Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Identification of novel pathogenic variants and novel gene-phenotype correlations in Mexican subjects with microphthalmia and/or anophthalmia by next-generation sequencing


Severe congenital eye malformations, particularly microphthalmia and anophthalmia, are one of the main causes of visual handicap worldwide. They can arise from multifactorial, chromosomal, or monogenic factors and can be associated with extensive clinical variability. Genetic analysis of individuals with these defects has allowed the recognition of dozens of genes whose mutations lead to disruption of normal ocular embryonic development. Recent application of next generation sequencing (NGS) techniques for genetic screening of patients with congenital eye defects has greatly improved the recognition of monogenic cases. In this study, we applied clinical exome NGS to a group of 14 Mexican patients (including 7 familial and 7 sporadic cases) with microphthalmia and/or anophthalmia. Causal or likely causal pathogenic variants were demonstrated in ~60% (8 out of 14 patients) individuals. Seven out of 8 different identified mutations occurred in well-known microphthalmia/anophthalmia genes (OTX2, VSX2, MFRP, VSX1) or in genes associated with syndromes that include ocular defects (CHD7, COL4A1) (including two instances of CHD7 pathogenic variants). A single pathogenic variant was identified in PIEZO2, a gene that was not previously associated with isolated ocular defects. NGS efficiently identified the genetic etiology of microphthalmia/anophthalmia in ~60% of cases included in this cohort, the first from Mexican origin analyzed to date. The molecular defects identified through clinical exome sequencing in this study expands the phenotypic spectra of CHD7-associated disorders and implicate PIEZO2 as a candidate gene for major eye developmental defects.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1
Fig. 2
Fig. 3
Fig. 4


  1. 1.

    Graw J. Eye development. Curr Top Dev Biol. 2010;90:343–86.

    Article  PubMed  Google Scholar 

  2. 2.

    Sinn R, Wittbrodt J. An eye on eye development. Mech Dev. 2013;130:347–58.

    CAS  Article  PubMed  Google Scholar 

  3. 3.

    Graw J, Löster J. Developmental genetics in ophthalmology. Ophthalmic Genet. 2003;24:1–33.

    Article  PubMed  Google Scholar 

  4. 4.

    Horsford DJ, Hanson I, Freund C, McInnes RR, van Heyningen V. Transcription factors in eye disease and ocular development. In. Valle D, Beaudet AL, Vogelstein B, et al. editors. Chapter 240. The Online Metabolic & Molecular Bases of Inherited disease, McGraw-Hill, New York, USA. (, accesed on February, 2018).

  5. 5.

    Morrison D, FitzPatrick D, Hanson I, Williamson K, van Heyningen V, Fleck B, et al. National study of microphthalmia, anophthalmia, and coloboma (MAC) in Scotland: investigation of genetic aetiology. J Med Genet. 2002;39:16–22.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. 6.

    Slavotinek AM. Eye development genes and known syndromes. Mol Genet Metab. 2011;104:448–56.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Skalicky SE, White AJ, Grigg JR, Martin F, Smith J, Jones M, et al. Microphthalmia, anophthalmia, and coloboma and associated ocular and systemic features: understanding the spectrum. JAMA Ophthalmol. 2013;131:1517–24.

    Article  PubMed  Google Scholar 

  8. 8.

    Freund C, Horsford DJ, McInnes RR. Transcription factor genes and the developing eye: a genetic perspective. Hum Mol Genet. 1996;5(Spec No):1471–88.

    CAS  Article  PubMed  Google Scholar 

  9. 9.

    Graw J. The genetic and molecular basis of congenital eye defects. Nat Rev Genet. 2003;4:876–88.

    CAS  Article  PubMed  Google Scholar 

  10. 10.

    Patel A, Sowden JC. Genes and pathways in optic fissure closure. Semin Cell Dev Biol. 2017; pii: S1084-9521(17)30149-0.

  11. 11.

    Verma AS, Fitzpatrick DR. Anophthalmia and microphthalmia. Orphanet J Rare Dis. 2007;2:47.

    Article  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Chassaing N, Causse A, Vigouroux A, Delahaye A, Alessandri JL, Boespflug-Tanguy O, et al. Molecular findings and clinical data in a cohort of 150 patients with anophthalmia/microphthalmia. Clin Genet. 2014;86:326–34.

    CAS  Article  PubMed  Google Scholar 

  13. 13.

    Williamson KA, FitzPatrick DR. The genetic architecture of microphthalmia, anophthalmia and coloboma. Eur J Med Genet. 2014;57:369–80.

    Article  PubMed  Google Scholar 

  14. 14.

    Gonzalez-Rodriguez J, Pelcastre EL, Tovilla-Canales JL, Garcia-Ortiz JE, Amato-Almanza M, Villanueva-Mendoza C, et al. Mutational screening of CHX10, GDF6, OTX2, RAX and SOX2 genes in 50 unrelated microphthalmia-anophthalmia-coloboma (MAC) spectrum cases. Br J Ophthalmol. 2010;94:1100–4.

    CAS  Article  PubMed  Google Scholar 

  15. 15.

    Gerth-Kahlert C, Williamson K, Ansari M, Rainger JK, Hingst V, Zimmermann T, et al. Clinical and mutation analysis of 51 probands with anophthalmia and/or severe microphthalmia from a single center. Mol Genet Genomic Med. 2013;1:15–31.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Riera M, Wert A, Nieto I, Pomares E. Panel-based whole exome sequencing identifies novel mutations in microphthalmia and anophthalmia patients showing complex Mendelian inheritance patterns. Mol Genet Genomic Med. 2017;5:709–19.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Richardson R, Sowden J, Gerth-Kahlert C, Moore AT, Moosajee M. Clinical utility gene card for: Non-Syndromic Microphthalmia Including Next-Generation Sequencing-Based Approaches. Eur J Hum Genet. 2017;25.

  18. 18.

    Jimenez NL, Flannick J, Yahyavi M, Li J, Bardakjian T, Tonkin L, et al. Targeted ‘next-generation’ sequencing in anophthalmia and microphthalmia patients confirms SOX2, OTX2 and FOXE3 mutations. BMC Med Genet. 2011;12:172.

    CAS  Article  PubMed  Google Scholar 

  19. 19.

    Slavotinek AM, Garcia ST, Chandratillake G, Bardakjian T, Ullah E, Wu D, et al. Exome sequencing in 32 patients with anophthalmia/microphthalmia and developmental eye defects. Clin Genet. 2015;88:468–73.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. 20.

    Prokudin I, Simons C, Grigg JR, Storen R, Kumar V, Phua ZY, et al. Exome sequencing in developmental eye disease leads to identification of causal variants in GJA8, CRYGC, PAX6 and CYP1B1. Eur J Hum Genet. 2014;22:907–15.

    CAS  Article  PubMed  Google Scholar 

  21. 21.

    Deml B, Reis LM, Lemyre E, Clark RD, Kariminejad A, Semina EV. Novel mutations in PAX6, OTX2 and NDP in anophthalmia, microphthalmia and coloboma. Eur J Hum Genet. 2016;24:535–41.

    CAS  Article  PubMed  Google Scholar 

  22. 22.

    Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016;44(W1):W3–W10.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Smigielski EM, Sirotkin K, Ward M, Sherry ST. dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res. 2000;28:352–5.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  24. 24.

    1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491:56–65.

    Article  CAS  Google Scholar 

  25. 25.

    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.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  26. 26.

    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.

    CAS  Article  Google Scholar 

  27. 27.

    Bendl J, Stourac J, Salanda O, Pavelka A, Wieben ED, Zendulka J, et al. PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations. PLoS Comput Biol. 2014;10:e1003440.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. 28.

    Schilter KF, Schneider A, Bardakjian T, Soucy JF, Tyler RC, Reis LM, et al. OTX2 microphthalmia syndrome: four novel mutations and delineation of a phenotype. Clin Genet. 2011;79:158–68.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  29. 29.

    Ragge NK, Brown AG, Poloschek CM, Lorenz B, Henderson RA, Clarke MP, et al. Heterozygous mutations of OTX2 cause severe ocular malformations. Am J Hum Genet. 2005;76:1008–22.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  30. 30.

    You T, Lv Y, Liu S, Li F, Zhao Y, Lv J, et al. Novel OTX2 mutation associated with congenital anophthalmia and microphthalmia in a Han Chinese family. Acta Ophthalmol. 2012;90:e501–2.

    CAS  Article  PubMed  Google Scholar 

  31. 31.

    Somashekar PH, Shukla A, Girisha KM. Intrafamilial variability in syndromic microphthalmia type 5 caused by a novel variation in OTX2. Ophthalmic Genet. 2017;38:533–6.

    CAS  Article  PubMed  Google Scholar 

  32. 32.

    Liu IS, Chen JD, Ploder L, Vidgen D, van der Kooy D, Kalnins VI, et al. Developmental expression of a novel murine homeobox gene (Chx10): evidence for roles in determination of the neuroretina and inner nuclear layer. Neuron. 1994;13:377–93.

    CAS  Article  PubMed  Google Scholar 

  33. 33.

    Ferda Percin E, Ploder LA, Yu JJ, Arici K, Horsford DJ, Rutherford A, et al. Human microphthalmia associated with mutations in the retinal homeobox gene CHX10. Nat Genet. 2000;25:397–401.

    CAS  Article  PubMed  Google Scholar 

  34. 34.

    Bar-Yosef U, Abuelaish I, Harel T, Hendler N, Ofir R, Birk OS. CHX10 mutations cause non-syndromic microphthalmia/ anophthalmia in Arab and Jewish kindreds. Hum Genet. 2004;115:302–9.

    CAS  Article  PubMed  Google Scholar 

  35. 35.

    Iseri SU, Wyatt AW, Nurnberg G, Kluck C, Nurnberg P, Holder GE, et al. Use of genome-wide SNP homozygosity mapping in small pedigrees to identify new mutations in VSX2 causing recessive microphthalmia and a semidominant inner retinal dystrophy. Hum Genet. 2010;128:51–60.

    CAS  Article  PubMed  Google Scholar 

  36. 36.

    Reis LM, Khan A, Kariminejad A, Ebadi F, Tyler RC, Semina EV. VSX2 mutations in autosomal recessive microphthalmia. Mol Vis. 2011;17:2527–32.

    CAS  PubMed  PubMed Central  Google Scholar 

  37. 37.

    Kameya S, Hawes NL, Chang B, Heckenlively JR, Naggert JK, Nishina PM. Mfrp, a gene encoding a frizzled related protein, is mutated in the mouse retinal degeneration 6. Hum Mol Genet. 2002;11:1879–86.

    CAS  Article  PubMed  Google Scholar 

  38. 38.

    Sundin OH, Leppert GS, Silva ED, Yang JM, Dharmaraj S, Maumenee IH, et al. Extreme hyperopia is the result of null mutations in MFRP, which encodes a Frizzled-related protein. Proc Natl Acad Sci USA. 2005;102:9553–8.

    CAS  Article  PubMed  Google Scholar 

  39. 39.

    Matsushita I, Kondo H, Tawara A. Novel compound heterozygous mutations in the MFRP gene in a Japanese patient with posterior microphthalmos. Jpn J Ophthalmol. 2012;56:396–400.

    Article  PubMed  Google Scholar 

  40. 40.

    Said MB, Chouchène E, Salem SB, Daoud K, Largueche L, Bouassida W, et al. Posterior microphthalmia and nanophthalmia in Tunisia caused by a founder c.1059_1066insC mutation of the PRSS56 gene. Gene. 2013;528:288–94.

    CAS  Article  PubMed  Google Scholar 

  41. 41.

    Ayala-Ramirez R, Graue-Wiechers F, Robredo V, Amato-Almanza M, Horta-Diez I, Zenteno JC. A new autosomal recessive syndrome consisting of posterior microphthalmos, retinitis pigmentosa, foveoschisis, and optic disc drusen is caused by a MFRP gene mutation. Mol Vis. 2006;12:1483–9.

    CAS  PubMed  Google Scholar 

  42. 42.

    Mukhopadhyay R, Sergouniotis PI, Mackay DS, Day AC, Wright G, Devery S, et al. A detailed phenotypic assessment of individuals affected by MFRP-related oculopathy. Mol Vis. 2010;16:540–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  43. 43.

    Zenteno JC, Buentello-Volante B, Quiroz-González MA, Quiroz-Reyes MA. Compound heterozygosity for a novel and a recurrent MFRP gene mutation in a family with the nanophthalmos-retinitis pigmentosa complex. Mol Vis. 2009;15:1794–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Xu Y, Guan L, Xiao X, Zhang J, Li S, Jiang H, et al. Identification of MFRP mutations in chinese families with high hyperopia. Optom Vis Sci. 2016;93:19–26.

    PubMed  Google Scholar 

  45. 45.

    Velez G, Tsang SH, Tsai YT, Hsu CW, Gore A, Abdelhakim AH, et al. Gene therapy restores Mfrp and corrects axial eye length. Sci Rep. 2017;7:16151.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  46. 46.

    Semina EV, Mintz-Hittner HA, Murray JC. Isolation and characterization of a novel human paired-like homeodomain-containing transcription factor gene, VSX1, expressed in ocular tissues. Genomics. 2000;63:289–93.

    CAS  Article  PubMed  Google Scholar 

  47. 47.

    Tanwar M, Kumar M, Nayak B, Pathak D, Sharma N, Titiyal JS, et al. VSX1 gene analysis in keratoconus. Mol Vis. 2010;16:2395–401.

    CAS  PubMed  PubMed Central  Google Scholar 

  48. 48.

    Dash DP, George S, O’Prey D, Burns D, Nabili S, Donnelly U, et al. Mutational screening of VSX1 in keratoconus patients from the European population. Eye (Lond). 2010;24:1085–92.

    CAS  Article  Google Scholar 

  49. 49.

    Mintz-Hittner HA, Semina EV, Frishman LJ, Prager TC, Murray JC. VSX1 (RINX) mutation with craniofacial anomalies, empty sella, corneal endothelial changes, and abnormal retinal and auditory bipolar cells. Ophthalmology. 2004;111:828–36.

    Article  PubMed  Google Scholar 

  50. 50.

    Chow RL, Snow B, Novak J, Looser J, Freund C, Vidgen D, et al. Vsx1, a rapidly evolving paired-like homeobox gene expressed in cone bipolar cells. Mech Dev. 2001;109:315–22.

    CAS  Article  PubMed  Google Scholar 

  51. 51.

    Clapier CR, Cairns BR. The biology of chromatin remodeling complexes. Annu Rev Biochem. 2009;78:273–304.

    CAS  Article  PubMed  Google Scholar 

  52. 52.

    Vissers LE, van Ravenswaaij CM, Admiraal R, Hurst JA, de Vries BB, Janssen IM, et al. Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nat Genet. 2004;36:955–7.

    CAS  Article  PubMed  Google Scholar 

  53. 53.

    Kim HG, Kurth I, Lan F, Meliciani I, Wenzel W, Eom SH, et al. Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome. Am J Hum Genet. 2008;83:511–9.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  54. 54.

    Jongmans MC, Hoefsloot LH, van der Donk KP, Admiraal RJ, Magee A, van de Laar I, et al. Familial CHARGE syndrome and the CHD7 gene: a recurrent missense mutation, intrafamilial recurrence and variability. Am J Med Genet A. 2008;146A:43–50.

    CAS  Article  PubMed  Google Scholar 

  55. 55.

    Pauli S, Pieper L, Häberle J, Grzmil P, Burfeind P, Steckel M, Lenz U, Michelmann HW. Proven germline mosaicism in a father of two children with CHARGE syndrome. Clin Genet. 2009;75:473–9.

    CAS  Article  PubMed  Google Scholar 

  56. 56.

    Legendre M, Gonzales M, Goudefroye G, Bilan F, Parisot P, Perez MJ, et al. Antenatal spectrum of CHARGE syndrome in 40 fetuses with CHD7 mutations. J Med Genet. 2012;49:698–707.

    CAS  Article  PubMed  Google Scholar 

  57. 57.

    Janssen N, Bergman JE, Swertz MA, Tranebjaerg L, Lodahl M, Schoots J, et al. Mutation update on the CHD7 gene involved in CHARGE syndrome. Hum Mutat. 2012;33:1149–60.

    CAS  Article  PubMed  Google Scholar 

  58. 58.

    Ishizaki M, Westerhausen-Larson A, Kino J, Hayashi T, Kao WW. Distribution of collagen IV in human ocular tissues. Invest Ophthalmol Vis Sci. 1993;34:2680–89.

    CAS  PubMed  Google Scholar 

  59. 59.

    Hann CR, Springett MJ, Wang X, Johnson DH. Ultrastructural localization of collagen IV, fibronectin, and laminin in the trabecular meshwork of normal and glaucomatous eyes. Ophthalmic Res. 2001;33:314–24.

    CAS  Article  PubMed  Google Scholar 

  60. 60.

    Gould DB, Phalan FC, Breedveld GJ, van Mil SE, Smith RS, Schimenti JC, et al. Mutations in COL4A1 cause perinatal cerebral hemorrhage and porencephaly. Science. 2005;308:1167–71.

    CAS  Article  PubMed  Google Scholar 

  61. 61.

    Gould DB, Phalan FC, vanMil SE, Sundberg JP, Vahedi K, Massin P, et al. Role of COL4A1 in small-vessel disease and hemorrhagic stroke. N Engl J Med. 2006;354:1489–96.

    CAS  Article  PubMed  Google Scholar 

  62. 62.

    Coupry I, Sibon I, Mortemousque B, Rouanet F, Mine M, Goizet C. Ophthalmological features associated with COL4A1 mutations. Arch Ophthalmol. 2010;128:483–9.

    Article  PubMed  Google Scholar 

  63. 63.

    Deml B, Reis LM, Maheshwari M, Griffis C, Bick D, Semina EV. Whole exome analysis identifies dominant COL4A1 mutations in patients with complex ocular phenotypes involving microphthalmia. Clin Genet. 2014;86:475–81.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  64. 64.

    Labelle-Dumais C, Dilworth DJ, Harrington EP, de Leau M, Lyons D, Kabaeva Z, et al. COL4A1 mutations cause ocular dysgenesis, neuronal localization defects, and myopathy in mice and Walker-Warburg syndrome in humans. PLoS Genet. 2011;7:e1002062.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  65. 65.

    Fernandez-Sanchez ME, Brunet T, Röper JC, Farge E. Mechanotransduction’s impact on animal development, evolution, and tumorigenesis. Annu Rev Cell Dev Biol. 2015;31:373–97.

    CAS  Article  PubMed  Google Scholar 

  66. 66.

    Geng J, Zhao Q, Zhang T, Xiao B. In Touch with the mechanosensitive Piezo channels: structure, ion Permeation, and mechanotransduction. Curr Top Membr. 2017;79:159–95.

    CAS  Article  PubMed  Google Scholar 

  67. 67.

    McMillin MJ, Beck AE, Chong JX, Shively KM, Buckingham KJ, Gildersleeve HI, et al. Mutations in PIEZO2 cause Gordon syndrome, Marden-Walker syndrome, and distal arthrogryposis type 5. Am J Hum Genet. 2014;94:734–44.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  68. 68.

    Bron R, Wood RJ, Brock JA, Ivanusic JJ. Piezo2 expression in corneal afferent neurons. J Comp Neurol. 2014;522:2967–79.

    CAS  Article  PubMed  Google Scholar 

  69. 69.

    Choi HJ, Sun D, Jakobs TC. Astrocytes in the optic nerve head express putative mechanosensitive channels. Mol Vis. 2015;21:749–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  70. 70.

    Szczot M, Pogorzala LA, Solinski HJ, Young L, Yee P, Le Pichon CE, et al. Cell-type-specific splicing of Piezo2 regulates mechanotransduction. Cell Rep. 2017;21:2760–71.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  71. 71.

    Schrander-Stumpel C, de Die-Smulders C, de Krom M, Schyns-Fleuran S, Hamel B, Jaeken D, et al. Marden-Walker syndrome: case report, literature review and nosologic discussion. Clin Genet. 1993;43:303–8.

    CAS  Article  PubMed  Google Scholar 

  72. 72.

    Sahni J, Kaye SB, Fryer A, Hiscott P, Bucknall RC. Distal arthrogryposis type IIB: unreported ophthalmic findings. Am J Med Genet A. 2004;127A:35–9.

    Article  PubMed  Google Scholar 

  73. 73.

    Güell JL, Verdaguer P, Elies D, Gris O, Manero F. Corneal impairment in a patient with type 2 distal arthrogryposis. Eye Contact Lens. 2015;41:e5–8.

    Article  PubMed  Google Scholar 

Download references


This work was partially supported by CONACYT grants 234413 and 233967. We would like to thank Daniel Moreno, M.D and Roger Fest-Parra, M.D for technical assistance, and Dr. Eduardo Perez-Campos for helpful observations on protocol organization.

Author information



Corresponding author

Correspondence to Juan C. Zenteno.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Matías-Pérez, D., García-Montaño, L.A., Cruz-Aguilar, M. et al. Identification of novel pathogenic variants and novel gene-phenotype correlations in Mexican subjects with microphthalmia and/or anophthalmia by next-generation sequencing. J Hum Genet 63, 1169–1180 (2018).

Download citation

Further reading


Quick links