptor-B (NPR2) gene as a cause of short stature. Hum Mutat. 2015;36:474–81. https://doi.org/10.1002/humu.22773.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hisado-Oliva A, Ruzafa-Martin A, Sentchordi L, Funari MFA, Bezanilla-López C, Alonso-Bernáldez M, et al. Mutations in C-natriuretic peptide (NPPC): a novel cause of autosomal dominant short stature. Genet Med. 2017;20:91–7. https://doi.org/10.1038/gim.2017.66.

Article  CAS  PubMed  Google Scholar 

Hauer NN, Sticht H, Boppudi S, Büttner C, Kraus C, Trautmann U, et al. Genetic screening confirms heterozygous mutations in ACAN as a major cause of idiopathic short stature. Sci Rep. 2017;7:12225. https://doi.org/10.1038/s41598-017-12465-6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vasques GA, Funari MFA, Ferreira FM, Aza-Carmona M, Sentchordi-Montané L, Barraza-García J, et al. IHH gene mutations causing short stature with nonspecific skeletal abnormalities and response to growth hormone therapy. J Clin Endocrinol Metab. 2017;103:604–14. https://doi.org/10.1210/jc.2017-02026.

Article  Google Scholar 

Kant SG, Cervenkova I, Balek L, Trantirek L, Santen GW, de Vries MC, et al. A novel variant of FGFR3 causes proportionate short stature. Eur J Endocrinol. 2015;172:763–70. https://doi.org/10.1530/EJE-14-0945.

Article  CAS  PubMed  Google Scholar 

Wang SR, Carmichael H, Andrew SF, Miller TC, Moon JE, Derr MA, et al. Large-scale pooled next-generation sequencing of 1077 genes to identify genetic causes of short stature. J Clin Endocrinol Metab. 2013;98:1428–37. https://doi.org/10.1210/jc.2013-1534.

Article  CAS  Google Scholar 

Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536:285–91. https://doi.org/10.1038/nature19057.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen T, Wu H, Zhang C, Feng J, Chen L, Xie R, et al. Clinical, genetics, and bioinformatic characterization of mutations affecting an essential region of PLS3 in patients with BMND18. Int J Endocrinol. 2018;2018:8953217. https://doi.org/10.1155/2018/8953217.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–95. https://doi.org/10.1093/bioinformatics/btp698.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, 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. https://doi.org/10.1038/gim.2015.30.

Article  PubMed  PubMed Central  Google Scholar 

Zhang J, Yao Y, He H, Shen J. Clinical interpretation of sequence variants. Curr Protoc Hum Genet. 2020;106:e98. https://doi.org/10.1002/cphg.98.

Article  PubMed  PubMed Central  Google Scholar 

Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, et al. Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genet Med. 2019;22:245–57. https://doi.org/10.1038/s41436-019-0686-8.

Article  PubMed  PubMed Central  Google Scholar 

Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10:giab008. https://doi.org/10.1093/gigascience/giab008.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4:1073–81. https://doi.org/10.1038/nprot.2009.86.

Article  CAS  PubMed  Google Scholar 

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248–9. https://doi.org/10.1038/nmeth0410-248.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Guo MH, Plummer L, Chan YM, Hirschhorn JN, Lippincott MF. Burden testing of rare variants identified through exome sequencing via publicly available control data. Am J Hum Genet. 2018;103:522–34. https://doi.org/10.1016/j.ajhg.2018.08.016.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16:284–7. https://doi.org/10.1089/omi.2011.0118.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lin YJ, Cheng CF, Wang CH, Liang WM, Tang CH, Tsai LP, et al. Genetic architecture associated with familial short stature. J Clin Endocrinol Metab. 2020;105:dgaa131. https://doi.org/10.1210/clinem/dgaa131.

Article  PubMed  Google Scholar 

Cescon M, Gattazzo F, Chen P, Bonaldo P. Collagen VI at a glance. J Cell Sci. 2015;128:3525–31. https://doi.org/10.1242/jcs.169748.

Article  CAS  PubMed  Google Scholar 

Deng FY, Dong SS, Xu XH, Liu YJ, Liu YZ, Shen H, et al. Genome-wide association study identified UQCC locus for spine bone size in humans. Bone. 2012;53:129–33. https://doi.org/10.1016/j.bone.2012.11.028.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huber C, Fradin M, Edouard T, Le Merrer M, Alanay Y, Da Silva DB, et al. OBSL1 mutations in 3-M syndrome are associated with a modulation of IGFBP2 and IGFBP5 expression levels. Hum Mutat. 2009;31:20–6. https://doi.org/10.1002/humu.21150.

Article  CAS  Google Scholar 

Blondelle J, Marrocco V, Clark M, Desmond P, Myers S, Nguyen J, et al. Murine obscurin and Obsl1 have functionally redundant roles in sarcolemmal integrity, sarcoplasmic reticulum organization, and muscle metabolism. Commun Biol. 2019;2:178. https://doi.org/10.1038/s42003-019-0405-7.

Article  PubMed  PubMed Central  Google Scholar 

Pavlakis E, Chiotaki R, Chalepakis G. The role of Fras1/Frem proteins in the structure and function of basement membrane. Int J Biochem Cell Biol. 2010;43:487–95. https://doi.org/10.1016/j.biocel.2010.12.016.

Article  CAS  PubMed  Google Scholar 

Turgut GT, Sarac Sivrikoz T, Komurcu-Bayrak E, Kalayci T. FREM2-related Fraser syndrome with popliteal pterygium and structural central nervous system anomalies. Eur J Med Genet. 2023;66:104712. https://doi.org/10.1016/j.ejmg.2023.104712.

Article  CAS 

Comments (0)

No login
gif