Table 1.
Rearrangement details and clinical features of patients included in the present study
| Case ID | SV structure | ISCN 2020/HGVS nomenclature | Main phenotype | Clinical assessment |
|---|---|---|---|---|
| P1 | Unbalanced translocation, DEL | seq[GRCh38] der(4)t(4;9)(q34.3;p23), del(16)(p12.1p11.2) NC_000004.12:g.181414917_qterdelins[NC_000009.12:g.pter_13043905] NC_000016.10:g.28455071_29508000del |
Mild ID and obesity. Strabismus (exotropia), hypermetropia, and astigmatism. Features include a large forehead, narrow eye slits, prominent labial furrows, and skin hyperpigmentation. | Pathogenic/pathogenic |
| P2 | Isodicentric chromosome | seq[GRCh38] 15q11.1q13.2(19799420_30095350x3-4)dn,15q13.2q13.3(30521460_32201830x2-3)dn | Suspected global developmental delay. Epilepsy, spasms. | Pathogenic |
| P3 | DEL-INV-DEL | seq[GRCh38] 22q13.33q13.33(50624868_50626276)x0 NC_000022.11:g.50618055_50626277delins[NC_000022.11:g.50624361_50624868inv] NM_000487.6(ARSA):c.[857_*277del];[857_*277del] p.(Pro286_Ala509delins8) |
Normal development in the first year. Progressive loss of functions, muscle weakness, areflexia, ptosis, and swallowing difficulties in the second year. | Pathogenic |
| P4 | DUP-TRIP-QUAD-TRIP-DUP-NML-DEL, DEL-INV-DEL | seq[GRCh38] der(2)ins(2)(p25.1p25.2p25.2)ins(2)(p25.1p25.1p25.2)ins(2)(p25.1p25.2p25.2)del(p25.1p25.1), del(q21.2)ins(2)(q21.2q22.1q21.2) NC_000002.12:g.7246507_7734100delins[g.5620671_6248808inv;g.5549092_7241289inv;g.5858296_6246303],g.132954122_141163928delins[g.133434126_137703180inv] |
Syndromic craniofacial condition | Likely pathogenic/likely pathogenic |
| P5 | DEL-INV-NML-DUP-NML-DUP | seq[GRCh38] der(3)del(3)(p14.3p14.2)inv(3)(p14.2p14.2)ins(3)(p14.2q22.2q22.2)ins(3)(p12.2q24q24) NC_000003.12:g.54518907_80981660delins[g.59407900_63614153inv;g.135767535_135891958;g.63614153_80981660inv] |
Motor delay | Pathogenic |
| P6 | Translocated insertion | seq[GRCh38] der(X)del(X)(q28q28)ins(X;9)(q28;q22.33q22.33) NC_000023.11:g.153724706_153779639delins[NC_000009.12:g.97596764_97598236inv] |
Adrenoleukodystrophy | Pathogenic |
| P7.1 | Translocation, INV | seq[GRCh38] t(1;10)(p36.2;q24), inv(2)(q32.2q33.2) NC_000001.11:g.19783172_qterdelins[NC_000010.11:g.pter_95395335] NC_000010.11:g.pter_95395328delins[NC_000001.11:g. 19783105_qter] NC_000002.12:g.189694535_202576083inv |
Recurrent miscarriages | Pathogenic Pathogenic |
| P7.2 | NA | NA | Healthy father of P7.1 | NA |
| P7.3 | NA | Same as P7.1 | Healthy mother of P7.1 | NA |
| P8.1 | DUP-INV-DUP | seq[GRCh38] der(X)ins(X)(p22.2q28q28)inv(X)(p22.2q28)ins(X)(q28p22.2p22.31) NC_000023.11:g.9768910_154113036delins[g.9420014_154208530inv] |
Short stature | Pathogenic |
| P8.2 | NA | Same as P8.1 | Healthy, normal height | NA |
| P9 | Translocation | 47,XX,t(X;9)(p22;q12)[27]/46,X,t(X;9)(p22;q12)[3].seq[GRCh38] t(X;9)(p22.33;q21.13) NC_000009.12:g.pter_(75862011)delins[NC_000023.11:g.3044233_qter] NC_000023.11:g.3044228_qterdelins[NC_000009.12:g.pter_(75862011)] |
Thrombocytopenia, early menopause, learning difficulties | Likely pathogenic |
| P10 | Ring chromosome, DEL | 46,XY,r(21)(p11q22)[9]/46,XY, del(21)(q22.3)[4]/46,XY[12] | Infertility, oligospermia | VUS |
| P11 | DUP-NML-DEL | seq[GRCh38] der(X)ins(X)(q22p11.21p22.33)del(X)(q22q28) NC_000023.11:g.101431832_qterdelins[g.pter_55349282inv] |
ID, delayed puberty | Likely pathogenic |
| P12 | Complex translocation | seq[GRCh38] t(1;4;6;4)(p32.2;q21.1;p22.3;q22.3q24), del(6)(p12.3p12.3) NC_000001.11:g.pter_58205785delins[NC_000004.12:g.106505092_qterinv] NC_000004.12:g. 80390384_qterdelins[NC_000006.12:g.pter_20052376inv] NC_000006.12:g.20052374_pterdelins[NC_000004.12:g.94218568_106505089inv;NC_000001.11:g.20052374_pter] NC_000006.12:g. 48002694_49160076 del |
Neonatal hypotonia, ID, short stature | Pathogenic |
| P13 | Unknown insertion | 46,XY,add(21)(p1?3) | Infertility, oligoasthenozoospermia | VUS |
(SV) structural variant, (DEL) deletion, (INV) inversion, (DUP) duplication, (TRIP) triplication, (QUAD) quadruplication, (NML) normal (copy number), (NA) not applicable, (ISCN) the international system of for human cytogenomic nomenclature, (HGVS) human genome variation society nomenclature, (DEL) deletion, (INV) inversion, (DUP) duplication, (TRIP) triplication, (QUAD) quadruplication, (NML) normal copy number, (ID) intellectual disability, (VUS) variant of uncertain significance. Unresolved rearrangements are shown in gray.