Table 2. Molecular Findings.

Patient No.	Genomic Coordinates	Gene	Transcript	cDNA	Protein Effect	Zygosity	Classification	Inheritance	Parental Origin	Diagnosis by
1	Chr1:160106162	ATP1A2	NM_000702.3	c.2563 + 2T>C		Het	Likely pathogenic	AD	Maternal	Panel
2	ChrX:53280248	IQSEC2	NM_001111125.2	c.1510C>T	p.Gln504*	Hem	Likely pathogenic	XLD	Unknown	Panel
3	ChrX:53279758-53279776	IQSEC2	NM_001111125.2	c.1983_1999del	p.Leu662fs	Het	Likely pathogenic	XLD	Unknown	Panel
4	Chr20:62038729	KCNQ2	NM_172107.2	c.1888-1G>A		Het	Likely pathogenic	AD	Unknown	Panel
5	ChrX:99662890	PCDH19	NM_001184880.1	c.706C>T	p.Pro236Ser	Het	Likely pathogenic	XL	Unknown	Panel
6	Chr22:32098112-32270694	PRR14L, DEPDC5		22q12.2 - q12.3 deletion		Het	Likely pathogenic	AD	Unknown	Panel
7	Chr16:29824948-29824950	PRRT2	NM_001256442.1	c.577delG	p.Glu193Lysfs*36	Het	Pathogenic	AD	Unknown	Panel
8	Chr2:166850723-166850726	SCN1A	NM_001165963.1	c.4783_4784delCT	p.Leu1595fs	Het	Pathogenic	AD	Unknown	Panel
9	Chr2:166905395	SCN1A	NM_001202435.1	c.1028 + 1G>T		Het	Pathogenic	AD	Unknown	Panel
10	Chr2:166848438	SCN1A	NM_001165963.1	c.5347G>A	p.Ala1783Thr	Het	Pathogenic	AD	Unknown	Panel
11	Chr16:29595483-30198151	PPRT2a		16p11.2 deletion		Het	Pathogenic	AD	Unknown	Panel
12	Chr16:29652999-30194001	PPRT2b		16p11.2 deletion		Het	Pathogenic	AD	Unknown	Panel
13	Chr9:130430431dup	STXBP1	NM_003165.3	c.867dup	p.Ala290Serfs*24	Het	Pathogenic	AD	Unknown	Panel
14	Chr9:130430439	STXBP1	NM_003165.3	c.875G>A	p.Arg292His	Het	Pathogenic	AD	Unknown	Panel
15c	Chr11:6638271; Chr11:6638385	TPP1	NM_000391.3	c.622C>T; c.509-1G>C	p.Arg208*; p.?	Compound het	Pathogenic; pathogenic	AR	Both	Panel
16c	Chr9:138651532	KCNT1	NM_020822.2	c.862G>A	p.Gly288Ser	Het	Pathogenic	AD	De novo, recurrent	Panel
17	Chr19:42482319	ATP1A3	NM_001256214.1	c.1829G>A	p.Arg610His	Het	Likely pathogenic	AD	Likely de novo	Parental testing
18	Chr19:13372340	CACNA1A	NM_023035.2	c.4186G>A	p.Val1396Met	Het	Likely pathogenic	AD	Likely de novo	Parental testing
19	Chr5:161309591	GABRA1	NM_000806.5	c.587A>G	p.Tyr196Cys	Het	Likely pathogenic	AD	Likely de novo	Parental testing
20	Chr2:166848464	SCN1A	NM_001165963.1	c.5321T>C	p.Phe1774Ser	Het, mosaic	Likely pathogenic	AD	De novo	Parental testing
21	Chr2:166231468	SCN2A	NM_001040142.1	c.4246C>T	p.Leu1416Phe	Het	Likely pathogenic	AD	likely de novo	Parental testing
22	Chr12:52200543	SCN8A	NM_014191.3	c.5273T>C	p.Val1758Ala	Het	Likely pathogenic	AD	De novo	Parental testing
23	Chr15:25584341	UBE3A	NM_000462.3	c.2550_2570dup	p.Glu851_Lys857dup	Het	Likely pathogenic	Imprinted	Likely de novo, unknown	Parental testing
24	Chr5:92921095	NR2F1	M_005654.5	c.366C>G	p.Cys122Trp	Het	Likely pathogenic	AD	De novo	ES trio
25	Chr18:42531889	SETBP1	NM_015559.2	c.2584G>A	p.Glu862Lys	Het	Pathogenic	AD	De novo	ES trio
26	ChrX:53440181	SMC1A	NM_006306.3	c.615 + 1G>C		Het, mosaic	Pathogenic	XLD	De novo	ES trio
27d	Chr1:40319721-40319723; 40319730	TRIT1	NM_017646.5	c.334delC; c.326T>C;	p.Arg112fs; p.Ile109Thr	Compound het	VUS; VUS	AR	Both	ES trio
Reanalysis Findings
28	Chr22:40036960	CACNA1I	NM_021096.3	c.829A>G	p.Ile277Val	Het	VUS	AD	Unknown	NA
29	Chr2:149267668	MBD5	NM_018328.4	c.4377T>A	p.His1459Gln	Het	VUS	AD	Unknown	NA
30	Chr2:166020387	SCN3A	NM_001081677.1	c.619G>C	p.Val207Leu	Het	VUS	AD	Unknown	NA
31	Chr2:166025265	SCN3A	NM_006922.3	c.454G>A	p.Asp152Asn	Het	VUS	AD	Unknown	NA
32	Chr6:118015256	NUS1	NM_138459.4	c.604A>G	p.Arg202Gly	Het	VUS	AD	Unknown	NA
33	Chr3:132394747	UBA5	NM_024818.4	c.1111G>A	p.Ala371Thr	Het	Pathogenic	AR	Unknown	NA

Abbreviations: AD, autosomal dominant; AR, autosomal recessive; ES, exome sequencing; Hem, hemizygous; Het, heterozygous; NA, not applicable; VUS, variant of unknown significance; XL, X-linked; XLD, X-linked dominant.

^aFull list of genes in the microdeletion: SEZ6L2, INO80E, SMG1P2, MIR3680-1, MIR3680-2, SPN, QPRT, C16orf54, ZG16, KIF22, MAZ, PRRT2, PAGR1, MVP, CDIPT, CDIPT-AS1, ASPHD1, KCTD13, TMEM219, TAOK2, HIRIP3, DOC2A, C16orf92, FAM57B, ALDOA, PPP4C, TBX6, YPEL3, LOC101928595, GDPD3, MAPK3, CORO1A.

^bMicrodeletion includes genes listed from SPN through MAPK3 in footnote a.

^cFindings noted in medically actionable genes.

^dThe report was marked as likely diagnostic owing to lack of definitive variant classification evidence and somewhat limited clinical validity of the gene.