PMC10277930_01
Brain magnetic resonance imaging (MRI), Sanger sequencing, and quantitative polymerase chain reaction (q-PCR). (A) Brain MRI of the patient at 8 months of age. T1: Cerebellar and brain stem hypoplasia with a characteristic flattening (red arrow). T2: Pachygyria-polymicrogyria of frontotemporal lobes (type "cobblestone pavement") (yellow arrows) and white matter lesions (white arrows). T2: Multiple subcortical cerebellar cysts (green arrows). (B) Sanger sequencing showed a homozygous c.636C>T variant in exon 7 of the POMGNT1 gene (NM_001243766) in the patient. His father had a heterozygous c.636C>T variant, and his mother had no variant in this site. (C) Q-PCR of DNA showed a normal copy number in exon 7 of POMGNT1 in the patient.
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Sanger sequencing revealed that the father had a heterozygous c.636C>T variant, but the mother had no variant at this site (Figure 1B). However, no abnormalities were found (Figure 1C), suggesting that there may be another cause of the homozygous variant.
PMC10277930_02
Brain magnetic resonance imaging (MRI), Sanger sequencing, and quantitative polymerase chain reaction (q-PCR). (A) Brain MRI of the patient at 8 months of age. T1: Cerebellar and brain stem hypoplasia with a characteristic flattening (red arrow). T2: Pachygyria-polymicrogyria of frontotemporal lobes (type "cobblestone pavement") (yellow arrows) and white matter lesions (white arrows). T2: Multiple subcortical cerebellar cysts (green arrows). (B) Sanger sequencing showed a homozygous c.636C>T variant in exon 7 of the POMGNT1 gene (NM_001243766) in the patient. His father had a heterozygous c.636C>T variant, and his mother had no variant in this site. (C) Q-PCR of DNA showed a normal copy number in exon 7 of POMGNT1 in the patient.
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Sanger sequencing revealed that the father had a heterozygous c.636C>T variant, but the mother had no variant at this site (Figure 1B). However, no abnormalities were found (Figure 1C), suggesting that there may be another cause of the homozygous variant.
Analysis of uniparental disomy (UPD) using trio-based whole-exome sequencing (trio-WES). It showed that paternal UPD existed on chromosome 1. UI_P: Uniparental Paternal Isodisomy. UA_P: Uniparental Paternal Heterdisomy. UI_M: Uniparental Maternal Isodisomy. UA_M: Uniparental Maternal Heterdisomy. BPI: Bi-Parental Inheritance. Het: Heterozygous. Hom: Homozygous.
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As a result, a possible paternal UPD on chromosome 1 of the patient was identified using trio-WES data analysis (Figure 2), which revealed the homozygous variant, and no other pathogenic variants were detected.
Chromosomal microarray analysis (CMA) and RNA sequencing (RNA-seq). (A) CMA showed a 120,451 kb loss of heterozygosity (LOH) on 1p36.33-p11.2 (888,658_121,339,317) and a 99,319 kb LOH on 1q21.2-q44 (149,879,544_249,198,164). The former encompassed the POMGNT1 gene. (B) RNA-seq showed skipped exon 7 in the POMGNT1 mRNA of the patient and the father. RPKM: Reads Per Kilobase per Million mapped reads. IncLevel: Inclusion Level.
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Finally, chromosomal microarray analysis (CMA) of the patient revealed a 120,451 kb loss of heterozygosity (LOH) on 1p36.33-p11.2 (888,658_121,339,317), encompassing POMGNT1, and a 99,319 kb LOH on 1q21.2-q44 (149,879,544_249,198,164) (Figure 3A). It was confirmed to cause the skipping of exon 7 in the POMGNT1 mRNA (Figure 3B), resulting in a frameshift change (p.Asp179Valfs*23).