Severe intellectual disability, omphalocele, hypospadia and high blood pressure associated to a deletion at 2q22.1q22.3: case report

abstract: ...Background Recently, array-comparative genomic hybridization (aCGH) platforms have significantly improved the resolution of chromosomal analysis allowing the identification of genomic copy number gains and losses smaller than 5Mb. Here we report on a young man with unexplained severe mental retardation, autism spectrum disorder, congenital malformations comprising hypospadia and omphalocele, and episodes of high blood pressure. An~6Mb interstitial deletion that includes the causative genes is identified by oligonucleotide-based aCGH. Results Our index case exhibited a de novo chromosomal abnormality at 2q22 [del(2)(q22.1q22.3)dn] which was not visible at the 550 haploid band level. The deleted region includes eight genes: HNMT, SPOPL, NXPH2, LOC64702, LRP1B, KYNU, ARHGAP15 and GTDC1 . Discussion aCGH revealed an~6Mb deletion in 2q22.1 to 2q22.3 in an as-yet unique clinical case associated with intellectual disability, congenital malformations and autism spectrum disorder. Interestingly, the deletion is co-localized with a fragile site (FRA2K), which could be involved in the formation of this chromosomal aberration. Further studies are needed to determine if deletions of 2q22.1 to 2q22.3 define a new microdeletion syndrome.

... case exhibited a de novo chromosomal abnormality at 2q22 [del(2)(q22.1q22.3)dn] which was not visible at the 550 haploid band level. The deleted region includes eight genes: HNMT, SPOPL, NXPH2, LOC64702, LRP1B, KYNU, ARHGAP15 and GTDC1 . Discussion aCGH revealed an~6Mb deletion in 2q22.1 to 2q22.3 in an as-yet unique clinical case associated with intellectual disability, congenital malformations and autism spectrum disorder. Interestingly, the deletion is co-localized with a fragile site (FRA2K

... and uses S-adenosyl-L-methionine as the methyl donor. This variant (1) represents the longest transcript and it encodes the longest protein (isoform 1). SPOPL NM_001001664 Homo sapiens speckle-type POZ protein-like (SPOPL), mRNA - NXPH2 NM_007226 604635 Homo sapiens neurexophilin 2 (NXPH2), m RNA. - LOC647012 NR_033658 Homo sapiens YY1 transcription factor pseudogene (LOC647012), non-coding RNA. - LRP1B NM_018557 608766 LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 1B LRP1B belongs to the low

... has a complex karyotype involving chromosomes 2, 3 and 5 [ 18 ]. None of the individuals listed in Table 3 shared the exact breakpoints at 2q22.1q22.3 as observed in our patient [ 17 ]. Table 3 Present case and four patients listed at Decipher with similar deletions, ranging from 2q22.1 to 2q22.3, are shown Patient Cytogenetic deletion sex Interval start-end (bp, hg19) Interval (Mb) RefSeq Gene Phenotype This report 2q22.1q22.3 Male 138,750,000144,750,000 6 HNMT, SPOPL, NXPH2, LOC647012, LRP1B, KYNU, ARHGAP15, GTDC1 Omphalocele, cryptorchidism, hypospadia. ID/MR, deep-set eyes, strabismus, thick eyebrow, protruding tongue, small teeth, pointed chin, bulbous nose, wide spaced nipples, hypoplastic nipples, bilateral clinodactyly of fifth finger, non-specific dermatoglyphic patterns, scoliosis, global developmental delay and behavioral disorder. Autism spectrum disorder. 1607 2q22.1q22.3 Female 139,813,180145,063,389 5,25 HNMT, SPOPL, NXPH2, LRP1B, KYNU, ARHGAP15, GTDC1 ID/MR, strabismus, bulbous nasal tip, hypoplastic/inverted/absent nipples. 2566 2q22.2q22.3 Female 143,635,233147,935,002 4,30 LRP1B, KYNU, ARHGAP15, GTDC1 ID/MR, strabismus, thick eyebrows. 250662 2q22.1q22.3 Male 141,232,786147,935,002 6,70 HNMT, SPOPL, NXPH2, LRP1B, KYNU, ARHGAP15, GTDC1 251811 2q22.2q22.3 Female 143,715,235146,369,069 2,65 LRP1B, KYNU, ARHGAP15, GTDC1 LEGEND: important data from five individuals with overlapping intervals are shown. The RefSeq genes and the phenotype columns list only the genes

... this gene is more likely to not exhibit haploinsufficiency [ 17 ]. Finally, genes and/or susceptibility loci on the long arm of chromosome 2 have been recently linked to blood pressure and hypertension by genome-wide association studies, such as STK39 at 2q24.3 [ 30 ]; PMS1 and MSTN , both at 2q32.2 [ 31 ]; DS2S2382 and DS2S338 at 2q35q37 [ 32 ]. Within the region 2q22.12q22.3, no functions have yet been assigned to SPOPL, NXPH2 or LOC647012. HNMT is the only gene currently associated with human

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Gene: NXPH2 - neurexophilin 2 - (NCBI)

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