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Table 4 Blood DMRs where genetic variation has previously been associated with OFCs

From: Distinct DNA methylation profiles in subtypes of orofacial cleft

Gene DMR Sidak-corrected P value Findings in this study N CpGs in DMR Example of previous findings
TBX1 c Chr22:19750918-19752870 Chr22:19736256-19736672 1.61 × 10−10 5.03 × 10−4 ↑ in CPO vs CLO ↑ in CPO vs CLO 6 2 Variants were associated with non-syndromic CL/P in a candidate gene study of a Brazilian population [41]
COL11A2 c Chr6:33132086-33132728 2.13 × 10−9 ↑ in CPO vs CLO 15 Multiple haplotypes have been associated with non-syndromic CPO compared to unaffected individuals [44]
HOXA2 b Chr7:27143046-27143807 Chr7:27143235-27143586 1.04 × 10−7 3.9 × 10−2 ↑ in CPO vs CLO ↑ in CPO vs CLP 7 7 Hoxa-2 mutant mice have abnormal palatogenesis [71, 72]
CRB2 a Chr9:126130901-126131310 5.14 × 10−4 ↑ in CPO vs CLO 2 Several non-syndromic CL/P susceptibility genes have been identified in the 9q22.32–34.1 region that includes CRB2 [73]
PDGFRA c Chr4:55090812-55091179 2.71 × 10−2 ↑ in CPO vs CLO 2 Mutations in PDGFRA have been associated with non-syndromic CPO [74]
CRISPLD2 c Chr16:84870066-84870204 3.41 × 10−2 ↑ in CPO vs CLO 2 Variants have been associated with non-syndromic CL/P, with some evidence for rs1546124 being associated with CPO in several populations [75]
SMOC1 c Chr14:70316898-70317240 1.39 × 10−5 ↓ in CPO vs CLP 5 A significant proportion of Smoc1 homozygous mutant mice have cleft palate [76]
PVRL1 c Chr11:119630144-119630363 1.52 × 10−5 ↓ in CPO vs CLO 2 Rare and common mutations within PVRL1 were associated with non-syndromic CLP in a family-based study of multiple populations [77]
CCL2 a Chr17:32582128-32582829 3.00 × 10−4 ↓ in CPO vs CLO 6 Variants mapping to CCL2 were associated with non-syndromic CL/P in a candidate gene study [78]
  1. aIdentified as OFC-related in DisGeNET
  2. bIdentified as OFC-related in Funato et al.
  3. cIdentified as OFC-related in both