Table 2.

Variants detected in CHD3 in our cohort. ACMG, American College of Medical Genetics. ^# Population frequency was estimated from pseudo-control databases: GnomAD genomes (v3.0); GnomAD exomes (v3.1); Kaviar (version160204-Public); Beacon (v2.0); 1000 G; Phase III; and Bravo (TOVMed Freeze 8).

Family	Proband	Genomic Coordinate (hg38)	cDNA and Protein Location	Exon/Intron	Mutation Type	Zygosity	Inheritance	Population Frequency #	CADD	REVEL	ACMG Prediction
1	1	chr17:7811001	NM_001005271.3:c.5184_5185del (p.Asp1730PhefsTer10)	33	Frameshift	Heterozygous	De novo	-	35	-	Likely Pathogenic
2	2	chr17:7804024	NM_001005271.3:c.3130C>T (p.Arg1044Trp)	18	Missense	Heterozygous	De novo	-	29.8	-	Pathogenic
3	3	chr17:7804650	NM_001005273.3:c.3209G>A (p.Arg1070Gln)	20	Missense	Heterozygous	De novo	0.0000159	24.9	0.161	Likely Pathogenic
4	4	chr17:7806590	NM_001005271.3:c.3673G>C (p.Ala1225Pro)	22	Missense	Heterozygous	De novo	-	33	-	Pathogenic
5	5	chr17:7805996	NM_001005271.3:c.3325_3327delGGT (p.Tyr1109del)	20	In frame deletion	Heterozygous	De novo	-	-	-	Likely Pathogenic
6	6	chr17:7806642	NM_001005271.3:c.3725G>A (p.Arg1242Gln)	23	Missense	Heterozygous	Inherited from father	-	32	0.947	Likely Pathogenic
7	7	chr17:7806600	NM_001005271.3:c.3683G>A (p.Arg1228Gln)	23	Missense	Heterozygous	De novo	-	31	0.957	Pathogenic
8	8	chr17:7903278	NM_001005273.3:c.3502_3504del (p.Ser1168del)	23	In frame deletion	Heterozygous	De novo	-	-	-	Likely Pathogenic
9	9	chr17:7902972	NM_001005273.3:c.3406A>C (p.Thr1136Pro)	22	Missense	Heterozygous	De novo	-	29.9	0.966	Likely Pathogenic
10	10	chr17:7895142	NM_001005273.3:c.1495C>T (p.Arg499Ter)	9	Nonsense	Heterozygous	De novo	-	-	-	Pathogenic
11	11	chr17:7903962	NM_001005273.3:c.3865G>A (p.Ala1289Thr)	24	Missense	Heterozygous	Unknown	-	29.1	0.831	Likely Pathogenic
12	12	chr17:7903962	NM_001005271.3:c.4042G>A (p.Ala1348Thr)	24	Missense	Heterozygous	Inherited from mother	-	29.1	0.831	Likely Pathogenic
12	13	chr17:7903962	NM_001005271.3:c.4042G>A (p.Ala1348Thr)	24	Missense	Heterozygous	Inherited from mother	-	29.1	0.831	Likely Pathogenic
12	14	chr17:7903962	NM_001005271.3:c.4042G>A (p.Ala1348Thr)	24	Missense	Heterozygous	Inherited from mother	-	29.1	0.831	Likely Pathogenic
13	15	chr17:7900707	NM_001005273.3:c.2954G>A (p.Arg985Gln)	18	Missense	Heterozygous	De novo	-	32	0.777	Pathogenic
14	16	chr17:7903281	NM_001005273.3:c.3505C>T p.Arg1169Trp	23	Missense	Heterozygous	De novo	-	25.7	0.899	Pathogenic
15	17	chr17:7903317	NM_001005273.3:c.3541A>T p.Ile1181Phe	23	Missense	Heterozygous	De novo	-	28.4	0.904	Likely Pathogenic
15	18	chr17:7903317	NM_001005273.3:c.3541A>T p.Ile1181Phe	23	Missense	Heterozygous	De novo	-	28.4	0.904	Likely Pathogenic
16	19	chr17:7903282	NM_001005273.3:c.3506G>A p.Arg1169Gln	23	Missense	Heterozygous	De novo	-	31	0.96	Pathogenic
17	20	chr17:7804024	NM_001005271.3:c.3130C>T (p.Arg1044Trp)	18	Missense	Heterozygous	De novo	-	29.8	-	Pathogenic