Table 1.

Overview of ATRT-SMARCA4 included in this study

Case No	Tumor location	Sex	Age at diagnosis [months]	Overall survival [months]	Dead/ alive	Brain Tumor Classifier Result (score)	SMARCA4 mutation in the tumor	Predicted AA change	Coding impact	Clinical significance (ClinVar)	Clinical significance (ACMG)	SMARCA4 germline mutation	DNA methylation data	RNA seq data	SMARC4 protein (IHC)	References
01	supra	Female	3	1	Dead	No matcha	c.3407delG	p.G1136Afs*4	Frameshift	n/a	Pathogenic	Yes	√	√	Lost	Patient #8 [17]
02	supra	Male	11	n/a	N/a	No matcha	c.1666C > Tb	p.Q556*	Nonsense	Pathogenic	Pathogenic	n/a	√	√	Lost
03	supra	Female	11	2	Dead	No matcha	c.352C > T	p.Q118*	Nonsense	n/a	Pathogenic	Yes	√	√	Lost
04	supra	Male	3	n/a	Dead	ATRT-SHH (0.99)	Breakage within the SMARCA4 region (FISH)	-	n/a	n/a	n/a	n/a	√	x	Lost
05	infra	Female	10	2	Dead	ATRT-SHH (0.99)	c.3565C > T	p.R1189*	Nonsense	Pathogenic	Pathogenic	Yesc	√	x	Lost	Patient #1 [17] Patient III2 [43]
06	infra	Female	7	1	Dead	ATRT-SHH (0.98)	c.4038_4075del38	p.I1347*	Nonsense	n/a	Pathogenic	Yes	√	x	Lost	Patient #4 [17]
07	supra, Multiple	Male	22	3	Dead	No matcha	Heterozygous SMARCA4 deletion (FISH)	-	n/a	n/a	n/a	no	√	√	Lost	Patient #5 [17]
08	infra	Male	17	28	Dead	No matcha	c.2335G > A	p.D779N	Missense	Uncertain significance	Uncertain significance	Yes	√	x	Retained	Patient #9 [17]
09	supra, metastatic	Male	3	1	Dead	ATRT-SHH (0.94)	c.2920delC	p.F975Sfs*44	Frameshift	Pathogenic	Pathogenic	Yes	√	x	Lost
10	infra	Female	46	21	Dead	ATRT-SHH (0.92)	c.3574C > T	p.R1192C	Missense	Uncertain significance	Uncertain significance	no	√	√	Retained	[32]
11	supra	Male	1	n/a	Dead	No matcha	n/a	n/a	n/a	n/a	n/a	n/a	√	x	Lost
12	infra	Male	13	22	Alive	No matcha	c.1757_1760del	p.K586Rfs*26	Framehsift	Pathogenic	Pathogenic	n/a	√	√	Lost
13	supra	Male	4	9	Alive	ATRT-SHH (0.96)	c.3168 + 5G > A	Intron	None	n/a	Uncertain significance	n/a	√	√	Lost
14	supra	Male	3	3	Dead	ATRT-SHH (0.99)	c.3277C > T	p.R1093*	Nonsense	Likely Pathogenic	Pathogenic	n/a	√	√	Lost

^aInterpreted by the brain tumor classifier (www.molecularneuropathology.org)

^bInferred from RNA Seq data

^cInferred since the same SMARCA4 mutation found in the patient’s tumor was found in her sister’s and father’s germline; infra infratentorial, n/a data not available, supra supratentorial, √ analysis done, x analysis not done