Table 3.

Genetic alterations in SMARCB1-deficient carcinomas of skin.

Case	Functional significance	Gene	cDNA	AA	Mutation type	Zygosity/ploidy status	Variant allele frequency
18 F	Likely oncogenic	SMARCB1	Whole gene deletion	N/A	Deep deletion	Homozygous deletion	N/A
	Unknown	LATS2	c.2888G>A	p.G963E	Missense		0.35
75 M	Likely or predicted oncogenic	SMARCB1	c.617G>A	p.W206*	Nonsense	LOH	0.44
		KDM6A	c.3878+2T>G	p.X1293_splice	Splice site	LOH	0.62
		EP300	c.4192C>T	p.L1398F	Missense	LOH	0.39
		TP53	c.529_546delCCCCACCATGAGCGCTGC	p.P177_C182del	In frame deletion	LOH	0.39
		TP53	c.867_868delinsTT	p.R290C	Missense	LOH	0.38
		FAT1	c.9568G>T	p.E3190*	Nonsense	LOH	0.38
		KMT2D	c.3810_3811delAC	p.L1271Ifs*14	Frameshift deletion	Diploid	0.27
		CIC	Inversion of exons 16–20	N/A	Structural variant	N/A	N/A
		CDK12	Intragenic deletion of exon 2	N/A	Structural variant	N/A	N/A
		CDKN2A/p16INK4A	Whole gene deletion	N/A	Deep deletion	Homozygous deletion	N/A
		CDKN2A/p14ARF	Whole gene deletion	N/A	Deep deletion	Homozygous deletion	N/A
		CDKN2B	Whole gene deletion	N/A	Deep deletion	Homozygous deletion	N/A
		PTPRD	Whole gene deletion	N/A	Deep deletion	Homozygous deletion	N/A
	Unknown	KDM5C	c.1318T>C	p.Y440H	Missense		0.57
		EIF4A2	c.307C>T	p.Q103*	Nonsense		0.49
		FGFR1	c.2378C>T	p.S793F	Missense		0.44
		MST1R	c.4189C>T	p.P1397S	Missense		0.40
		INPP4B	c.1672G>A	p.G558R	Missense		0.40
		NOTCH1	c.517C>T	p.P173S	Missense		0.40
		AGO2	c.1276G>A	p.A426T	Missense		0.37
		U2AF1	c.598C>T	p.R200W	Missense		0.36
		JAK2	c.2780T>C	p.L927S	Missense		0.36
		MEF2B	c.980C>G	p.P327R	Missense		0.32
		IKBKE	c.571C>T	p.R191*	Nonsense		0.31
		ASXL2	c.2060G>A	p.G687E	Missense		0.31
		RET	c.3095G>A	p.G1032D	Missense		0.30
		MDM4	c.272C>T	p.S91F	Missense		0.30
		CIC	c.338C>T	p.P113L	Missense		0.29
		EPAS1	c.1558G>A	p.D520N	Missense		0.29
		TERT	c.1247G>T	p.R416L	Missense		0.29
		MDC1	c.5498C>T	p.S1833F	Missense		0.29
		NSD2	c.2089C>T	p.L697F	Missense		0.29
		KIT	c.447_448delinsAA	p.G150R	Missense		0.29
		SF3B1	c.104C>T	p.S35F	Missense		0.29
		ROS1	c.2822C>T	p.S941F	Missense		0.28
		SDHA	c.589G>A	p.G197S	Missense		0.28
		ZFHX3	c.4027G>A	p.D1343N	Missense		0.28
		POLD1	c.1139_1140delinsTT	p.A380V	Missense		0.28
		KMT2D	c.4388_4389delinsTT	p.T1463I	Missense		0.28
		ASXL1	c.3500C>T	p.P1167L	Missense		0.28
		FGFR2	c.1268C>T	p.P423L	Missense		0.28
		ROS1	c.1855C>T	p.P619S	Missense		0.28
		CENPA	c.263C>T	p.A88V	Missense		0.27
		MGA	c.775C>T	p.R259W	Missense		0.27
		NOTCH2	c.3707T>C	p.L1236P	Missense		0.27
		ERBB4	c.716C>T	p.S239L	Missense		0.26
		CBL	c.1282C>T	p.P428S	Missense		0.26
		ARID2	c.1418C>T	p.S473F	Missense		0.25
		CDC73	c.251C>T	p.P84L	Missense		0.25
		BLM	c.2186C>T	p.S729F	Missense		0.25
		PREX2	c.1673C>T	p.P558L	Missense		0.24
		IL7R	c.801–1G>T	p.X267_splice	Splice site		0.24
		RPS6KA4	c.2300G>A	p.G767D	Missense		0.24
		EPHB1	c.2732C>T	p.T911M	Missense		0.23
		ARID5B	c.1759_1760delinsAT	p.E587I	Missense		0.22
		TGFBR1	c.1183T>C	p.S395P	Missense		0.18
		PAK5	c.1259_1260delinsTT	p.S420F	Missense		0.12
		PTCH1	c.1322G>A	p.R441H	Missense		0.10
		MDC1	Intragenic deletion of exons 10–12	N/A	Structural variant		0
		TEK	Whole gene deletion	N/A	Deep deletion		N/A

Abbreviations: AA, amino acid; LOH, loss of heterozygosity; N/A, not available