Table 2.
CNVs detected in this study.
| Family-ID | Family members | Affected region | Ensembl genome browser | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Location (hg19) CytoscanHD nomenclature | Location (hg19) HGVS nomenclaturea | Start | End | Size (Kbp) | CN status | Gene count | Within known CNVb | Gene of interest | Physical locationc | Physical locationd (sequence direction) | Transcript ID | Exons order (numbering) | Exons harboring the CNV start-end (physical location) | Introns harboring the CNV start-end (physical location) | ||
| F5 | P (M) | arr[hg19] 22q13.33(51,073,379–51,197,838)×1 | NC_000022.10:g.(?_51073379)_(51197838_?)del | 51,073,379 | 51,197,838 | 124.459 | Loss (het) | 3 | Y | SHANK3 | chr22:51,113,070–51,171,640 | chr22: 51,113,070–51,171,641 forward strand | NM_033517/ENST00000262795.3 | 1–23 | Entire gene | Entire gene |
| US (F) | arr[hg19] 22q13.33(51,073,379–51,197,725)×1 | NC_000022.10:g.(?_51073379)_(51197725_?)del | 51,073,379 | 51,197,725 | 124.346 | Loss (het) | 3 | Y | ||||||||
| US (M) | arr[hg19] 22q13.33(51,130,158–51,183,869)×1 | NC_000022.10:g.(?_51130158)_(51183869_?)del | 51,130,158 | 51,183,869 | 53.711 | Loss (het) | 3 | Y | ||||||||
| UM | arr[hg19] 22q13.33(51,073,379–51,197,838)×1 | NC_000022.10:g.(?_51073379)_(51197838_?)del | 51,073,379 | 51,197,838 | 124.459 | Loss (het) | 3 | Y | ||||||||
| UF | arr[hg19] 22q13.33(51,073,265–51,197,838)×1 | NC_000022.10:g.(?_51073265)_(51197838_?)del | 51,073,265 | 51,197,838 | 124.573 | Loss (het) | 3 | Y | ||||||||
| F10 | P (F) | arr[hg19] 9q34.3(139,252,010–139,435,356)×3 | NC_000009.11:g.(?_139252010)_(139435356_?)dup | 139,252,010 | 139,435,356 | 183.346 | Gain | 11 | Y | NOTCH1 | chr9:139,388,896–139,440,238 | chr9: 139,388,896–139,440,314 reverse strand | NM_017617/ENST00000277541.6 | 1–34 | From exon 3 to exon 34 139,418,431–139,388,896 | From intron (2–3) to (33–34) 139,438,475–139,392,011 |
| AS (M) | No change | – | – | – | – | – | – | – | ||||||||
| UF | No change | – | – | – | – | – | – | – | ||||||||
| UM | arr[hg19] 9q34.3(139,114,307–139,435,356)×3 | NC_000009.11:g.(?_139114307)_(139435356_?)dup | 139,114,307 | 139,435,356 | 321.049 | Gain | 13 | Y | ||||||||
| F15 | P (F) | arr[hg19] 22q13.33(51,127,896–51,197,725)×1 | NC_000022.10:g.(?_51127896)_(51197725_?)del | 51,127,896 | 51,197,725 | 69.829 | Loss (het) | 3 | Y | SHANK3 | chr22:51,113,070–51,171,640 | chr22: 51,113,070–51,171,641 forward strand | NM_033517/ENST00000262795.3 | 1–23 | From exon 10 to exon 23 51,133,203–51,160,865 | Parts of intron (9–10) to intron (22–23) 51,123,080–51,160,865 |
| US (M) | No change | – | – | – | – | – | – | – | ||||||||
| US (F) | No change | – | – | – | – | – | – | – | ||||||||
| US (F) | No change | – | – | – | – | – | – | – | ||||||||
| UM | No change | – | – | – | – | – | – | – | ||||||||
| UF | No change | – | – | – | – | – | – | – | ||||||||
| F17 | P (F) | arr[hg19] 9q34.3(139,375,930–139,435,356)×3 | NC_000009.11:g.(?_139375930)_(139435356_?)dup | 139,375,930 | 139,435,356 | 59.426 | Gain | 4 | Y | NOTCH1 | chr9:139,388,896–139,440,238 | chr9: 139,388,896–139,440,314 reverse strand | NM_017617/ENST00000277541.6 | 1–34 | From exon 3 to exon 34 139,418,431–139,388,896 | From intron (2–3) to (33–34) 139,438,475–139,392,011 |
| AS (M) | No change | – | – | – | – | – | – | – | ||||||||
| US (M) | No change | – | – | – | – | – | – | – | ||||||||
| US (M) | arr[hg19] 9q34.3(139,053,501–139,654,647)×3 | NC_000009.11:g.(?_139053501)_(139654647_?)dup | 139,053,501 | 139,654,647 | 601.146 | Gain | 27 | Y | ||||||||
| UM | No change | – | – | – | – | – | – | – | ||||||||
| UF | arr[hg19] 9q34.3(139,056,879–139,431,947)×3 | NC_000009.11:g.(?_139056879)_(139431947_?)dup | 139,056,879 | 139,431,947 | 375.068 | Gain | 14 | Y | ||||||||
| F19 | P (M) | arr[hg19] 14q31.1(79,342,954–79,397,500)×1 | NC_000014.8:g.(?_79342954)_(79397500_?)del | 79,342,954 | 79,397,500 | 54.546 | Loss (het) | 1 | Y | NRXN3 | chr14:78,870,074–80,334,633 | chr14: 78,870,093–80,328,786 forward strand | NM_004796/ENST00000554719.1 | 1–17 | NA | Parts of intron (7–8) 79,276,688–79,423,584 |
| US (F) | arr[hg19] 14q31.1(79,342,954–79,401,388)×1 | NC_000014.8:g.(?_79342954)_(79401388_?)del | 79,342,954 | 79,401,388 | 58.434 | Loss (het) | 1 | Y | ||||||||
| US (F) | arr[hg19] 14q31.1(79,342,954–79,397,500)×1 | NC_000014.8:g.(?_79342954)_(79397500_?)del | 79,342,954 | 79,397,500 | 54.546 | Loss (het) | 1 | Y | ||||||||
| AF | No change | – | – | – | – | – | – | – | ||||||||
| UM | arr[hg19] 14q31.1(79,342,954–79,401,337)×1 | NC_000014.8:g.(?_79342954)_(79401337_?)del | 79,342,954 | 79,401,337 | 58.383 | Loss (het) | 1 | Y | ||||||||
P proband, UM unaffected mother, AF affected father, AS affected sibling, UF unaffected father, M male, F female.
aInformation about deletion/duplication breakpoints were not available nor the position of the first or last normal nucleotides. Therefore CNV description was based on HGVS recommendations for describing variants for which not all details are available.
bCNVs identified here that are wholly or partially contained within regions reported in the Database of Genomic Variants (DGV) [http://dgv.tcag.ca/dgv/app/home].
cGenes positions are based on UCSC Genome Browser on Human Feb. 2009 (GRCh37/hg19) Assembly.
dPhysical location based on Ensembl Genome browser.