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

Andersson, Kristofer; Malmgren, Barbro; Åström, Eva; Nordgren, Ann; Taylan, Fulya; Dahllöf, Göran

doi:10.1186/s13023-020-01361-4

Orphanet Journal of Rare Diseases

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.	Chrom^a	Start	End	Gene	Transcript	Codon change	Aa^b change	Aa^b Position/Total length	Impact	Polyphen pred^c	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

^aChrom chromosome number
^bAa amino acid
^cPolyphen pred Polyphen-2 prediction

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ISSN: 1750-1172

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