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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 2038600 2078713 40,113
16p13.3 0 SEVERE RSTS 3' CREBBP plus
DNASE1
DNASE1 (NM_005223) at chr16:3642941-3648096 3642941 3648096 5,155
16p13.3 #180849 RUBINSTEIN-TAYBI
SYNDROME; RSTS
CREBBP; 600140 CREBBP (U85962) at chr16:3717720-3870723 3717720 3870723 153,003
16p13.1
0 16p13.1 MICRODUPLICATION/ DELETION SYNDROME 1.5 Mb CR (Ullmann et al, 2007) BACs RP11-566I03 to RP11-413I10 14,899,000 16,390,000 1,491,000
16q21-q22 0 16q21-q22 microdeletion
syndrome
CBFB (Khan et al,
2006
)
CBFB (NM_022845) at chr16:65620551-65692457 65620551 65692457 71,906
16q24.3 *607139 FANCA GENE; FANCA FANCA - large
intragenic deletions
FANCA (NM_000135) at chr16:88331460-88410555 88331460 88410555 79,095
               
17p13.3 #247200 MILLER-DIEKER
LISSENCEPHALY SYNDROME; MDLS
CR1 LIS1 itself (PAFAH1B1;
601545); MDS
deletions extend telomerically to
CR2 from YWHAE
(14-3-3-epsilon) to
ABR (600365)
(Cardoso et al,
2003
).
CR1 PAFAH1B1 (NM_000430) at chr17:2443686-2535638 to CR2 YWHAE (NM_006761) at chr17:1194595-1250267 to ABR (NM_021962) at chr17:853510-1029881 inclusive 1029881 1194595 164,714
17p13.3 #607432 LISSENCEPHALY I; LIS1 CR LIS1
(PAFAH1B1;
601545) (extends to
PITPNA but NOT
YWHAE) (Cardoso
et al, 2003
)
PAFAH1B1 chr17:2,443,686-2,535,638 (PITPNA at chr17:1368035-1412835 ) 2,443,686 2,535,638 91,952
17p11.2 #118220 CHARCOT-MARIE-TOOTH DISEASE, DEMYELINATING,
TYPE 1A MICRODUPLICATION SYNDROME
PMP22 PMP22 (NM_000304) at chr17:15073822-15109369 15073822 15109369 35,547
17p11.2 #162500 NEUROPATHY, HEREDITARY, WITH LIABILITY TO
PRESSURE PALSIES; HNPP MICRODELETION SYNDROME
PMP22 PMP22 (NM_000304) at chr17:15073822-15109369 15073822 15109369 35,547
17p11.2 #182290 SMITH-MAGENIS SYNDROME; SMS RAI1 *607642 RAI1 (NM_030665) at chr17:17525512-17655488 17525512 17655488 129,976
17p11.2 0 17p11.2 MICRODUPLICATION SYNDROME RAI1 *607642
(Potocki et al, 2007)
RAI1 (NM_030665) at chr17:17525512-17655488 17525512 17655488 129,976
17q11.2 162200 NEUROFIBROMATOSIS, TYPE
I; NF1
NF1; JJAZ1
(interrupted in
common mosaic
cases (buccal
smear better than
blood) Kehrer-
Sawatzki et al,
2004
)
NF1 (NM_000267) at chr17:26446243-26725590; JJAZ1chr17:27,288,185-27,352,162 27,288,185 27,352,162 63,977
17q12 0 17q12 MICRODUPLICATION SYNDROME (1 patient so far) 2.5 Mb CR between
seg dups (Sharp et
al, 2006
)
31.5 - 34 Mb from tel 31,500,000 34,000,000 2,500,000
17q12-q21 *605740 SCLEROSTIN; SOST INC VAN BUCHEM DISEASE 52kb SOST control
region deletion 35kb downstream (1
family, Balemans et
al, 2002
)
SOST (NM_025237) at chr17:39186625-39191682 39186625 39191682 5,057
17q21.31 *610443 CHROMOSOME 17q21.31 MICRODELETION SYNDROME 478kb CR inc MAPT
and CRHR1 (Sharp
et al, 2006
) RP11-
769P22 - RP11-
100C5
RP11-769P22 chr17:41,288,423-41,466,041 to RP11-100C5 chr17:41,178,738-41,346,570 inclusive 41,288,423 41,346,570 58,147
               
18p11.31 #142946 HOLOPROSENCEPHALY 4;
HPE4
TGIF (2 microdels in
339 severe HPEs - Bendavid et al, 2006)
TGIF (NM_170695) at chr18:3441591-3448404 3441591 3448404 6,813
18q12.3-q21.1
0 PROXIMAL 18q MICRODELETION SYNDROME 5 Mb CR (Cody et al, 2007) Multiple candidate genes 37,500,000 42,500,000 5,000,000
18q21.2
#610954 PITT HOPKINS SYNDROME 0.5 Mb CR inc part TCF4 *602272 (Brockschmidt et al, 2007) TCF4 chr18:51,040,560-51,406,858 51,040,560 51,406,858 366,298
18q22.3 0 18q22.3-q23 microdeletion
syndrome
2.3 MB CR from
ZNF407 to GALR1
ZNF407 (NM_017757) at chr18:70474282-70762002 to GALR1 (NM_001480) at chr18:73090721-73111081 70474282 73111081 2,636,799
               
19q13.2 #105650 DIAMOND-BLACKFAN ANEMIA; DBA with MR 3.2 Mb CR inc
RPS19; 603474 (
Tentler et al, 2000)
RPS19 (NM_001022) at chr19:47055828-47067322 47055828 47067322 11,494
               
20p12.2 #118450 ALAGILLE SYNDROME 1;
ALGS1
JAG1; 601920 JAG1 (NM_000214) at chr20:10566334-10602590 10566334 10602590 36,256
20q13.32 #103580 ALBRIGHT HEREDITARY OSTEODYSTROPHY; AHO; PSEUDOHYPOPARATHYROID
ISM, TYPE IA, INCLUDED
GNAS1 (Aldred et al,
2002
)
GNAS (NM_016592) at chr20:56848190-56919640 56848190 56919640 71,450
               
21q22.3 #190685 DOWN SYNDROME DSCR1 (602917) DSCR1 (U28833) at chr21:34810658-34908012 34810658 34908012 97,354
" " " DYRK1A (600855) DYRK1A (NM_130438) at chr21:37714471-37809347 37714471 37809347 94,876
21q22.3 236100% HOLOPROSENCEPHALY 1;
HPE1
TMEM1 candidate
gene only
cTMEM1 (NM_003274) at chr21:44256634-44350858     0
               
22q11.1 #115470 CAT EYE SYNDROME; CES 450-650 kb CR from D22S427 to D22S36 (not in UCSC) (McTaggart et al, 1998); core CR from Il-17R to ATP6E (Footz et al, 2001 esp patient 25105)
D22S427 chr22:16,865,871-17,066,188 plus 450kb equals 17,521,634; IL-17R 15,940,412-15,965,941 and ATP6E 16,449,479-16,486,089 15,940,412 16,486,089 545,677
22q11.2
#188400 DIGEORGE SYNDROME; DGS 3.0 and 1.5 Mb CRs inc TUPLE1 (HIRA) and TBX1 TUPLE1 (HIRA) HIRA (NM_003325) at chr22:17692778-17793773; TBX1 (NM_005992) at chr22:18118780-18145664 18118780 18145664 26,884
22q11.2
#608363 MICRODUPLICATION 22q11.2 TUPLE1 (HIRA) and TBX1 TUPLE1 (HIRA) HIRA (NM_003325) at chr22:17692778-17793773; TBX1 (NM_005992) at chr22:18118780-18145664 18118780 18145664 26,884
22q12.2
#101000 NF2 MICRODELETION SYNDROME (NEUROFIBROMATOSIS TYPE II) NF2, *607379 (Bruder et al, 2001) NF2 (NM_181835) at chr22:28324119-28419137 28,324,119 28,419,137 95,018
22q13.3 #606232 CHROMOSOME 22q13.3
DELETION SYNDROME
Last 100kb of 22q
(Bonaglia et al,
2006
) SHANK3
(ProSAP2) (606230)
SHANK3 *606230 chr22:49403214-49459884 ("non-human Ref Seq gene") 49403214 49459884 56,670
               
Xp22.33 *312865; #127300 SHOX AND LERI-WEILL DYSCHONDROSTEOSIS; LWD SHOX and DPE 30
to 530 kb downstream
SHOX chrX:505,079-532,318 Ref Joh Crolla     0
Xp22.32-p22.31 #300495 AUTISM, X-LINKED, SUSCEPTIBILITY TO, 2 CR PAR boundary- DXS7103 (Thomas
et al, 1999
) inc
NLGN4 (300427)
NLGN4 chrX:5,818,085-6,155,888 5,818,085 6,155,888 337,803
Xp22.31 308100 ICHTHYOSIS, X-LINKED STS chrX:7,147,497-7,282,680 7,147,497 7,282,680 135,183
Xp22.31 308700 KALLMANN SYNDROME 1;
KAL1
KAL1 chrX:8,456,916-8,660,227 8,456,916 8,660,227 203,311
Xp22 #309801 MICROPHTHALMIA,
SYNDROMIC 7; MCOPS7
HCCS gene (300056) chrX:11,039,373-11,051,122 11,039,373 11,051,122 11,749
Xp21.3-p21.2 #300200; #300018 ADRENAL HYPOPLASIA, CONGENITAL; AHC
microdeletions; DOSAGE-
SENSITIVE SEX REVERSAL;
DSS duplications
DAX1 ("non-human RefSeq gene")
(=NR0B1)
DAX1 chrX:30,232,609-30,237,205 30,232,609 30,237,205 4,596
Xp21.2 #310200 MUSCULAR DYSTROPHY, DUCHENNE TYPE; DMD DMD chrX:31,048,667-33,139,448 31,048,667 33,139,448 2,090,781
Xp21.2 *300474 Complex GLYCEROL KINASE; cGKD (Stanczak et al, 2006) DAX1, DMD and GK GK chrX:30,581,461-30,658,645 30,581,461 30,658,645 77,184
Xq13.2 *314670 X INACTIVATION-SPECIFIC TRANSCRIPT; XIST XIST chrX:72,863,307-73,063,491 72,863,307 73,063,491 200,184
Xq22.1 300300 BRUTON
AGAMMAGLOBULINEMIA TYROSINE KINASE; BTK; DEAFNESS/DYSTONIA
PEPTIDE 1 (Richter D et al,
2001
)
BTK + TIMM8A
(DDP) *300356
TIMM8A (NM_004085) at chrX:100406795-100409832; BTK (NM_000061) at chrX:100410587-100447327 100,406,795 100,447,327 40,532
Xq22 #312080 PELIZAEUS-MERZBACHER DISEASE; PMD PLP1; 300401 chrX:102,918,410-102,934,201 102,918,410 102,934,201 15,791
Xq25 #308240 LYMPHOPROLIFERATIVE SYNDROME, X-LINKED
(DUNCAN's DISEASE)
XLP chrX:123,205,729-123,232,540 123,205,729 123,232,540 26,811
Xq27.1 #300123 MENTAL RETARDATION, X-
LINKED, WITH ISOLATED
GROWTH HORMONE
DEFICIENCY; MRGH
SOX3 (313430) chrX:139,310,672-139,312,745 139,310,672 139,312,745 2,073
Xq27.3 309550 FRAGILE SITE MENTAL RETARDATION 1 GENE; FMR1 FMR1 chrX:146,699,055-146,738,157 146,699,055 146,738,157 39,102
Xq28 #300475 CONTIGUOUS
ABCD1/DXS1375E DELETION SYNDROME
ABCD1 chrX:152,511,183-152,531,028 152,511,183 152,531,028 19,845
Xq28 #312750 RETT SYNDROME; RTT MECP2 chrX:152,808,111-152,883,976 152,808,111 152,883,976 75,865
               
Yp11.31 *480000 SEX-DETERMINING REGION Y; SRY SRY chrY:2,698,257-2,699,153 2,698,257 2,699,153 896
Yq11.21 *400003 DELETED IN AZOOSPERMIA;
DAZ
AZFa STSs sY740 chrY:12,781,306-12,981,666 to sY709 chrY:13,532,211-13,732,321 (Blanco et al, 2000); Sharp et al polymorphism chrY:12757298-12924529 12,981,666 13,532,211 550,545
Yq11.223-Yq11.23 *400003 DELETED IN AZOOSPERMIA;
DAZ
AZFc STS SY579 at chrY:23592473-23792736 - (SY579) and at chrY:25206858-25407121 23592473 25407121 1,814,648
        BPY2 (NM_004678) at chrY:23468535-23489733 - variable charge, Y chromosome, 2 protein, at chrY:25102276-25123475 and at chrY:25515177-25536376 23468535 25536376 2,067,841
        DAZ1 (NM_004081) at chrY:23613633-23683282 - deleted in azoospermia and at chrY:25318189-25391306 23613633 25391306 1,777,673
        GOLGA2LY (AF332229) at chrY:24694239-24699103 - golgi autoantigen, golgin subfamily a, 2-like, Y-linked and at chrY:25939583-25944447 24694239 25944447 1,250,208
        CDY1 (NM_170723) at chrY:24530067-24532286 - Y chromosome chromodomain protein 1, telomeric; CDY1 (NM_170723) at chrY:26106389-26108608 - Y chromosome chromodomain protein 1, telomeric; CDY1 (NM_004680) at chrY:24529504-24532286 - Y chromosome chromodomain protein 1, telomeric; CDY1 (NM_004680) at chrY:26106389-26109171 - Y chromosome chromodomain protein 1, telomeric 24529504 26109171 1,579,667
2006 National Genetics Reference Laboratory (Wessex), Salisbury District Hospital, Salisbury SP2 8BJ; Tel: +44 (0)1722 429080; E-mail:ncpc@soton.ac.uk