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Hemizygous mutations in SNAP29 unmask autosomal recessive conditions and contribute to atypical findings in patients with 22q11.2DS.

McDonald-McGinn DM, Fahiminiya S, Revil T, Nowakowska BA, Suhl J, Bailey A, Mlynarski E, Lynch DR, Yan AC, Bilaniuk LT, Sullivan KE, Warren ST, Emanuel BS, Vermeesch JR, Zackai EH, Jerome-Majewska LA - J. Med. Genet. (2012)

Bottom Line: We utilised whole exome, targeted exome and/or Sanger sequencing to examine the genome of 17 patients with 22q11.2 deletions and phenotypic features found in <10% of affected individuals.This work confirms that the phenotypic variability observed in a subset of patients with 22q11.2DS is due to mutations on the non-deleted chromosome, which leads to unmasking of autosomal recessive conditions such as CEDNIK, Kousseff, and a potentially autosomal recessive form of Opitz G/BBB syndrome.Furthermore, our work implicates SNAP29 as a major modifier of variable expressivity in 22q11.2 DS patients.

View Article: PubMed Central - PubMed

Affiliation: Division of Human Genetics, The Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA.

ABSTRACT

Background: 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder, affecting an estimated 1 : 2000-4000 live births. Patients with 22q11.2DS have a broad spectrum of phenotypic abnormalities which generally includes congenital cardiac abnormalities, palatal anomalies, and immunodeficiency. Additional findings, such as skeletal anomalies and autoimmune disorders, can confer significant morbidity in a subset of patients. 22q11.2DS is a contiguous gene DS and over 40 genes are deleted in patients; thus deletion of several genes within this region contributes to the clinical features. Mutations outside or on the remaining 22q11.2 allele are also known to modify the phenotype.

Methods: We utilised whole exome, targeted exome and/or Sanger sequencing to examine the genome of 17 patients with 22q11.2 deletions and phenotypic features found in <10% of affected individuals.

Results and conclusions: In four unrelated patients, we identified three novel mutations in SNAP29, the gene implicated in the autosomal recessive condition cerebral dysgenesis, neuropathy, ichthyosis and keratoderma (CEDNIK). SNAP29 maps to 22q11.2 and encodes a soluble SNARE protein that is predicted to mediate vesicle fusion at the endoplasmic reticulum or Golgi membranes. This work confirms that the phenotypic variability observed in a subset of patients with 22q11.2DS is due to mutations on the non-deleted chromosome, which leads to unmasking of autosomal recessive conditions such as CEDNIK, Kousseff, and a potentially autosomal recessive form of Opitz G/BBB syndrome. Furthermore, our work implicates SNAP29 as a major modifier of variable expressivity in 22q11.2 DS patients.

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Identification of a homozygous 2 bp frameshift insertion within the gene SNAP29 by exome and Sanger sequencing. (A) The SNAP29 gene is located on the long arm of chromosome 22 at position 22q11.2. It is 32 kb in size and is composed of five exons. (B) The grey horizontal arrows depict the 100 bp paired-end reads aligned to the positive strand of human genome (hg19) and cover the 2 bp ‘GA’ homozygous insertion at position 388_389 in exon 2. Of 19 unique reads mapped at the genomic position chr22:21224770, 17 reads displayed the 2 bp homozygous insertion. Note that the BWA (Burrows-Wheeler Aligner) placed the insertion at position c.383_384, whereas the correct HGVS (Human Genome Variation Society) notation is c.387_388dup. (C) Chromatograms show the result of Sanger sequencing in patient 1 and his parents. Patient 1 carries a homozygous 2 bp insertion resulting in a frameshift and a premature stop codon 17 amino acids downstream (p.T130fs). The father is a heterozygous carrier for the 2 bp insertion at the same position. The position of the insertion is indicated by the green arrow on the chromatograms of patient 1 and his father. In the lower part of figure, the frameshift DNA sequence and the respective translation into protein are given.
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JMEDGENET2012101320F2: Identification of a homozygous 2 bp frameshift insertion within the gene SNAP29 by exome and Sanger sequencing. (A) The SNAP29 gene is located on the long arm of chromosome 22 at position 22q11.2. It is 32 kb in size and is composed of five exons. (B) The grey horizontal arrows depict the 100 bp paired-end reads aligned to the positive strand of human genome (hg19) and cover the 2 bp ‘GA’ homozygous insertion at position 388_389 in exon 2. Of 19 unique reads mapped at the genomic position chr22:21224770, 17 reads displayed the 2 bp homozygous insertion. Note that the BWA (Burrows-Wheeler Aligner) placed the insertion at position c.383_384, whereas the correct HGVS (Human Genome Variation Society) notation is c.387_388dup. (C) Chromatograms show the result of Sanger sequencing in patient 1 and his parents. Patient 1 carries a homozygous 2 bp insertion resulting in a frameshift and a premature stop codon 17 amino acids downstream (p.T130fs). The father is a heterozygous carrier for the 2 bp insertion at the same position. The position of the insertion is indicated by the green arrow on the chromatograms of patient 1 and his father. In the lower part of figure, the frameshift DNA sequence and the respective translation into protein are given.

Mentions: Patient 1 presented with a history of laryngotracheomalacia, a small patent ductus arteriosus, gastro-oesophageal reflux disease, failure to thrive and feeding difficulty requiring G-tube placement, chronic infection, polymicrogyria, and dysmorphic features including hypertelorism. In addition, he had: microcephaly, strabismus, optic nerve hypoplasia, bilateral sensorineural hearing loss, obstructive sleep apnoea, immunoglobulin G (IgG) and IgM deficiency, a unilateral inguinal hernia and undescended testis. More recently, he was noted to have palmoplantar keratoderma and ichthyosis, (figure 1: 1A–F). The homozygous frameshift insertion within SNAP29, c.388_389insGA (p.T130fs), has not previously been seen in dbSNP, 1000 Genomes Project or EVS, and was subsequently confirmed by Sanger sequencing (figure 2A–C). Sanger sequencing of parental blood DNA revealed a heterozygous insertion in the father at the same position (figure 2C), suggesting that the proband was hemizygous for the 22q11.2 chromosome, as determined by fluorescence in situ hybridisation. (FISH), and inherited a non-functional SNAP29 gene from the father and by inference a de novo deletion on the 22q11.2 chromosome inherited from his mother. Truncating mutations in SNAP29 are associated with CEDNIK syndrome, an autosomal recessive condition characterised by cerebral dysgenesis, neuropathy, ichthyosis, and keratoderma.1415 The frameshift mutation identified in SNAP29 is predicted to result in a truncated protein with 129 amino acids of the SNAP29 protein, and insertion of 17 novel amino acids before a premature stop (figure 2C).


Hemizygous mutations in SNAP29 unmask autosomal recessive conditions and contribute to atypical findings in patients with 22q11.2DS.

McDonald-McGinn DM, Fahiminiya S, Revil T, Nowakowska BA, Suhl J, Bailey A, Mlynarski E, Lynch DR, Yan AC, Bilaniuk LT, Sullivan KE, Warren ST, Emanuel BS, Vermeesch JR, Zackai EH, Jerome-Majewska LA - J. Med. Genet. (2012)

Identification of a homozygous 2 bp frameshift insertion within the gene SNAP29 by exome and Sanger sequencing. (A) The SNAP29 gene is located on the long arm of chromosome 22 at position 22q11.2. It is 32 kb in size and is composed of five exons. (B) The grey horizontal arrows depict the 100 bp paired-end reads aligned to the positive strand of human genome (hg19) and cover the 2 bp ‘GA’ homozygous insertion at position 388_389 in exon 2. Of 19 unique reads mapped at the genomic position chr22:21224770, 17 reads displayed the 2 bp homozygous insertion. Note that the BWA (Burrows-Wheeler Aligner) placed the insertion at position c.383_384, whereas the correct HGVS (Human Genome Variation Society) notation is c.387_388dup. (C) Chromatograms show the result of Sanger sequencing in patient 1 and his parents. Patient 1 carries a homozygous 2 bp insertion resulting in a frameshift and a premature stop codon 17 amino acids downstream (p.T130fs). The father is a heterozygous carrier for the 2 bp insertion at the same position. The position of the insertion is indicated by the green arrow on the chromatograms of patient 1 and his father. In the lower part of figure, the frameshift DNA sequence and the respective translation into protein are given.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3585484&req=5

JMEDGENET2012101320F2: Identification of a homozygous 2 bp frameshift insertion within the gene SNAP29 by exome and Sanger sequencing. (A) The SNAP29 gene is located on the long arm of chromosome 22 at position 22q11.2. It is 32 kb in size and is composed of five exons. (B) The grey horizontal arrows depict the 100 bp paired-end reads aligned to the positive strand of human genome (hg19) and cover the 2 bp ‘GA’ homozygous insertion at position 388_389 in exon 2. Of 19 unique reads mapped at the genomic position chr22:21224770, 17 reads displayed the 2 bp homozygous insertion. Note that the BWA (Burrows-Wheeler Aligner) placed the insertion at position c.383_384, whereas the correct HGVS (Human Genome Variation Society) notation is c.387_388dup. (C) Chromatograms show the result of Sanger sequencing in patient 1 and his parents. Patient 1 carries a homozygous 2 bp insertion resulting in a frameshift and a premature stop codon 17 amino acids downstream (p.T130fs). The father is a heterozygous carrier for the 2 bp insertion at the same position. The position of the insertion is indicated by the green arrow on the chromatograms of patient 1 and his father. In the lower part of figure, the frameshift DNA sequence and the respective translation into protein are given.
Mentions: Patient 1 presented with a history of laryngotracheomalacia, a small patent ductus arteriosus, gastro-oesophageal reflux disease, failure to thrive and feeding difficulty requiring G-tube placement, chronic infection, polymicrogyria, and dysmorphic features including hypertelorism. In addition, he had: microcephaly, strabismus, optic nerve hypoplasia, bilateral sensorineural hearing loss, obstructive sleep apnoea, immunoglobulin G (IgG) and IgM deficiency, a unilateral inguinal hernia and undescended testis. More recently, he was noted to have palmoplantar keratoderma and ichthyosis, (figure 1: 1A–F). The homozygous frameshift insertion within SNAP29, c.388_389insGA (p.T130fs), has not previously been seen in dbSNP, 1000 Genomes Project or EVS, and was subsequently confirmed by Sanger sequencing (figure 2A–C). Sanger sequencing of parental blood DNA revealed a heterozygous insertion in the father at the same position (figure 2C), suggesting that the proband was hemizygous for the 22q11.2 chromosome, as determined by fluorescence in situ hybridisation. (FISH), and inherited a non-functional SNAP29 gene from the father and by inference a de novo deletion on the 22q11.2 chromosome inherited from his mother. Truncating mutations in SNAP29 are associated with CEDNIK syndrome, an autosomal recessive condition characterised by cerebral dysgenesis, neuropathy, ichthyosis, and keratoderma.1415 The frameshift mutation identified in SNAP29 is predicted to result in a truncated protein with 129 amino acids of the SNAP29 protein, and insertion of 17 novel amino acids before a premature stop (figure 2C).

Bottom Line: We utilised whole exome, targeted exome and/or Sanger sequencing to examine the genome of 17 patients with 22q11.2 deletions and phenotypic features found in <10% of affected individuals.This work confirms that the phenotypic variability observed in a subset of patients with 22q11.2DS is due to mutations on the non-deleted chromosome, which leads to unmasking of autosomal recessive conditions such as CEDNIK, Kousseff, and a potentially autosomal recessive form of Opitz G/BBB syndrome.Furthermore, our work implicates SNAP29 as a major modifier of variable expressivity in 22q11.2 DS patients.

View Article: PubMed Central - PubMed

Affiliation: Division of Human Genetics, The Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA.

ABSTRACT

Background: 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder, affecting an estimated 1 : 2000-4000 live births. Patients with 22q11.2DS have a broad spectrum of phenotypic abnormalities which generally includes congenital cardiac abnormalities, palatal anomalies, and immunodeficiency. Additional findings, such as skeletal anomalies and autoimmune disorders, can confer significant morbidity in a subset of patients. 22q11.2DS is a contiguous gene DS and over 40 genes are deleted in patients; thus deletion of several genes within this region contributes to the clinical features. Mutations outside or on the remaining 22q11.2 allele are also known to modify the phenotype.

Methods: We utilised whole exome, targeted exome and/or Sanger sequencing to examine the genome of 17 patients with 22q11.2 deletions and phenotypic features found in <10% of affected individuals.

Results and conclusions: In four unrelated patients, we identified three novel mutations in SNAP29, the gene implicated in the autosomal recessive condition cerebral dysgenesis, neuropathy, ichthyosis and keratoderma (CEDNIK). SNAP29 maps to 22q11.2 and encodes a soluble SNARE protein that is predicted to mediate vesicle fusion at the endoplasmic reticulum or Golgi membranes. This work confirms that the phenotypic variability observed in a subset of patients with 22q11.2DS is due to mutations on the non-deleted chromosome, which leads to unmasking of autosomal recessive conditions such as CEDNIK, Kousseff, and a potentially autosomal recessive form of Opitz G/BBB syndrome. Furthermore, our work implicates SNAP29 as a major modifier of variable expressivity in 22q11.2 DS patients.

Show MeSH
Related in: MedlinePlus