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The Chromosome Microdeletion/duplication Collection

References

Band OMIM Condition Critical region/gene Location Start End Difference
        UCSC Genome Browser on Human May 2004 Assembly (hg17)  
1p36.33 #607872 

1p36 DELETION SYNDROME
(inc HYPERTRICHOTIC OSTEOCHONDRODYSPLASIA 239850%)

 SKI *603055  chr1:2,192,296-2,271,618 2,192,296 2,271,618 79,322
1q21.1 0 1q21.1 MICRODELETION/Thrombocyto
penia-Absent Radius
syndrome (TAR) SYNDROME		 RP11-431G14 -
RP11-772D10
(Redon et al, 2006);
RP11 698N18
(Klopocki et al,
2007)

431G14 chr1:143,845,668-144,024,663 to 772D10 chr1:144,459,424-144,617,808; RP11-698N18: chr1 Chromosome 1 144,111,610 - 144,289,841

 144,111,610 144,289,841 178,231
1q32-q41  #119300 VAN DER WOUDE
SYNDROME; VWS		 no CR        
1q42-q43 #241410  HYPOPARATHYROIDISM-RETARDATION-
DYSMORPHISM SYNDROME
(HRD) MICRODUPLICATION SYNDROME (inc Sanjad-Sakati syndrome and Kenny-Caffey
syndrome 244460)		 TBCE  *604934 chr1:231,856,812-231,938,321 231,856,812 231,938,321 81,509
               
2p24.1  #164280  FEINGOLD SYNDROME MYCN *608025 and surrounding 1 Mb chr2:16,031,281-16,037,726 16,031,281 16,037,726 6,445
2p21 157170 HOLOPROSENCEPHALY 2  SIX3 *603714 (4
microdels in 339
severe HPEs -
Bendavid et al, 2006)		 chr2:45,080,512-45,084,092 45,080,512 45,084,092 3,580
2p15-p16.1 0 2p15-p16.1 MICRODELETION SYNDROME 4.5 Mb (Rajcan-
Separovic et al,
2006)		 57.2 - 61.7 Mb  57,200,000 61,700,000 4,500,000
2p16.3 #606407 HYPOTONIA-CYSTINURIA
SYNDROME		 SLC3A1 and PREPL chr2:44,414,250-44,459,588 and chr2:44,459,617-44,500,595 44,414,250 44,500,590 86,340
2q13 #256100 NEPHRONOPHTHISIS 1 NPHP1 (179,311bp homozygous
deletion)		 chr2:110,237,281-110,319,969 110,237,281 110,319,969 82,688
2q22.3 #235730  MOWAT-WILSON SYNDROME ZFXH1B chr2:144,979,317-145,111,648 144,979,317 145,111,648 132,331
2q31-q32  *142991 SYNPOLYDACTYLY 1; SPD1 EVX2 chr2:176,768,723-176,774,307 176,768,723 176,774,307 5,584
2q31-q32  #186000  SYNPOLYDACTYLY 1 SPD1; BRACHYDACTYLY, TYPE D
BDD 113200;
BRACHYDACTYLY, TYPE E
BDE #113300; 		 HOXD13 (esp
Goodman et al,
2002)		 chr2:176,783,039-176,785,307 176,783,039 176,785,307 2,268
2q31-q32  *142982   SYNPOLYDACTYLY 1; SPD1 HOXD9 chr2:176,812,595-176,815,031 176,812,595 176,815,031 2,436
  188600% SPLIT-HAND/FOOT MALFORMATION 5 No SHFM5 gene yet Centromeric to EVX2 (Goodman et al, 2002)      
2q32.2-q33 0 del(2)(q32.2q33) deletion
syndrome		 8.1 Mb CR from
RP11-347P5 - RP11-
507C18 with aCGH
(Van Buggenhout G
et al, 2005)		 197.2 Mb - 205.3 Mb; SATB2 (NM_015265) at chr2:199959730-200150707 candidate gene (see Britanova O et al, 2006) 199,959,730 200,150,707 190,977
2q37.1 605934% HOLOPROSENCEPHALY 6 No gene yet        
2q37 600430% BRACHYDACTYLY/MR; AHO-
like 3		 HDAC4-tel (Aldred
et al,2004); 1.5Mb
CR		 HDAC4 (NM_006037) at chr2:239706636-240058897; poss subtel polymorphism 239706636 240058897 352,261
               
3p25-p26 0 DISTAL 3p DELETION
SYNDROME		 CR  D3S3630-
D3S1304 (Cargile et
al, 2006); 1.5 Mb CR
from D3S3630 to
RP11-32f23
(Dijkhuizen et al,
2006)		 D3S3630 chr3:2,575,496-2,775,754 to D3S1304 chr3:6,794,242-6,994,583; D3S3630 to RP11-32F23 4,016,397-4,198,468 2,575,496 4,198,468 1,622,972
3p25-p26 *608537  Von Hippel Lindau disease VHL chr3:10,158,319-10,168,744 10,158,319 10,168,744 10,425
3q23 #110100  BLEPHAROPHIMOSIS,
PTOSIS, AND EPICANTHUS INVERSUS; BPES		 FOXL2  chr3:140,145,766-140,148,499;  140,145,766 140,148,499 2,733
    " Upstream position
effect (UPE)		 UPE CR 140,377,649-140,503,837 140,377,649 140,503,837 126,188
    " downstream
position effect
(DPE)		 DPE CR 139,959,089-140,147,132 139,959,089 140,147,132 188,043
3q24 220200% DANDY-WALKER SYNDROME; DWS 7Mb CR inc ZIC1
and ZIC4 (Grinberg
et al, 2004)		 ZIC 1 chr3:148,609,879-148,615,046; ZIC 4 chr3:148,586,535-148,607,105 148,586,535 148,615,046 28,511
3q27 605289 SPLIT-HAND/FOOT MALFORMATION 4 TP73L no deletions      
3q29 609425% 3q29 MICRODELETION
SYNDROME		 1.5 Mb CR  from 1st centromeric deleted
clone to tel		 chr3:197,126,186-197,313,823 - qter 197,126,186 199,505,740 2,379,554
               
4p16.3 #194190 WOLF-HIRSCHHORN
SYNDROME; WHS; WHSCR1		 D4S166 - D4S3327
(Zollino et al, 2003)

chr4: CR 2,043,468(RP11
-262P20) - pter; WHSC1 gene chr4:1,908,239-1,948,753

 1,908,239 1,948,753 40,514
4p16.3 #194190 WOLF-HIRSCHHORN
SYNDROME; WHS; WHSCR2		 D4S3327 - D4S98-
D4S168 (Zollino et
al, 2003)		 WHSC2 gene chr4:1,951,684-1,977,980 1,951,684 1,977,980 26,296
4p16.3 #262350 PITT-ROGERS-DANKS
syndrome		 Allelic to above        
4q21.1-q21.3 0 4q21 microdeletion syndrome inc polycystic kidney disease 4q21 CR for larger
deletions of 4q
(Velinov et al, 2005)		 PKD2 gene (NM_000297) (OMIM 173910)  89285999 89356107 70,108
4q25 180500 RIEGER TYPE 1 PTX2 (RIEG1) chr4:111,758,031-111,777,957 111,758,031 111,777,957 19,926
               
5p15.33-p15.2 123450 CRI-DU-CHAT etc  See Zhang X et al,
2005)		        
5p15.33-p15.32   speech delay CR 3.2 Mb D5S417-D5S635 chr5:3,074,203-3,274,461 - chr5:6,265,580-6,465,938 3,274,461 6,265,580 2,991,119
5p15.32-p15.31   cat cry CR 1.5 Mb D5S2054 - D5S676 chr5:5,844,886-6,045,198 - chr5:7,392,488-7,592,901 6,045,198 7,392,488 1,347,290
5p15.31-p15.31   mental retardation 1 CR 1.2 Mb Clones 15 and 18 chr5:8,021,000 - 9,288,000 8,021,000 9,288,000 1,267,000
5p15.31-p15.2   dysmorphology CR 2.4Mb D5S208-D5S2887 chr5:8,939,505-9,139,654 - chr5:11,388,086-11,588,196 9,139,654 11,388,086 2,248,432
5p13.2 #122470 CORNELIA DE LANGE
SYNDROME; CDLS		 NIPBL chr5:11,388,086-11,588,196 11,388,086 11,588,196 200,110
5q22.2 175100 ADENOMATOUS POLYPOSIS
OF THE COLON; APC
(GARDNER SYNDROME)		 APC chr5:112,101,483-112,209,834 112,101,483 112,209,834 108,351
5q35.1 #187500  5q35 microdeletion syndrome inc TETRALOGY OF FALLOT 2.2 Mb CR inc NKX2-
5 (Baekvad-Hansen
et al, 2006)/NKX2E		 chr5:172,591,744-172,594,868 172,591,744 172,594,868 3,124
5q35.1 264480 HOLOPROSENCEPHALY-POLYDACTYLY SYNDROME; Pseudotrisomy 13 syndrome FBXW11 Koolen et
al, 2006		 chr5:171,221,161-171,366,482 171,221,161 171,366,482 145,321
5q35.2 #168500  PARIETAL FORAMINA; PFM 206kb CR inc MSX2 (123101) (Wilkie et
al, 2000)		 MSX2 (NM_002449) at chr5:174084208-174090507  174084208 174090507 6,299
5q35 #117550  SOTOS (WEAVER SYNDROME) NSD1 chr5:176,493,532-176,655,367 176,493,532 176,655,367 161,835
5q35 0 SOTOS MICRODUPLICATION SYNDROME NSD1 (Kirchhoff et
al, 2006)		 chr5:176,493,532-176,655,367 176,493,532 176,655,367 161,835
               
6p25.3 602482% AXENFELD-RIEGER ANOMALY WITH CARDIAC DEFECTS AND SENSORINEURAL HEARING
LOSS 		 terminal deletion of
6p25 inc FOXC1		 chr6:1,555,680-1,557,341 1,555,680 1,557,341 1,661
6p21.3 201910 0011 ADRENAL
HYPERPLASIA, CONGENITAL,
DUE TO 21-HYDROXYLASE DEFICIENCY, SALT-WASTING TYPE 		 CYP21A2, 30-KB
DEL		 chr6:32,114,061-32,117,398 32,114,061 32,117,398 3,337
6q16.2 *603128 Prader-Willi like  - SINGLE-
MINDED, DROSOPHILA,
HOMOLOG OF, 1; SIM1 		 SIM1 deletion (see
Faivre et al 2002)		 chr6:100,943,472-101,018,272 100,943,472 101,018,272 74,800
6q24.2 601410% TRANSIENT NEONATAL
DIABETES MELLITUS (TNDM) MICRODUPLICATION
SYNDROME		 ZAC (PLAGL1) chr6:144,303,132-144,371,246 144,303,132 144,371,246 68,114
               
7p21.1 #101400 SAETHRE-CHOTZEN
SYNDROME; SCS		 TWIST1 chr7:18,928,331-18,930,265 18,928,331 18,930,265 1,934
7p14.1 #175700 GREIG CEPHALOPOLYSYNDACTYLY SYNDROME GLI3 chr7:41,776,920-42,036,135 41,776,920 42,036,135 259,215
7q11.23 #194050 WILLIAMS-BEUREN
SYNDROME; MICRODELETION AND MICRODUPLICATION SYNDROMES		 1.55 Mb CR between repeats inc ELN1
gene		 ELN chr7:72,887,122-72,927,681 72,887,122 72,927,681 40,559
7q11.23 #609757   WILLIAMS-BEUREN REGION DUPLICATION SYNDROME 1.55 Mb CR between repeats inc ELN1
gene		 ELN chr7:72,887,122-72,927,681 72,887,122 72,927,681 40,559
7q21.3 183600% SPLIT-HAND/FOOT MALFORMATION 1 DSS1 chr7:95,962,731-95,983,854 95,962,731 95,983,854 21,123
7q31.1 #602081 SPEECH-LANGUAGE
DISORDER 1; SPCH1; (inc Developmental verbal
dyspraxia DVD)		 FOXP2 chr7:113,649,227-113,924,106 113,649,227 113,924,106 274,879
7q36 *600725 HOLOPROSENCEPHALY 3 SONIC
HEDGEHOG; SHH
(7 microdels in 339
severe HPEs -
Bendavid et al, 2006)		 chr7:155,095,034-155,104,443 155,095,034 155,104,443 9,409
7q36 #176450  SACRAL AGENESIS
(CURRARINO SYNDROME)		 HLXB9 chr7:156,297,023-156,302,701 156,297,023 156,302,701 5,678
               
8p23.1 0 8p23.1 MICRODELETION/DUPLICATION SYNDROME (inc FRYNS SYNDROME accd Slavotinek et
al (2005))		 REPD-REPP
MFHAS1-CTSB (DECIPHER) 		 chr8:8,680,942-8,787,978 to chr8:11,739,236-11,763,044 (8,156,705-11,803,128) 8,680,942 11,763,044 3,082,102
8p11.2 #147950 KALLMAN 2 FGFR1 chr8:38,389,449-38,445,293 38,389,449 38,445,293 55,844
8q12.2 #214800  CHARGE SYNDROME CHD7 chr8:61,753,893-61,942,017 61,753,893 61,942,017 188,124
8q21.3-q22.1 608156% NABLUS MASK-LIKE FACIAL SYNDROME RP11-100L22 -
RP11-90N3 (RP11-
31K23 not on UCSC browser)		 chr8:93,721,478-93,889,438 - chr8:96,904,503-97,062,457 93,721,478 97,062,457 3,340,979
8q23.3-q24.11 #150230 TRICHORHINOPHALANGEAL SYNDROME, TYPE II; TRPS2 (LANGER-GIEDION) TRPS1 to EXT1 TRPS1 chr8:116,489,900-116,750,429; EXT1 chr8:118,880,787-119,193,239 116,489,900 119,193,239 2,703,339
                
9p24.3 *602424; *604935 9p24 sex reversal deletion sydrome DMRT1 and DMRT2 DMRT1 chr9:831,690-959,088  831,690 959,088 127,398
9p24.3 *602424; *604935   9p24 sex reversal deletion sydrome DMRT1 and DMRT2 DMRT2 chr9:1,041,614-1,047,550 1,041,614 1,047,550 5,936
9p #158170 MONOSOMY 9p SYNDROME 4.7-Mb CR from
RP11-933C16 in
9p23 to D9S285 in
9p22.3 		 (chr9:11,355,596-11,546,331) to  (chr9:15,967,945-16,168,221) 11,355,596 16,168,221 4,812,625
9p13.1-9q21.11 0 PERICENTROMERIC 9p/q euchromatic variant regions 402N8 - 88I18 (ref
Willatt et al, 2006)		 39 Mb and 70 Mb from telomere full of 9p/q duplicons 39,000,000 70,000,000 31,000,000
9q22.32 601309 HOLOPROSENCEPHALY 7 PTCH chr9:95,285,955-95,350,386 95,285,955 95,350,386 64,431
9q22.32 #109400 BASAL CELL NEVUS
SYNDROME;		 PTCH chr9:95,285,955-95,350,386 95,285,955 95,350,386 64,431
9q22.3 0 9q22.3 microdeletion syndrome 6.5 Mb CR (Redon et
al, 2006)		 RP11-333I7 to RP11-96L7 94415600 99098674 4683074
9q33.3 #161200  NAIL-PATELLA SYNDROME;
NPS		 LMX1B chr9:126,456,352-126,538,284 126,456,352 126,538,284 81,932
9q34.3 #610253  9q SUBTELOMERIC DELETION SYNDROME EHMT1 EHMT1 (NM_024757) at chr9:137,881,254-138,006,413 137,881,254 138,006,413 125,159
               
10p14 #146255 HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE GATA3 GATA3 (NM_001002295) at chr10:8136673-8157170  8136673 8157170 20,497
10p12.31 605491 DGS2 NEBL NEBL (NM_006393) at chr10:21110096-21226537  21110096 21226537 116,441
10q22-q23
0 10q22-q23 MICRODELETION SYNDROME 7.2 Mb CR between LCR3 and 4 (Balciuniene et al, 2007) inc candidates NRG3, BMPR1A, SNCG and GLUD1 32 genes inc LOC387693 at chr10:81,654,634-81,700,763 through to FAM22A at chr10:89107457-89120432 81,654,634 89,120,432 7,465,798
10q23.2-q23.3
174900 JUVENILE POLYPOSIS CONTIGUOUS DELETION SYNDROME 2Mb CR inc PTEN and BMPR1A (Delnatte et al, 2006) 1.8 Mb bewteen BMPR1A and LIPF genes 88,623,207 90,446,243 1,823,036
10q24.32 #600095; *608071  SPLIT-HAND/FOOT MALFORMATION 3; SHFM3; MICRODUPLICATION WITH DACTYLIN (FBXW4)
DISRUPTION		 ~ 0.5 Mb dup [inc
LBX1, BTRC, POLL (606343), and
DPCD] with
disruption of FBXW4		 LBX1 (NM_006562) at chr10:102976724-102978707; BTRC (NM_033637) at chr10:103103815-103307058; POLL (NM_013274) at chr10:103328629-103337963 ; RP11-529I10.4 (NM_015448) at chr10:103338079-103359399; FBXW4 (NM_022039) at chr10:103360412-103444733  102976724 103444733 468,009
               
11p15.5 #130650; BECKWITH-WIEDEMAN  SYNDROME INC H19, 1.8-KB
DEL AND LIT1, DEL 		 BWS Microdels H19 chr11:1,972,984-1,975,280 1,972,984 1,975,280 2,296
" " " " KCNQ10T1 (LIT1)     0
11p13 #106210  ANIRIDIA, TYPE II; AN2 PAX6; 607108 PAX6 (NM_001604) at chr11:31768058-31789341 31768058 31789341 21,283
11p14-p13 #194072 WAGR SYNDROME PAX6, WT1 etc PAX6 (NM_001604) at chr11:31768058-31789341; WT1 (X51630) at chr11:32365897-32413643  31768058 32413643 645,585
11p11.2 #601224; #168500
POTOCKI-SHAFFER
SYNDROME (PSS) INC
MULTIPLE EXOSTOSES
(#133701 EXT2) AND PARIETAL FORAMINA (#168500  ALX4);
PSS MR CR		 2.1 Mb, spanning
from D11S1393 to D11D1385/D11S1319
(Wakui et al, 2005);
MR; 1.1 Mb of
11p11.2 between
D11S1361 and
D11S1344		 CR chr11:43,851,376-44,051,689 - chr11:45,893,944-46,094,274; MR chr11:44,802,107-45,002,385 - chr11:46,023,436-46,223,802 43,851,376 46,223,802 2,372,426
11q14.1-q14.2 #133780 *604579 11q14 microdeletion syndrome inc Exudative VitreoRetinopathy (EVR)  ~ 78.6 Mb - 88 Mb
inc FZD4 (Li et al,
2006)		 FZD4 (NM_012193) at chr11:86334370-86344081 - frizzled 4 86,334,370 86,344,081 9,711
11q23.3-qter #147791 11q TERMINAL DELETION SYNDROME JACOBSEN SYNDROME) (inc Paris-
Trousseau thrombocytopenia)		 42 known genes
between FRA11B
and qter
 chr11: 118,100,000 - qter 118,100,000 134,452,384 16,352,384
               
12q14
#166700 12q14 MICRODELETION SYNDROME INC OSTEOPOIKILOSIS (BUSCHKE-OLLENDORFF SYNDROME) 3.44 Mb CR inc LEMD3, HMGA2 and GRIP1 (Menten et al, 2007) LEMD3 (NM_014319) at chr12:63849638-63928374 63849638 63928374 78,736
12q24.1 #163950 NOONAN SYNDROME PTPN11 PTPN11 (NM_002834) at chr12:111319256-111410436 111319256 111410436 91,180
               
13q12.3-q13.1 600185 del(13)(q12.3q13.1) MICRODELETION SYNDROME
INC AR PETERS PLUS
SYNDROME AND BRCA2		 1.5 Mb CR from
RP11-95N14 to
RP11-37E23 (Lesnik Oberstein, S et al,
2005)		 CR INC LGR8 LGR8 (NM_130806) at chr13:31211679-31275009 (assoc testicular maldescent) and BRCA2  31211679 31275009 63,330
" " " " BRCA2 (NM_000059) at chr13:31787617-31871805 31787617 31871805 84,188
13q14.2 180200 RETINOBLASTOMA; RB1 RB1 RB1 (NM_000321) at chr13:47775912-47954023 47775912 47954023 178,111
13q22 #600155 HIRSCHSPRUNG DISEASE 2; HSCR2 INC 13q22 DELETION SYNDROME EDNRB EDNRB (NM_003991) at chr13:77368544-77390935  77368544 77390935 22,391
13q32.3 #609637 HOLOPROSENCEPHALY 5;
HPE5		 ZIC2 *603073 (3
microdels in 339
severe HPEs -
Bendavid et al, 2006)		 ZIC2 (NM_007129) at chr13:99432320-99437019 99432320 99437019 4,699
               
14q12-q13 #604625 OLIGODONTIA PAX9  167416  PAX9 (NM_006194) at chr14:36200656-36215621 36200656 36215621 14,965
14q22-q23 0 14q22-q23 microdeletion
syndrome		 9.66 Mb CR inc
BMP4, OTX2, TRN1,
SIX6, SIX1 and SIX4		 BMP4 (NM_001202) at chr14:53486207-53493362 to SIX4 (NM_017420) at chr14:60246011-60260545  53486207 60260545 6,774,338
               
15q11.2-q13
#176270; #105830 PRADER-WILLI; ANGELMAN MICRODELETION SYNDROME 5 Mb CR inc SNRPN/UBE3A (Sahoo et al, 2005) 5.3 Mb CR between BP2 at chr15:21,129,692-21,314,466 and BP3 at chr15:26,598,041-26,709,341 21,314,466 26,598,041 5,283,575
15q11.2-q13 0 15q11.2-q13 MICRODUPLICATION SYNDROME 5 Mb CR inc SNRPN/UBE3A 5.3 Mb CR between BP2 at chr15:21,129,692-21,314,466 and BP3 at chr15:26,598,041-26,709,341 21,314,466
26,598,041 5,283,575
15q11.2-q13
  PWS/AS IMPRINTING CENTRE MICRODELETIONS ? ~ 880 bp        
15q13.1-q13.3
0 15q13 MICRODELETION SYNDROME (not yet published) 1.2 MB minimum CR between BP3 and BP4 BP3 at chr15:26,598,041-26,709,341 and BP4 at chr15:27,906,178-28,091,821 26,709,341 27,906,178 1,196,837
15q15.3
0 15q15.3 DEAFNESS AND INFERTILITY SYNDROME 100 kb CR inc KIAA0377, CKMT1B, STRC and CATSPER2 (Zhang et al, 2007) KIAA0377 at chr15:41612967-41664383 and CATSPER2 at chr15:41710065-41728331 41612967 41728331 115,364
15q21-q22 0 15q21 MICRODELETION SYNDROME (1 patient so far) 8 Mb CR (See
Pramparo et al,
2005)		       0
15q23-q25.1
 0 15q24 MICRODELETION SYNDROME 1.7Mb minimum CR between BP1 and 2 (Sharp et al, 2007) 72.15 and 73.85 Mb from telomere  72,150,000  73,850,000 1,700,000
15q26.2 142340 DIAPHRAGMATIC HERNIA, CONGENITAL (INC FRYNS SYNDROME) 1 - 2 Mb CR
(Slavotinek et al,
2005)		 chr15: 94,434,555 - 95,865,430 94,434,555 95,865,430 1,430,875
               
16p13.3 #191100  TUBEROUS SCLEROSIS; TS TSC2 (191092) TSC2 (NM_021056) at chr16:2038600-2078713