Table 1:

Clinical, Pathologic, and Genetic Features of Cases

Case	Age/Sex	Tumor Size/Stage	IHC+	IHC-	Comment	NF2 Variant	Other Molecular Findings
1	78/M	4.2cm; pT1bNX;	HNF-1 beta, PAX8, CK7, EMA (focal)	WT-1, Melan A, cathepsin k-, GATA3, SF-1, inhibin; FH, SDHB intact	TFE3/B FISH -; died of complications 1 month after operation	p.Tyr66*	Chr loss: 1p, 6, 22q; Chr gain: 16, 20. XPO1 p.Asn735Lys; POLQ p.Phe944Val; SPTBN1 p.Trp1893*; EXT2 p.Tyr421*; NPM1 p.Asp165_Glu169del; NCOA1 p.Met476Ile; AUTS2 p.Gly216Arg; ARID2 p.Arg314Ser; LMO7 p.Pro715Ser; CYLD p.Pro78Thr; MIB1 p.Ser408Asn; CSNK1G2 c.187+1G>T
2	60/U	7cm; pT2NX	PAX8, EMA,CK7	WT-1, TFE3,cathepsin k, TFEB, HMB45, Melan A chromogranin, synaptophysin, GATA3, SF-1, inhibin	TFE3/B FISH -; ESRD; tumor in native kidney 21 years after transplant	p.Asn293fs	Chr loss: 1p, 6, 22q; Chr gain: 16, 20. WNT4 p.Val97Ile; RAD54L p.Arg202Cys; MRE11A p.Asp495His; ERBB2 p.Asp880Tyr; PI4KA p.Pro514Leu
3	69/M	4cm; pT1cNXM1 (bone metastasis)	CK7, racemase, HNF-1 beta	TFE3, HMB45, Melan A, cathepsin K, AR,ER, CA-IX, GATA3	Lung metastasis; died of disease 2 months later	p.Gln111*	Chr loss: 9; Chr gain: 20. GLI1 p.Gly1097fs; RB1 p.Glu539_Thr543del; TERT promoter variant g.1295228C>T
4	53/F	2.5cm; pT1NX		GATA3, WT-1, cathepsin K, inhibin, SF-1	TFE3/B FISH -; h/o bilateral ovarian cystectomy	c.600–1G>A	Chr loss: 1p, 4, 6, 21q, 22q; Chr gain: 1, 7, 20. ARID1A p.Pro1619fs; CDK6 p.Thr198fs; RAD50 p.Gln479Arg; MLLT6 p.Ser608Tyr; SUGP2 p.Ala75Ser; THBS1 p.Arg458Gly; LRIG3 p.Asp56Glu; PLCG2 p.Glu567Lys; KMT2B p.Gly100Asp
5	73/M	3cm L partial nephrectomy variegated pink orange multilobulated	CK7	CA-IX, cathepsin K, GATA3, WT-1, inhibin, SF-1 -; FH, SDHB intact	TFE3/B FISH-	p.Lys364*	Chr loss: 1, 6, 9q, 15q, 19q; Chr gain: 9p, 16. CHD6 p.Asn2152Ser; NUP98 p.Ser103*; SAMD9 p.Phe801fs; MIB1 c.2211+1G>A; CIITA p.Gly174Arg; MECOM p.Glu81Gln; FLT4 p.Trp1233Cys; ABL2 p.Asn152fs; ASPSCR1 p.Asp217fs; HIST1H2AG p.Pro81Arg; FBXW7 p.Arg505His; KDM1A p.Val400Ile; SQSTM1 p.Cys27Ser
6	71/M	1.5cm; pT3NX (perirenal fat and vascular invasion)	PAX8, CK7	Cathepsin k, GATA3, WT-1, inhibin, SF-1-; FH intact	Concurrent clear cell RCC; TFE3/B FISH-,	p.Leu316fs	Chr loss: 1p, 6, 9, 15q; Chr gain: 16, 17q, 20. SMARCA4 c.3546+3A>T; FANCD2 p.Ser352Leu; BCL2 p.Leu185Met; PAK5 p.Ala120Val; PPP2R1B p.His661Leu; NOTCH2 p.Phe2091Ser; PICALM p.Val183Gly; HIP1 c.2891–2A>G; AKAP9 p.Glu2697Gln; STAT1 p.Ala531Thr; DLEC1 p.Gln1740Arg; PRICKLE1 p.Pro786Thr; LAMA5 p.Asn479Ser
7	52/M	1cm; pTXNX	PAX8	Chromogranin, Synaptophysin, cathepsin K, Melan A, WT-1, inhibin, SF-1, calretinin, GATA3	Renal-adrenal fusion; concurrent renal cyst	p.Arg516_Lys523delinsGln	Chr loss: 14q, 19q, 22q; Chr gain: 2p, 5, 13q, 20. PPP2R2B p.Arg129fs; RPL22 p.Lys13fs; BICC1 p.Val254Leu; WDFY3 c.1591+4A>C; TFEB p.Arg4Pro; FZD3 p.Gly595Ala; TNC p.Phe1196Tyr
8	51/M	1.5cm; pT1NX			Concurrent renal cyst	p.Lys130fs	Chr loss: 1p, 3, 6, 11, 14q, 19, 22q; Chr gain: 20. ERCC5 p.Leu844*; CLTC p.Asp662fs; WHSC1 c.1674+6dupT; SNX29 p.Lys513Ile; CNTN1 c.2185–4T>A; SGK1 p.Lys338Glu; ITGA7 p.Glu120Val; GNAI1 p.Arg142Ile; TPR p.Glu1594Asp; RASGRF1 p.Asn1075Tyr; LIFR p.Met773Leu

U=unknown gender; FH=fumarate hydratase; SDHB=succinate dehydrogenase subunit B; Chr=chromosome; IHC=immunohistochemistry