Table 3.

Pathogenic mutations in urethral clear cell adenocarcinoma

Case	Gene	Driver	Role	Effect	Type	Reference	Alternate	Chr.	cDNA change	Protein change	VAF (%)
1	WBSCR27	-	-	Splice site	Indel	CTGTG	C	7	c.389-5_389-2delCACA		30.76
2	APC2	-	-	Nonsense variant	SNV	C	A	19	c.2855C>A	p.Ser952*	42.85
	CSMD3	-	TSG	Missense variant	SNV	C	T	16	c.2972G>A	p.Arg991His	14.28
	LAMC2	-	-	Missense variant	SNV	C	T	1	c.301C>T	p.Arg101Trp	12.5
3	ZNF219	-	-	In-frame deletion	Indel	GGAGGCT	G	14	c.698_703delAGCCTC	p.Gln233_Pro234del	46.34
	KRAS	+	OG	Missense variant	SNV	C	A	12	c.35G>T	p.Gly12Val	11.79
4	KEAP1	-	TSG	Missense variant	SNV	C	T	19	c.1085G>A	p.Arg362Gln	37.5
	SMARCA4	-	TSG	Missense variant	SNV	T	C	19	c.3461T>C	p.Leu1154Pro	25.45
	CACNA1D	-	OG	Missense variant	SNV	C	G	3	c.4780C>G	p.Arg1594Gly	24.17
	AMER1	+	TSG	Missense variant	SNV	C	T	X	c.2254G>A	p.Glu752Lys	24.07
	PIK3R1	+	TSG	Missense variant	SNV	G	A	5	c.1670G>A	p.Arg557Gln	19.17
	TNK2	-	-	Missense variant	SNV	G	T	3	c.1700C>A	p.Ser567Tyr	17.97
5	PBRM1	+	TSG	Frameshift variant	Indel	AC	A	3	c.3245delG	p.Gly1082fs	31.75
	ARID1A	+	TSG	Nonsense variant	SNV	G	A	1	c.4634G>A	p.Trp1545*	45.26
	NKD1	-	-	Missense variant	SNV	G	A	16	c.92G>A	p.Arg31Gln	40.35
	ACVRL1	+	-	Missense variant	SNV	C	A	12	c.532C>A	p.Leu178Met	30.76
	CAPN2	-	-	Missense variant	SNV	C	T	1	c.1433C>T	p.Pro478Leu	29.52
	CC2D1B	-	-	Missense variant	SNV	C	G	1	c.1208G>C	p.Arg403Pro	28.82
	CHD4	-	OG,TSG	Missense variant	SNV	C	T	12	c.4822G>A	p.Val1608Ile	28.4
	KMT2D	+	OG, TSG	Missense variant	SNV	G	T	12	c.2312C>A	p.Ser771Tyr	28
	TCF12	-	TSG	Missense variant	SNV	C	T	15	c.280C>T	p.His94Tyr	26.51

Chr., chromosome; Indel, insertion and deletion; OG, oncogene, SNV, single nucleotide variation; TSG, tumor suppressor gene, VAF, variant allele frequency.