Identification of potential causal variants for premature ovarian failure by whole exome sequencing

BMC Medical Genomics

Table 1 Potential causal variants detected in 8 patients with POF by whole-exome sequencing

GENE	Locus	dbSNP ID	Transcript ID	Sequence charge		Allele Frequency				Pathogenicity
GENE	Locus	dbSNP ID	Transcript ID	cDNA	AA	ExAC	gnomAD	1000G	KRGDB	VEST	CADD	Patient ID
EIF2B3	chr1:45446711	rs201162647	NM_020365.4	c.130G>A	P.Glu44Lys	0.00001	0.00001	0.00020	0.00080	0.823	33.0	P15
ERCC6	chr10:50682161	rs77027474	NM_000124.3	c.2510G>A	P.Arg837His	0.00011	0.00007	0.00060	0.00500	0.822	32.0	P5
HFM1	chr1:91781465	rs755200362	NM_001017975.4	c.3047A>G	P.Gln1016Arg	0.00001	0.00001	.	0.00080	0.583	23.6	P23
MCM8	chr20:5943969	rs749490653	NM_001281521.1	c.839C>G	P.Ser280Cys	0.00022	0.00022	.	0.00273	0.616	22.9	P32
MCM8	chr20:5958571	rs201813827	NM_001281521.1	c.1565C>T	P.Thr522Met	0.00008	0.00010	0.00020	0.00409	0.612	27.5	P14, P28
MCM9	chr6:119150409	rs757364893	NM_017696.2	c.1330G>C	P.Val444Leu	.	0.00002	.	0.00136	0.630	25.9	P26
PRE PL	chr2:44549950	rs140355063	NM_001171603.1	c.1940G>A	P.Arg647Gln	0.00009	0.00009	.	0.00500	0.672	32.0	P15
SALL4	chr20:50400817	rs189552205	NM_020436.3	c.3149T>C	P.Ile1050Thr	0.00002	0.00002	0.00020	0.00136	0.978	25.1	P23
TG	chr8:134107412	rs2272707	NM_003235.4	c.7364G>A	P.Arg2455His	0.00070	0.00078	0.00120	0.00818	0.857	27.3	P3

VEST analysis generates values between 0 and 1, and scores ≥ 0.5 were classified as pathogenic variants and those < 0.5 as benign. CADD analysis generates a PHRED-like scaled value. Scores ≥ 20 were classified as pathogenic variants and those < 20 as benign. Variants satisfying both CADD ≥ 20 and VEST ≥ 0.5 were classified as pathogenic

ISSN: 1755-8794