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Table 3 Detected heterozygous variants in selected genes related to tooth development based on literature (n = 26)

From: Mutations in COL1A1/A2 and CREB3L1 are associated with oligodontia in osteogenesis imperfecta

Pat. No. Chroma Start End Gene Transcript Codon change Aab change Aab Position/Total length Impact Polyphen predc GERP CADD
1 chr17 63,533,621 63,533,622 AXIN2 ENST00000307078 aCg/aTg T/M 511/843 Missense variant Probably damaging 5.08 24.7
1 chr19 3,527,018 3,527,019 FZR1 ENST00000395095 aaC/aaT N 143/496 Synonymous variant −7.42 9.43
1 chr2 70,683,580 70,683,581 TGFA ENST00000295400 gcG/gcA A 85/160 Synonymous variant −11.1 18.95
1 chr20 10,393,438 10,393,439 MKKS ENST00000347364 Gca/Tca A/S 242/570 Missense variant Probably damaging 5.71 29.3
1 chr9 98,220,506 98,220,507 PTCH1 ENST00000331920 Gac/Tac D/Y 986/1447 Missense variant Probably damaging 3.32 26.4
1 chrX 44,921,995 44,921,996 KDM6A ENST00000377967    −/1401 Splice region variant   2.96 13.3
2 chr17 46,607,103 46,607,104 HOXB1 ENST00000239174 gcC/gcA A 237/301 Synonymous variant 6.94 10.1
2 chr2 189,861,948 189,861,949 COL3A1 ENST00000304636    −/1466 Splice region variant 2.2 7.63
2 chr2 189,871,109 189,871,110 COL3A1 ENST00000304636 Gct/Act A/T 1045/1466 Missense variant Possibly damaging 2.8 25.7
2 chr7 42,005,900 42,005,901 GLI3 ENST00000395925 Gcc/Acc A/T 924/1580 Missense variant Possibly damaging 4.85 32.0
2 chr7 128,851,226 128,851,227 SMO ENST00000475779 gCt/gTt A/V 65/70 Missense variant Benign 5.17 25.2
2 chr8 145,741,869 145,741,870 RECQL4 ENST00000428558 gaT/gaC D 211/1208 Synonymous variant 2.86 0.01
3 chr5 149,762,683 149,762,684 TCOF1 ENST00000451292 agG/agT R/S 973/1525 Missense variant Benign 0.150 1.76
4 chr16 68,842,671 68,842,672 CDH1 ENST00000261769 gGt/gAt G/D 203/882 Missense variant Probably damaging 4.82 23.9
4 chr5 176,636,763 176,636,764 NSD1 ENST00000347982 aTg/aCg M/T 186/2427 Missense variant Benign 5.50 3.09
4 chr4 5,642,346 5,642,347 EVC2 ENST00000310917 aCa/aGa T/R 375/1228 Missense variant Possibly damaging 3.33 25.6
4 chr4 111,539,693 111,539,694 PITX2 ENST00000306732 Gcc/Acc A/T 188/324 Missense variant Benign 3.15 17.28
5 chr4 5,721,083 5,721,084 EVC ENST00000264956 gAc/gGc D/G 95/992 Missense variant Possibly damaging 3.42 23.8
6 chr12 115,112,599 115,112,600 TBX3 ENST00000257566 gaG/gaC E/D 380/743 Missense variant Benign −5.58 1.22
6 chr5 174,151,756 174,151,757 MSX2 ENST00000239243 gAg/gTg E/V 32/267 Missense variant Benign 3.23 17.0
7,8 chr3 50,211,278 50,211,279 SEMA3F ENST00000002829 Gac/Tac D/Y 56/785 Missense variant Probably damaging 5.25 25.2
7,8 chr3 58,135,715 58,135,716 FLNB ENST00000295956 gaC/gaT D 2077/2602 Synonymous variant −9.81 9.72
7,8 chr4 5,713,114 5,713,115 EVC ENST00000264956 cGc/cCc R/P 3/992 Missense variant Possibly damaging 2.20 25.3
9 chr12 49,446,069 49,446,070 KMT2D ENST00000301067 Cgc/Tgc R/C 466/5537 Missense variant Unknown 3.31 18.42
9 chr2 200,246,463 200,246,464 SATB2 ENST00000260926 atG/atA M/I 142/733 Missense variant Probably damaging 5.76 24.6
10 chrX 13,778,622 13,778,623 OFD1 ENST00000340096 Att/Ctt I/L 682/1012 Missense variant Benign −2.97 0.03
  1. aChrom chromosome number
  2. bAa amino acid
  3. cPolyphen pred Polyphen-2 prediction