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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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Schematic representation of SNAP29 gene, cDNA and protein structure. (A) Upper panel is genomic structure of the SNAP29 gene, comprises five exons (numbered 1–5) and 5′ and 3′ untranslated regions (UTRs). Introns are represented by a straight grey line. The structure of 777 bp SNAP29 cDNA is shown in the middle panel. Numbers above the cDNA diagram show the exons (named E1–E5) boundary nucleotide. The vertical dashed grey lines align the location of each exon to the regions of SNAP29 protein that each exon encodes. Numbers below the protein diagram show the contribution of each exon to the amino acid sequence. The SNAP29 protein has a length of 258 amino acid residues and is composed of two domains: coiled-coil (orange box) and t-SNARE (purple box). The position of seven mutations identified in SNAP29 is shown by arrows on cDNA and protein levels. The three mutations identified in this study are coloured in green for insertion and in red for deletion. Black arrows show the position of four previously reported SNAP29 mutations, associated with cerebral dysgenesis, neuropathy, ichthyosis and keratoderma syndrome. (B) Sanger sequencing confirmed all of the mutations identified in this study. Patient 2 and his mother are homozygous for a 5 bp deletion (c.28_32delCCGTT) resulting in a frameshift (p.P10fs) and a premature stop codon 42 amino acids downstream. Patient 3 and 4 carry a homozygous sequence variant resulting in glutamic acid to lysine (p.E89K) and arginine to cysteine (p.R90C) changes, respectively.
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JMEDGENET2012101320F3: Schematic representation of SNAP29 gene, cDNA and protein structure. (A) Upper panel is genomic structure of the SNAP29 gene, comprises five exons (numbered 1–5) and 5′ and 3′ untranslated regions (UTRs). Introns are represented by a straight grey line. The structure of 777 bp SNAP29 cDNA is shown in the middle panel. Numbers above the cDNA diagram show the exons (named E1–E5) boundary nucleotide. The vertical dashed grey lines align the location of each exon to the regions of SNAP29 protein that each exon encodes. Numbers below the protein diagram show the contribution of each exon to the amino acid sequence. The SNAP29 protein has a length of 258 amino acid residues and is composed of two domains: coiled-coil (orange box) and t-SNARE (purple box). The position of seven mutations identified in SNAP29 is shown by arrows on cDNA and protein levels. The three mutations identified in this study are coloured in green for insertion and in red for deletion. Black arrows show the position of four previously reported SNAP29 mutations, associated with cerebral dysgenesis, neuropathy, ichthyosis and keratoderma syndrome. (B) Sanger sequencing confirmed all of the mutations identified in this study. Patient 2 and his mother are homozygous for a 5 bp deletion (c.28_32delCCGTT) resulting in a frameshift (p.P10fs) and a premature stop codon 42 amino acids downstream. Patient 3 and 4 carry a homozygous sequence variant resulting in glutamic acid to lysine (p.E89K) and arginine to cysteine (p.R90C) changes, respectively.

Mentions: In light of this finding, we concluded that the SNAP29 mutation, in conjunction with the 22q11.2 deletion, unmasked the symptoms of CEDNIK syndrome in this patient, including diffuse polymicrogyria (similar to the 2011 Fuchs-Telem et al report14), an ichthyosiform dermatitis with secondary hypohidrosis, atopic dermatitis, and palmoplantar keratoderma. To determine if other patients with 22q11.2DS and similar atypical findings might also have mutations in this gene, we screened the coding exons 5′ and 3′ splice sites of SNAP29 in 12 additional patients by Sanger sequencing. Thereafter, we identified a 5 bp deletion in exon 1 (c.28_32delCCGTT, p.P10fs) in patient 2 (figure 3B). Atypical findings in patient 2 included features consistent with CEDNIK syndrome, as well as with patient 1: microcephaly, polymicrogyria (similar to the structural differences reported by Sprecher et al13), optic nerve hypoplasia, hypertelorism, sensorineural hearing loss, palmoplantar keratoderma, and ichthyosis; additional findings also included a preauricular tag, amblyopia, hypospadias, and type 1 diabetes (figure 1: 2A–F and supplementary data). Sanger sequencing of DNA from the parents of this patient revealed the c.28_32delCCGTT mutation in the mother's DNA (figure 3B). This deletion is predicted to result in a frameshift insertion of 42 novel amino acids before a premature stop in the SNAP29 protein (figure 3B). In addition, these studies also revealed a heterozygous A to G transition (c.317A>G) that would generate a missense (p.Q106R) mutation in the father (see supplementary figure 1). Parent of origin studies, using microsatellite markers, revealed that the proband shares the D22S264 allele with his mother, indicating the 22q11.2 deletion was paternal in origin, consistent with the SNAP29 findings.


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)

Schematic representation of SNAP29 gene, cDNA and protein structure. (A) Upper panel is genomic structure of the SNAP29 gene, comprises five exons (numbered 1–5) and 5′ and 3′ untranslated regions (UTRs). Introns are represented by a straight grey line. The structure of 777 bp SNAP29 cDNA is shown in the middle panel. Numbers above the cDNA diagram show the exons (named E1–E5) boundary nucleotide. The vertical dashed grey lines align the location of each exon to the regions of SNAP29 protein that each exon encodes. Numbers below the protein diagram show the contribution of each exon to the amino acid sequence. The SNAP29 protein has a length of 258 amino acid residues and is composed of two domains: coiled-coil (orange box) and t-SNARE (purple box). The position of seven mutations identified in SNAP29 is shown by arrows on cDNA and protein levels. The three mutations identified in this study are coloured in green for insertion and in red for deletion. Black arrows show the position of four previously reported SNAP29 mutations, associated with cerebral dysgenesis, neuropathy, ichthyosis and keratoderma syndrome. (B) Sanger sequencing confirmed all of the mutations identified in this study. Patient 2 and his mother are homozygous for a 5 bp deletion (c.28_32delCCGTT) resulting in a frameshift (p.P10fs) and a premature stop codon 42 amino acids downstream. Patient 3 and 4 carry a homozygous sequence variant resulting in glutamic acid to lysine (p.E89K) and arginine to cysteine (p.R90C) changes, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

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JMEDGENET2012101320F3: Schematic representation of SNAP29 gene, cDNA and protein structure. (A) Upper panel is genomic structure of the SNAP29 gene, comprises five exons (numbered 1–5) and 5′ and 3′ untranslated regions (UTRs). Introns are represented by a straight grey line. The structure of 777 bp SNAP29 cDNA is shown in the middle panel. Numbers above the cDNA diagram show the exons (named E1–E5) boundary nucleotide. The vertical dashed grey lines align the location of each exon to the regions of SNAP29 protein that each exon encodes. Numbers below the protein diagram show the contribution of each exon to the amino acid sequence. The SNAP29 protein has a length of 258 amino acid residues and is composed of two domains: coiled-coil (orange box) and t-SNARE (purple box). The position of seven mutations identified in SNAP29 is shown by arrows on cDNA and protein levels. The three mutations identified in this study are coloured in green for insertion and in red for deletion. Black arrows show the position of four previously reported SNAP29 mutations, associated with cerebral dysgenesis, neuropathy, ichthyosis and keratoderma syndrome. (B) Sanger sequencing confirmed all of the mutations identified in this study. Patient 2 and his mother are homozygous for a 5 bp deletion (c.28_32delCCGTT) resulting in a frameshift (p.P10fs) and a premature stop codon 42 amino acids downstream. Patient 3 and 4 carry a homozygous sequence variant resulting in glutamic acid to lysine (p.E89K) and arginine to cysteine (p.R90C) changes, respectively.
Mentions: In light of this finding, we concluded that the SNAP29 mutation, in conjunction with the 22q11.2 deletion, unmasked the symptoms of CEDNIK syndrome in this patient, including diffuse polymicrogyria (similar to the 2011 Fuchs-Telem et al report14), an ichthyosiform dermatitis with secondary hypohidrosis, atopic dermatitis, and palmoplantar keratoderma. To determine if other patients with 22q11.2DS and similar atypical findings might also have mutations in this gene, we screened the coding exons 5′ and 3′ splice sites of SNAP29 in 12 additional patients by Sanger sequencing. Thereafter, we identified a 5 bp deletion in exon 1 (c.28_32delCCGTT, p.P10fs) in patient 2 (figure 3B). Atypical findings in patient 2 included features consistent with CEDNIK syndrome, as well as with patient 1: microcephaly, polymicrogyria (similar to the structural differences reported by Sprecher et al13), optic nerve hypoplasia, hypertelorism, sensorineural hearing loss, palmoplantar keratoderma, and ichthyosis; additional findings also included a preauricular tag, amblyopia, hypospadias, and type 1 diabetes (figure 1: 2A–F and supplementary data). Sanger sequencing of DNA from the parents of this patient revealed the c.28_32delCCGTT mutation in the mother's DNA (figure 3B). This deletion is predicted to result in a frameshift insertion of 42 novel amino acids before a premature stop in the SNAP29 protein (figure 3B). In addition, these studies also revealed a heterozygous A to G transition (c.317A>G) that would generate a missense (p.Q106R) mutation in the father (see supplementary figure 1). Parent of origin studies, using microsatellite markers, revealed that the proband shares the D22S264 allele with his mother, indicating the 22q11.2 deletion was paternal in origin, consistent with the SNAP29 findings.

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