Table a1 An overview of 63 genes tested using MAPH analysis among 105 DD/CM patients

From: Copy number variation in regions flanked (or unflanked) by duplicons among patients with developmental delay and/or congenital malformations; detection of reciprocal and partial Williams-Beuren duplications

Gene	Chrom. band	Description	GeneID	Location on chromosome	Regions flanked by duplicons	Distance between duplicon
P29	1p35.3	GCIP-interacting protein p29	25949	28755625	28834059–28932575	98 516
PRKAB2	1q21.1	Protein kinase, AMP-activated, beta 2	5565	173584889	171036140–177249592	62 13 452
CAPN2	1q42.11	Calpain 2, large subunit	824	259601508	258169103–259907561	1 738 458
FLJ2204	2q13	Hypothetical protein FLJ22004		117458997	117178230–117635198	456 968
NPHP1	2q13	Nephrocystin	4867	114316563	109925083–116080082	6 154 999
UMPS	3q21.2	Uridine monophosphate synthetase (orotate)	7372	141469386	140479577–143078865	2 599 288
GLUC	4p15.2	Cytosolic beta-glucosidase	2629	25264898	24981138–25427505	446 367
EVC	4p16.2	Ellis van Creveld syndrome protein	2121	6019414	4420622–10868121	6 447 499
P25	5p15.33	Brain-specific protein p25 alpha	11076	1251194	1180464–1306142	125 678
RANBP17	5q35.1	RAN binding protein 17	64901	188–189 Mb	189063686–189213481	149 795
MLN	6p21.31	Motilin	4295	37345065	34908829–40172081	5 263 252
DDC	7p12.2	Dopa decarboxylase (aromatic L-amino acid)	1644	55065653	49777336–61172562	11 395 226
GSBS	7p14.3	G-substrate	10842	34265228	31828578–37665179	5 836 601
JTV1	7p22.1	Multisynthetase complex auxiliary component	7965	6767988	6652376–7723723	1 071 347
TPST1	7q11.21	Tyrosylprotein sulphotransferase 1	8460	68961571	68899125–69000004	100 879
FKBP6 ^a	7q11.23	FK506-binding protein 6	8468	70913203	70865853–71592416	726 563
TBL2 ^a	7q11.23	Transducin (beta)-like 2	26608	^*	70865853–71592416	see above
ELN ^a	7q11.23	Elastin	2006	^*	70865853–71592416	see above
CYLN2 ^a	7q11.23	Cytoplasmic linker 2	7461	^*	70865853–71592416	see above
ARHGEF5	7q35	Rho guanine nucleotide exchange factor 5	7984	156140962	155961558–156151892	190 334
CENTG3	7q36.1	MRIP-1 protein	116988	163305750	161981314–166427628	4 446 314
di-RAS2	9q22.2	GTP-binding RAS-like 2	54769	99459475	99072373–99615625	543 252
PTCH	9q22.32	Patched (Drosophila) homolog	5727	107463432	105649233–108546485	2 897 252
FANCC	9q22.33	Fanconi anaemia, complementation group C	2176	107816739	105649233–108546485	See above
RSU1	10p13	ras suppressor protein 1	6251	17763985	17343558–17953656	610 098
KIAA0187	10q11.21	KIAA0187 gene product	9790	45421390	45331297–47906414	2 575 117
SDF1	10q11.21	Stromal cell-derived factor 1	6387	47064383	45331297–47906414	See above
PPYR1	10q11.22	Pancreatic polypeptide receptor 1	5540	49145372	49021238–54773984	5 752 746
SGPL1	10q22.1	Sphingosine-1-phosphate lyase 1	8879	77278049	75454903–80191770	4 736 867
TACR2	10q22.1	Tachykinin receptor 2	6865	75719214	75454903–80191770	See above
PAPSS2	10q23.31	3′ phosphoadenosine 5′ phosphosulphate	9060	88057489	86760491–88848332	2 087 841
FLJ22794	11q12.1	Hypothetical protein FLJ22794	63901	65208275	65086253–65169286	83 033
CD5	11q12.2	CD5 antigen (p56–62)	921	67565428	67348654–67606043	257 389
FADD	11q13.3	Fas (TNFRSF6)-associated via death domain	8772	79700968	77157096–82393752	5 236 656
ICEBERG	11q22.3	ICEBERG caspase-1 inhibitor	59082	120243026	120179983–120328323	148 340
HNT	11q25	Neurotrimin precursor	50863	151230535	151288128–151483616	195 488
CLECSF12	12p13.2	C-type lectin domain family c7, member Ca dep.	64581	10905383	10753561–11533368	779 807
CNTN1	12q12	Contactin 1	1272	45800931	45700335–47233112	1 532 777
DKFZp434B0417	12q12	Hypothetical protein DKFZp434B0417		46680635	45700335–47233112	see above
TMEM5	12q14.2	Transmembrane protein 5	10329	72955978	72479865–73099895	620 030
CKAP2	13q14.3	Cytoskeleton-associated protein 2	26586	52929838	52126921–53081328	954 407
NDN ^b	15q11.2	Necdin	4692	19787505^*	17304292–19469943	2 165 651
UBE3A ^c	15q12	Ubiquitin protein ligase E3A	7337	21515963^*	20279911–20507618	227 707
LTK	15q15.1	Tyrosine kinase	4058	38501171	35955283–41645045	5 689 762
NMB	15q25.2	Neuromedin B	4828	88362943	85255238–88736771	3 481 533
NADRIN	16p12.1	Neuronal protein	55114	29985255	14335149–35125392	20 790 243
NUDE1	16p13.11	Lis-1 interacting protein	54820	18763116	14335149–35125392	See above
TAT	16q22.2	Tyrosine aminotransferase	6898	85891517	82945639–89466425	6 520 786
CFDP1	16q23.1	Craniofacial development protein 1	10428	90635426	90575990–90735398	159 408
DRG2 ^d	17p11.2	Developmentally regulated GTP binding protein 2	1819	19787405	15371266–27948279	12 577 013
COPS3 ^d	17p11.2	Homo sapiens COP9 complex subunit 3	8533	19038181	15371266–27948279	See above
RAI1 ^d	17p11.2	Retinoic acid induced 1	10743	19492572	15371266–27948279	See above
NF1	17q11.2	Neurofibromin	4763	32548362	31949051–33721569	1 772 518
ACACA	17q12	Acetyl-coenzyme A carboxylase alpha	31	38913111	37945776–39868543	1 922 767
ASPA	17p13.2	Aspartoacylase	443	3267932	3120079–3546982	426 903
CLTC	17q23.2	Clathrin heavy chain	1213	65270461	65066121–65736364	670 243
TBX2	17q23.2	T-box 2	6909	67106821	65739747–68308666	2 568 919
IMPA2	18p11.21	Inositol(myo)-1(or 4)-monophosphatase 2	3613	13146682	12188020–13392618	1 204 598
LIPG	18q21.1	Endothelial lipase precursor	9388	54173714	54104840–54449609	344 769
FLJ14686	19q13.12	Zinc-finger protein 382	84911	44915972	44764587–46070350	1 305 763
NOSIP	19q13.33	Nitric oxide synthase interacting protein	51070	61526455	59278949–62006526	2 727 577
SPIB	19q13.33	Spi-B transcription factor (Spi-1/PU.1 related)	6689	62489290	62019412–62726350	706 938
ECR2 ^e	22q11.1	Cat eye syndrome chromosome region, candidate	27443	14900358	13950072–21770926	7 820 854
DGCR2 ^f	22q11.2	DiGeorge syndrome critical region gene 2	9993	15882238	13950072–21770926	See above
ADRBK2	22q12.1	Beta adrenergic receptor kinase 2	157	22657045	13950072–21770926	See above

The probes were designed using exon-specific single-copy sequences located in regions defined at a first pass by Bailey et al.¹¹ The localisation of the sequences is based on the Human Working draft of August 2001, as the duplicon data of Bailey is based on this information. Some of the probes tested were localised within the regions related to microdeletion syndromes: ^aWilliams syndrome. ^bPrader Willi. ^cAngelman syndrome. ^dSmith Magenis syndrome. ^eCat eye syndrome. ^f22q11del/dup syndrome. ^*These genes are now known to be located in the WBCR; however, in the Human Working Draft of August 2001, these genes were located outside the Williams-related duplicons.
The sum of all basepairs that are localised between two homologous intrachromosomal duplicons and tested in this study is 155 556 588 bp. This resembles 5.2% of the total human genome. The sum of all basepairs localised between duplicons and not tested in this study is 4.6% (calculation not shown). The total percentage of the genome flanked by duplicons identified at a first pass in 2001 is 9.8%.

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Table a1 An overview of 63 genes tested using MAPH analysis among 105 DD/CM patients

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