Table 2.

Confirmed germ-line de novo variants in the DDD study

Insertion coord.	RT type	Genomic compartment	ENSEMBL gene ID	HGNC gene ID	pLI	DDG2P annotation	Decipher ID57	Diagnostic?	Parental origin	Notes
chr3:9495459	Alu	Exonic	ENSG00000168137	SETD5	1.000	Confirmed, monoallelic	280818	True	Father
chr5:176638159	Alu	Exonic	ENSG00000165671	NSD1	1.000	Confirmed, monoallelic	259118	True	Unknown	Included in Wright et. al.58
chr6:159190834	Alu	Exonic	ENSG00000092820	EZR	0.988	None	300984	False	Unknown
chr7:77552086	Alu	Exonic	ENSG00000006576	PHTF2	0.024	None	271388	False	Father
chr3:135913800	Alu	Intronic	ENSG00000174579	MSL2	0.890	None	292325	False	Unknown
chr3:148614204	Alu	Intronic	ENSG00000163751	CPA3	<0.001	None	270426; 270428	False	Unknown	Monozygotic twins
chr3:172480619	Alu	Intronic	ENSG00000114346	ECT2	<0.001	None	307591	False	Unknown
chr12:46246325	L1	Exonic	ENSG00000189079	ARID2	1.000	Probable, monoallelic	264759	True	Unknown
chr5:88100580	L1	Exonic	ENSG00000081189	MEF2C	0.004	Confirmed, monoallelic	285645	True	Unknown
chr6:10847968	Retrogene-SLC35F2	Intergenic	N/A	N/A	N/A	N/A	291670	False	Unknown
chr1:25074202	Retrogene-SERINC5	Intronic	ENSG00000169504	CLIC4	0.009	None	301168	False	Father

Relevant clinical and annotation information for MEI and PPG de novo variants identified as part of this study. Location of the insertion event is given in human build GRCh37 reference coordinates (Insertion coord.). A true value in the Diagnostic column indicates, at the time of publication, that this variant intersected a known DD gene, and was deemed likely to be involved in the patient’s phenotype by the referring clinician; false does not indicate whether or not, with additional future evidence, the gene may become associated with DD and the variant thus deemed diagnostically relevant. If applicable, ENSEMBL⁵⁹ gene IDs indicate the gene impacted, not the gene from which the event is derived (i.e., for PPGs)