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Table 2 Developmental regulatory genes with assigned human disease

From: Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes

Target gene Disease/syndrome (OMIM) Conserved gene order hs/gg Conserved gene orderhs/dr/tn (distance in human genome) Number of neighboring genes kept (hs/gg-hs/dr) Chromosome locus human Ref.
PTCH Nevoid basal cell carcinoma (#109400), medulloblastoma (#155255), basal cell carcinoma (#605462), holoprosencephaly-7 (#610828) 2.5 Mb; gene desert 1.6 MB 8/5 9q22.3 [93]
WT1 a Wilms tumor (#194070), Deny-Drash syndrome (#194080) >4 Mb 3 Mb/0.4 Mb >16/9/1 11p13 [94]
MAF (position effect) Cataract (#610202) >3.5 Mb; gene desert; WWOX bystander 2.5 Mb 5/2 16q23 [95]
CHD7 Charge syndrome (#214800) >2 Mb; gene desert 0.8 Mb 2/1 8q12.1 [96]
DLX5/DLX6 (position effect) Ectrodactyly; split hand/foot malformation 1 (%183600) >2 Mb; gene desert; shfm1 bystander 1.5 Mb 4/2 7q22 [97]
SOX9a (position effect) Campomelic dysplasia (#114290) >6 Mb; gene desert ? >8/0 17q24.3 [98]
FOXC1/FOXQ1/FOXF2 (position effect) Glaucoma; Rieger's anomaly (#601631) >2 Mb GMDS bystander 1 Mb 2/2 6p25.3 [99]
FOXC2/FOXF1/FOXL1 Lymphedema distiachis syndrome (#153400) >3 Mb; gene desert 0.5 Mb 8/1 16q24.1 [100]
FOXL2 (position effect) Blepharophimosis, ptosis, and epicanthus inversus (BPES; #110100) 1 Mb; gene desert; PK3CB bystander 0.7 Mb 3/3 3q22.3 [101]
GLI3 (position effect) Greig cephalopolysyndactyly syndrome (GCPS; #175700) 4 Mb 0.4 Mb 2/0 7p14.1 [102]
PITX2 Rieger syndrome, type 1 (RIEG1; #180500) >4 Mb; gene desert 2 Mb 8/2 4q25 [103]
POU3F4 (position effect) Deafness 3, conductive, with stapes fixation (DFN3; #304400) 10 Mb (including DACH2) 2 Mb 8/3 xq21.1 [85]
SIX3/SIX2 Holoprosencephaly 2 (#157170) >3 Mb 2 Mb 9/6 2p21 [104]
SHHa (position effect) Holoprosencephaly 3 (#142945), preaxial polydactyly 2 (#174500) >2 Mb 1/1.5 Mb 7/4/3 7q36.3 [83]
TWIST Saethre-Chotzen syndrome (#101400) 8 Mb (including sp8 and sp4); gene desert 2 Mb >20/3 7p21 [105]
SALL1 a Townes-Brocks syndrome (#107480) >8 Mb; gene desert 1.5/0.1 Mb 18/3/0 16q12.1 [106]
SOX2 Microphthalmia (MCOPS3; #206900) 8 Mb; gene desert 2.5 Mb >20/2 3q26.33 [86]
PAX6a (position effect) Aniridia, type II (AN2; #106210) >4 Mb 1 Mb 18/1/3 11p13 [107]
SOX3 Mental Retardation, X-linked (#300123) 4 Mb 2 Mb ?/3 Xq27.1 [108]
SHOX (position effect) Langer mesomelic dyplasia (#248700) 3 Mb 2 Mb 6/5 Xp22.33 [109]
  1. Provided is a list of developmental regulatory genes known to harbor human disease mutations. These genes retain extended regions of conserved synteny around them. Length of conserved gene or highly conserved noncoding element (HCNE) order was estimated through alignments between human and chicken (hs/gg) genomes, or through alignment between human and teleost genomes (either zebrafish [dr] or tetraodon [tn]). Those loci in which position effect mutations have been found are indicated in the left-most column. The size of these loci suggests that position effect mutations should eventually be found in all of them (see text for further detail). aTarget genes retained in duplicate in teleost genomes. Mb, megabases.