Identification of anHMGB3Frameshift Mutation in a Family With an X-linked Colobomatous Microphthalmia Syndrome Using Whole-Genome and X-Exome Sequencing

Abstract

IMPORTANCE Microphthalmias are rare disorders whose genetic bases are not fully understood. HMGB3 is a new candidate gene for X-linked forms of this disease. OBJECTIVE To identify the causative gene in a pedigree with an X-linked colobomatous microphthalmos phenotype. DESIGN, SETTING, AND PARTICIPANTS Whole-genome sequencing and chromosome X-exome-targeted sequencing were performed at the High Throughput Sequencing Laboratory of the Genetic Resources Core Facility at the Johns Hopkins University School of Medicine on the DNA of the male proband and informatically filtered to identify rare variants. Polymerase chain reaction and Sanger sequencing were used to confirm the variant in the proband and the carrier status of his mother. Thirteen unrelated male patients with a similar phenotype were also screened. MAIN OUTCOMES AND MEASURES Whole-genome and X-exome sequencing to identify a frameshift variant in HMGB3. RESULTS A 2-base pair frameshift insertion (c.477_478insTA, coding for p.Lys161Ilefs*54) in the HGMB3 gene was found in the proband and his carrier mother but not in the unrelated patients. The mutation, confirmed by 3 orthogonal methods, alters an evolutionarily conserved region of the HMGB3 protein from a negatively charged polyglutamic acid tract to a positively charged arginine-rich motif that is likely to interfere with normal protein function. CONCLUSIONS AND RELEVANCE In this family, microphthalmia, microcephaly, intellectual disability, and short stature are associated with a mutation on the X chromosome in the HMGB3 gene. HMGB3 should be considered when performing genetic studies of patients with similar phenotypes.

NAA10 polyadenylation signal variants cause syndromic microphthalmia

“…Clinical presentation in one-third of affected individuals is syndromic,1 2 and it is genetically heterogeneous 3. X-linked syndromic anophthalmia and microphthalmia have been shown to result from pathogenic variants in four genes: BCOR 4 (MIM:300485, MCOPS2), HCCS 5 (MIM:300056, MCOPS7), HMGB3 6 (MIM:300193, MCOPS13), and NAA10 7 (MIM:309800, MCOPS1). A fifth locus, MCOPS4 (MIM:301590, also designated as ANOP1), with linkage to Xq27-q28, was specified without identification of an associated gene.…”

“…HMGB3 and NAA10 reside on Xq27-q28. A single HGMB3 variant has been reported in one family to cause syndromic colobomatous microphthalmia 6. Forrester et al 8 described a family segregating what they termed Lenz microphthalmia syndrome (LMS) and linkage to Xq27-q28.…”

FOXE3 mutations: genotype‐phenotype correlations

“…1 Only a few studies have determined the mutation detection rate using whole exome sequencing (WES). Deml et al 8 [10][11][12] The FOXE3 gene encodes a transcription factor of 319 amino acids with a DNA-binding domain, the forkhead domain, located from amino acid 71 to 165. 13 FOXE3 is specifically expressed during lens development in humans, mouse and zebrafish.…”

The long tail and rare disease research: the impact of next-generation sequencing for rare Mendelian disorders

“…While exome sequencing may be particularly suited to solving known Mendelian diseases for which the genetic aetiology is unknown, the authors claim that the data generated from WGS is more suited to the task of discovering the genetic basis of yet unknown diseases. Another group also used a combination of WGS and WES to identify a frameshift mutation in HMGB3 as the cause for X-linked colobomatous microphthalmia (OMIM 309800) (Scott et al, 2014). The authors write that the increased coverage generated from multiple orthogonal sequencing methods improved their ability to identify variants over a single-technique approach (Scott et al, 2014).…”

“…Another group also used a combination of WGS and WES to identify a frameshift mutation in HMGB3 as the cause for X-linked colobomatous microphthalmia (OMIM 309800) (Scott et al, 2014). The authors write that the increased coverage generated from multiple orthogonal sequencing methods improved their ability to identify variants over a single-technique approach (Scott et al, 2014). Enns et al also used a combination of WGS and WES to identify NGLY-1 deficiency as the cause of a glycosylation disorder found in eight patients in 2014 .…”