Table 2 Potential missense causal variants in prioritized genes.

CHR	BP	rs ID	Gene	AA change	MAF	SIFT	PolyPhen2	MT	FATHMM	CADD
1	7879401	rs147327372	PER3	Thr519Ala	0.002	T	B	N	T	0.01
1	7890153	rs144178755	PER3	Thr1040Asn	0.001	D	B	N	T	0.962
1	216138793	rs554957414	USH2A	Pro2329Leu	2e−6	D	D	D	D	29.1
1	216373416	rs148135241	USH2A	Ser1122Pro	0.004	D	D	D	D	22.8
1	216419934	rs201527662	USH2A	Cys934Trp	0.0002	D	D	D	D	36
3	33840234	rs200697599	PDCD6IP	Ile5Ser	0.0007	D	D	D	T	32
3	33879764	rs199990824	PDCD6IP	Asp376Asn	4e−6	D	B	D	T	26
3	33905532	rs62620697	PDCD6IP	Ala719Thr	4e−6	T	B	D	T	23.8
3	33905587	rs145293758	PDCD6IP	Pro737Arg	0.001	T	B	N	T	20.2
3	49039984	rs140290144	P4HTM	Ile227Val	0.006	T	B	D	T	22.1
3	49043292	rs144279528	P4HTM	Asp386Asn	8e−5	T	B	D	T	27.3
8	102570910	rs142411476	GRHL2	Arg183Gln	0.0002	T	D	D	T	22
16	75512734	rs140699573	CHST6	Gln331His	4e−6	D	D	D	D	27.4
17	44055786	rs139796158	MAPT	Ala118Gly	6e−5	D	D	D	T	26.4
17	44060807	rs76375268	MAPT	Gly213Arg	0.004	D	D	N	T	11.71
17	44060859	rs63750072	MAPT	Gln230Arg	0.04	D	D	D	T	4.652
17	44067341	rs143956882	MAPT	Ser427Phe	0.001	D	D	D	T	28.5
17	44101481	rs63750191	MAPT	Gln741Lys	3e−5	D	D	D	T	27.5

Legend: The best potential missense causal variants in our top prioritized genes. The headers represent: CHR = chromosome, BP = physical position in basepairs (hg19), Gene = gene location, AA change = amino acid change caused by mutation, MAF = minor allele frequency of the variant obtained from gnomAD, SIFT = pathogenicity prediction from SIFT (where T = tolerated and D = damaging), PolyPhen2 = pathogenicity prediction from PolyPhen2 (where B = benign and D = damaging), MT = pathogenicity prediction from MutationTaster (where N = neutral and D = damaging), FATHMM = pathogenicity prediction from FATHMM (where T = tolerated and D = damaging), CADD = CADD phred score.

Quick links

Search