Table 1.

Syndromes Caused by Recurrent Deletions and Duplications

Deletion/Duplication Syndrome (Chromosome Locus) 1Approximate SizeISCA ID 2Region Location 3Genes of
Interest in
This Region
1q21.1 recurrent microdeletion 1.35 MbISCA-37421GRCh38/hg38 chr1: 147,105,904-147,922,392 GJA5
GJA8
3q29 recurrent deletion 1.6 MbISCA-37443GRCh38/hg38 chr3: 196,029,183-197,617,791 DLG1
FBXO45
PAK2
RNF168
3q29 duplication syndrome (OMIM 611936)
Sotos syndrome
(5q35 deletion)		1.9 MbISCA-37425GRCh38/hg38 chr5: 176,301,976-177,620,792 NSD1
Williams syndrome (7q11.23 deletion)1.5-1.8 MbISCA-37392GRCh38/hg38 chr7: 73,330,452-74,728,172 LIMK1
FTF2I
STX1A
BAZ1B
CLIP2
GTF2IRD1
NCF1
7q11.23 duplication syndrome ELN
GTF2I
10q22.3-q23.2 deletion syndrome (OMIM 612242)7 MbISCA-37424GRCh38/hg38 chr10: 79,923,087-86,979,631 BMPR1A
GRID1
NRG3
Angelman syndrome
(15q11.2-q13 maternal deletion)		7 Mb 4ISCA-37404GRCh38/hg38 chr15: 22,782,170-28,134,728 UBE3A
5 Mb 5ISCA-37478GRCh38/hg38 chr15: 23,465,365-28,134,728
Prader-Willi syndrome
(15q11.2-q13 paternal deletion)		7 Mb 4ISCA-37404GRCh38/hg38 chr15: 22,782,170-28,134,728 SNURF-SNRPN
OCA2
NECDIN
MAGEL2
SNORD116
5 Mb 5ISCA-37478GRCh38/hg38 chr15: 23,465,365-28,134,728
15q duplication syndrome 6
(15q11.2-q13.1)		7 Mb 4ISCA-37404GRCh38/hg38 chr15: 22,782,170-28,134,729 UBE3A
GABRB3
GABRA5
GABRG3
HERC2
5 Mb 5ISCA-37478GRCh38/hg38 chr15: 23,513,243-28,312,040
15q13.3 microdeletion ~2.0 Mb 7ISCA-37411GRCh38/hg38 chr15: 30,900,686-32,153,204 CHRNA7
OTUD7A
16p12.2 recurrent deletion 520 kbNAGRCh37/ hg19 chr 16: ~21,950,000-~22,470,000 UQCRC2
CDR2
POLR3E
EEF2K
MOSMO
16p11.2 recurrent microdeletion 593 kbISCA-37400GRCh38/hg38 chr16: 29,638,676-30,188,531 PRRT2
KCTD13
TBX6
16p11.2 duplication syndrome (OMIM 614671)593 kbUnknown
16p11.2 deletion syndrome, 220-kb (OMIM 613444)220 kbISCA-37486GRCh38/hg38 chr16: 28,811,314-29,035,178 SH2B1
Hereditary neuropathy with liability to pressure palsies
(17p12 deletion)		1.5 MbISCA-37436GRCh38/hg38 chr17: 14,194,598-15,519,638 PMP22
Charcot-Marie-Tooth neuropathy type 1A (17p12 duplication; OMIM 118220)
Smith-Magenis syndrome (17p11.2 deletion)3.7 MbISCA-37418GRCh38/hg38 chr17: 16,906,714-20,309,889 RAI1
Potocki-Lupski syndrome (17p11.2 duplication)
Neurofibromatosis 1 (17q11.2 deletion)1.0-1.4 MbISCA-37431GRCh38/hg38 chr17: 30,780,079-31,937,008 NF1
17q11.2 duplication syndrome (OMIM 613675)
17q12 recurrent deletion syndrome 1.4 MbISCA-37432GRCh38/hg38 chr17: 36,458,167-37,854,616 ACACA
LHX1
HNF1B
17q12 recurrent duplication HNF1B
Koolen-de Vries syndrome (17q21.31 deletion)500 kbISCA-37420GRCh38/hg38 chr17: 45,627,800-46,087,514 KANSL1
22q11.2 deletion syndrome 1.5 MbISCA-37433GRCh38/hg38 chr22: 18,924,718-20,299,685 TBX1
3 MbISCA-37446GRCh38/hg38 chr22: 18,924,718-21,111,383
22q11.2 duplication (OMIM 608363)1.5 MbISCA-37433GRCh38/hg38 chr22: 18,924,718-20,299,685Unknown
3 MbISCA-37446GRCh38/hg38 chr22: 18,924,718-21,111,383
22q11.2 deletion syndrome, distal (OMIM 611867)1.1-2.1 Mb 9ISCA-37397GRCh38/hg38 chr22: 21,562,828-23,306,924 TOP3B
22q11.2 duplication syndrome, distal 8Unknown
Xq28 duplication (OMIM 300815)0.3 MbISCA-37439GRCh38/hg38 chrX: 154,396,223-154,555,683 GDI1
Xq28 duplication syndrome, Int22h1/Int22h2 mediated 0.5 MbISCA-37494GRCh38/hg38 chrX: 154,890,328-155,335,092 CLIC2
RAB39B
1.

Data are compiled from the following standard references: chromosome locus from OMIM, genes from HGNC.

2.

Standardized clinical annotation and interpretation for genomic variants from the Clinical Genome Resource (ClinGen) project (formerly the International Standards for Cytogenomic Arrays [ISCA] Consortium)

3.

Genomic coordinates represent the minimum deletion/duplication size as designated by ClinGen. Coordinates may vary slightly based on array design used by the testing laboratory. Note that the size of the microdeletion/microduplication as calculated from these genomic positions may differ from the expected size due to the presence of segmental duplications near breakpoints.

4.

Class 1 deletion/duplication, extending from BP1 to BP3

5.

Class 2 deletion/duplication, extending from BP2 to BP3

6.

Approximately 80% of individuals have a maternal isodicentric 15q11.2-q13.1 supernumerary chromosome – idic(15) – that typically comprises two extra copies of 15q11.2-q13.1, resulting in tetrasomy for 15q11.2-q13.1. Approximately 20% of individuals have one extra copy.

7.

Extending from BP4 to BP5

8.
9.

Includes deletions extending from LCR22-D to either LCR22-E or –F

From: Educational Materials — Genetic Testing: Current Approaches

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