title: Apparent homozygosity due to compound heterozygosity of one point mutation and an overlapping exon deletion mutation in ABCA12: A genetic diagnostic pitfall.
abstract: BACKGROUND
  Harlequin ichthyosis (HI), one of the most severe genetic skin disorders, is autosomal recessively inherited. Mutations in ABCA12, which encodes ATP-binding cassette transporter A12 (ABCA12), are known to be the cause of HI. It is very difficult to make precise genetic diagnosis when an exon deletion mutation overlaps the site of another causative point mutation. This combination of mutations may lead us to conclude incorrectly that the patient has the point mutation homozygously, a phenomenon called "apparent homozygosity".
  
  
  OBJECTIVE
  To demonstrate that the present HI patient has apparent homozygosity in ABCA12 mutations.
  
  
  METHODS
  We performed direct sequencing of gDNA in the entire coding region, including exon-intron boundaries, of ABCA12 in the HI patient and her parents. To further elucidate the mutations in the patient, parental mutation segregation study was done and SNP analysis was conducted on the region flanking ABCA12 in the patients and her parents. Quantitative PCR of gDNA in exon 11 of ABCA12 was also performed. Direct sequencing of cDNA from exon 9 to exon 13 and of gDNA between intron 9 and intron 11 of ABCA12 was done in the HI patient and her parents.
  
  
  RESULTS
  Direct sequencing of gDNA in the entire coding region, including exon-intron boundaries, of ABCA12 seemed to indicate that the patient had the novel homozygous nonsense mutation c.1216A>T (p.Lys406X) in exon 11. However, mutation segregation analysis, SNP analysis, qRTPCR of gDNA in exon 11 of ABCA12 and direct sequencing of cDNA from exon 9 to exon 12 of ABCA12 and of gDNA between intron 9 and intron 11 of ABCA12 in the HI patient and her parents demonstrated that the present patient was compound heterozygous for two ABCA12 mutations: c.1216A>T (p.Lys406X) in exon 11 and g.111346_113217del1872 (p.Leu355_Lys428del, Gln354fs7*) which was overlapping exon deletion mutations involving exons 10 and 11.
  
  
  CONCLUSIONS
  When direct sequencing indicates that a patient from a non-consanguineous family has an apparently homozygous non-founder point mutation, the homozygosity may be "apparent homozygosity", and we should keep in mind the possibility of overlapping exon deletion mutation.
authors.affiliation: Department of Dermatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan.
authors.forename: Akitaka
authors.initials: A
authors.lastname: Shibata
authors.affiliation: Department of Dermatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan.
authors.forename: Kazumitsu
authors.initials: K
authors.lastname: Sugiura
authors.affiliation: Department of Pediatrics, Kainan Hospital, 396 Minami-Honda, Maegasu-cho, Yatomi 498-8502, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Suzuki
authors.affiliation: Department of Pediatrics, Kainan Hospital, 396 Minami-Honda, Maegasu-cho, Yatomi 498-8502, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Ichiki
authors.affiliation: Department of Dermatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan. Electronic address: makiyama@med.nagoya-u.ac.jp.
authors.forename: Masashi
authors.initials: M
authors.lastname: Akiyama
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics*; D001483:Base Sequence; D004252:DNA Mutational Analysis; D005091:Exons; D005260:Female; D006580:Genetic Carrier Screening; D005820:Genetic Testing; D006239:Haplotypes; D006579:Heterozygote; D006720:Homozygote; D006801:Humans; D017490:Ichthyosis, Lamellar / Q000175:diagnosis / Q000235:genetics*; D007223:Infant; D007231:Infant, Newborn; D007438:Introns; D008297:Male; D017354:Point Mutation; D020641:Polymorphism, Single Nucleotide; D017384:Sequence Deletion
chemical_list: C473801:ABCA12 protein, human; D018528:ATP-Binding Cassette Transporters
keywords: ABCA12; Apparent homozygosity; Exon deletion; Partial paternal uniparental disomy of a chromosome