Table 2 Fifty-five cases with potentially disease-associated variants identified by genome sequencing

From: Genome sequencing provides high diagnostic yield and new etiological insights for intellectual disability and developmental delay

Case	Gene	Variant	Zygosity	Pathogenicity^a	ES-detectable^b	Clinical diagnosis category^c
Pt0348	TNPO2	c.466G>C p.(Asp156His)	Het	LP	Yes	EIEE
Pt0442	TBR1	c.1474del p.(Arg492Glyfs*30)	Het	P	Yes	Unclassified (Other)
Pt0457	DLG4	c.686A>T p.(Asp229Val)	Het	P	Yes	West syndrome
Pt0616	POLR2A	c.3275C>T p.(Ala1092Val)	Het	P	Yes	Shprintzen-Goldberg syndrome
Pt0688	SCN8A	c.667A>G p.(Arg223Gly)	Het	P	Yes	West syndrome
Pt2049	TOR1A	c.936_937del p.(Arg312Serfs*5)	Comp het	LP	Yes	Unclassified (Other)
Pt2049	TOR1A	c.284C>T p.(Pro95Leu)	Comp het	VUS	Yes	Unclassified (Other)
Pt2199	TMEM67	c.2086C>T p.(Leu696Phe)	Homo	LP	Yes	Unclassified (Other)
Pt2283	VPS4A	c.617A>G p.(Glu206Gly)	Het	P	Yes	Unclassified (White matter)
Pt2385	SMC1A	c.3131_3132del p.(Glu1044Valfs*2)	Het	P	Yes	Unclassified (Cerebellar)
Pt2420	SPTBN1	c.614G>C p.(Gly205Ala)	Het	LP	Yes	Unclassified (Cerebellar)
Pt2553	HNRNPH2	c.617G>T p.(Arg206Leu)	Het	P	Yes	Unclassified (Other)
Pt2637	NTRK2	c.2167_2169del p.(Tyr723del)	Het	LP	Yes	Unclassified (Other)
Pt2908	RBMX	c.1051_1053dup p.(Pro351dup)	Het	LP	Yes	Unclassified (Epilepsy)
Pt7180	LMBRD2	c.1448G>A p.(Arg483His)	Het	P	Yes	West syndrome
Pt7186	ALDH3A2	c.57_132dup p.(Ile45Serfs*34)	Comp het	P	Yes	Unclassified (Epilepsy)
Pt7186	ALDH3A2	c.1339A>G p.(Lys447Glu)	Comp het	LP	Yes	Unclassified (Epilepsy)
Pt2235	PTP4A1	c.199G>A p.(Asp67Asn)	Het	VUS	Yes	Donnai-Barrow syndrome
Pt2289	HIC1	c.1562_1563delinsTT p.(Cys521Phe)	Het	VUS	Yes	Unclassified (White matter)
Pt0712	RNU4-2	n.69C>G	Het	P	No	Unclassified (Epilepsy)
Pt2092	RNU4-2	n.64_65insT	Het	P	No	Claes-Jensen syndrome
Pt2190	CHASERR	Ex1 to 4 DEL	Het	P	No	Unclassified (Other)
Pt2902	LINC02789	Disruptive large INV	Het	VUS	No	West syndrome
Pt0600	FTO	c.1334G>A p.(Arg445His)	Comp het	VUS	Yes	Unclassified (Other)
Pt0600	FTO	Ex3 to 7 DEL	Comp het	LP	Yes	Unclassified (Other)
Pt0607	HACE1	Ex24 DEL	Homo	P	No	Unclassified (Other)
Pt0707	SCN1A	Ex18 to 19 DUP	Het	P	No	Dravet syndrome
Pt2277	ADGRG1	Ex14 DEL	Homo	P	No	Unclassified (White matter)
Pt2317	WWOX	c.517-1G>A	Comp het	P	Yes	Unclassified (Epilepsy)
Pt2317	WWOX	Ex5 DEL	Comp het	P	No	Unclassified (Epilepsy)
Pt2450	NPHP1	Gross DEL	Homo	P	Yes	Joubert syndrome
Pt2547	EHMT1	Ex18 DEL	Het	LP	No	Unclassified (Other)
Pt2632	ASXL3	Ex11 DEL	Het	LP	No	Rett syndrome
Pt2779	PNPT1	c.1520C>G p.(Ala507Gly)	Comp het	LP	Yes	PEHO syndrome
Pt2779	PNPT1	Ex16 to 18 DEL	Comp het	P	Yes	PEHO syndrome
Pt7249	MEF2C	Ex5 DEL	Het	P	No	Unclassified (Epilepsy)
Pt2292	SATB2	Ex6 to 7 INV	Het	P or LP	No	Inherited GPI deficiency
Pt0445	SMC1A	MEI in Ex16	Het	P or LP	Yes	Unclassified (Epilepsy)
Pt2538	CC2D2A	c.3863C>G p.(Thr1288Arg)	Comp het	VUS	Yes	Joubert syndrome
Pt2538	CC2D2A	MEI in Ex7	Comp het	P or LP	Yes	Joubert syndrome
Pt0448		Chr2 large CNVs	Het	P	Yes	Unclassified (Epilepsy)
Pt2074		Chr16p13.3 multiplication	Het	VUS	Yes	Unclassified (Cerebellar)
Pt2361		Unbalanced CTX	Het	P	Yes	Unclassified (Cortical)
Pt2539		Chr18 large CNVs	Het	P	Yes	Cornelia de Lange syndrome
Pt7147		ChrX large multiplication	Het	P	Yes	West syndrome
Pt7252		Chr16 large DEL	Het	P	Yes	Dravet syndrome
Pt0538	SCN1A	c.265-2104G>A	Het	VUS	No	Unclassified (Epilepsy)
Pt2061	PXDN	c.506G>A p.(Arg169Gln)	Comp het	VUS	Yes	Unclassified (Other)
Pt2061	PXDN	c.200+3254A>G	Comp het	VUS	No	Unclassified (Other)
Pt2101	CTU2	c.282+471C>G	Comp het	P	No	Unclassified (Epilepsy)
Pt2101	CTU2	c.483G>A p.(Trp161*)	Comp het	P	Yes	Unclassified (Epilepsy)
Pt2178	STXBP1	INS of a DLX4 transcript in Int10	Het	LP	No	EIEE
Pt2232	POLRMT	c.3422+197G>T	Comp het	VUS	No	Unclassified (Other)
Pt2232	POLRMT	c.2214_2231del p.(Pro739_Ala744del)	Comp het	VUS	Yes	Unclassified (Other)
Pt2341	WDR62	c.3514+43C>T .	Homo	LP	Yes	Unclassified (Cortical)
Pt2447	CEP290	c.6012-12T>A .	Homo	P	Yes	Joubert syndrome
Pt2878	NPC1	c.1554-1009G>A .	Homo	P	No	Unclassified (Epilepsy)
Pt7183	FDFT1	c.99+543A>G .	Comp het	P	No	EIEE
Pt7183	FDFT1	c.382-15C>G .	Comp het	P	Yes	EIEE
Pt7234	TMEM237	c.325C>T p.(Arg109*)	Comp het	P	Yes	Joubert syndrome
Pt7234	TMEM237	c.275-972G>T	Comp het	P	No	Joubert syndrome
Pt2286		CTX near TBL1XR1	Het	VUS	No	Inherited GPI deficiency
Pt2800		Chromothripsis near NR2F1	Het	VUS	No	Unclassified (Epilepsy)
Pt0481	CHD3	Repeat expansion	Het	VUS	No	West syndrome
Pt0526	ATN1	Repeat expansion	Het	P	Yes	Neuronal ceroid lipofuscinosis
Pt2351	DMPK	Repeat expansion	Het	P	No	Unclassified (Other)

DEL deletion, DUP duplication, INV inversion, INS insertion, MEI mobile element insertion, CNV copy number variant, CTX chromosomal translocation, Ex exon, Int intron, Het heterozygous, Comp compound, Homo homozygous, P Pathogenic, LP Likely pathogenic, VUS variant of unknown significance, EIEE early infantile epileptic encephalopathy, Unclassified unclassified DD/ID syndrome, Other other or non-specific features, White matter white matter abnormalities, Cerebellar cerebellar abnormalities, Cortical cortical and cerebral malformations.
^aSee Supplemental Information for classification criteria.
^bSee Table 1 for the criteria.
^cSee Table 1.

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Table 2 Fifty-five cases with potentially disease-associated variants identified by genome sequencing

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