Table 2:

FGFR2 Extracellular Activating In-Frame Deletions Identified in Intrahepatic Cholangiocarcinoma Patients by Oncopanel and in any Malignancy by GENIE

Tumor Type	Amino Acid Change	Database	Prediction	Confidencea	Domain	Role of WT Amino Acid	Figure	Mapping #b
Intrahepatic Cholangiocarcinoma	p.H167_N173del	Oncopanel Sample 46	Pathogenic	High	Ig-like C2-type D2	Extended recognition of FGF Dimerization Beta-strand structure	2A, 2B	1
Intrahepatic Cholangiocarcinoma	p.H167_N173del	Oncopanel Sample 50	Pathogenic	High	Ig-like C2-type D2	Extended recognition of FGF Dimerization Beta-strand structure	2A, 2B	1
Intrahepatic Cholangiocarcinoma	p.W290_L312delinsC	Oncopanel Sample 39	Pathogenic	Moderate	Ig-like C2-type D3	Beta-sheet and turn, folding of D3 domain.	Supp. 8	2
Intrahepatic Cholangiocarcinoma	p.I288_E295delinsT	Oncopanel Sample 285	Pathogenic	High	Ig-like C2-type D3	Recognition of FGF Beta-strand structure, folding of D3 domain	Supp. 9	3
Intrahepatic Cholangiocarcinoma	p.W290_I291WI>C	Oncopanel Sample 3	Pathogenic	Reported (43)	Ig-like C2-type D3	Beta-strand structure, folding of D3 domain	Supp. 10	4
Breast Mixed Ductal and Lobular Carcinoma	p.A97_G103del	GENIE MSK-P-0011392-T01-IM5	Pathogenic	Low (not in X-ray)	Ig-like C2-type D1	Beta-strand structure, folding of D1 domain (not in X-ray, inferred from FGFR1 NMR)	Supp. 11	5
Intrahepatic Cholangiocarcinoma	p.H167_N173del	GENIE MSK-P-0032563-T01-IM6	Pathogenic	High	Ig-like C2-type D2	Extended recognition of FGF Dimerization Beta-strand structure	2A, 2B	1
Poorly Differentiated Carcinoma, NOS	p.H167_N173del	GENIE MSK-P-0020056-T01-IM6	Pathogenic	High	Ig-like C2-type D2	Extended recognition of FGF Dimerization Beta-strand structure	2A, 2B	1
Intrahepatic Cholangiocarcinoma	p.P170_K176del	GENIE VICC-482349-unk-1	Pathogenic	High	Ig-like C2-type D2	Recognition of FGF Dimerization Beta-strand structure	Supp. 12	6
High-Grade Serous Ovarian Cancer	p.P256_G261delinsR	GENIE UHN-OCT998164-ARC1	Pathogenic	Moderate	Ig-like C2-type D3	Extended non-structural region linking D3 to D2	Supp. 13	7
Intrahepatic Cholangiocarcinoma	p.P263_A266del	GENIE MSK-P-0033098-T01-M6	Pathogenic	Moderate	Ig-like C2-type D3	Beta-strand structure, folding of D3 domain	Supp. 14	8
Adenocarcinoma, unspecified	p.P263_A266del	GENIE NKI-9NDA-J5ML	Pathogenic	Moderate	Ig-like C2-type D3	Beta-strand structure, folding of D3 domain	Supp. 14	8
Miscellaneous Brain Tumor	p.T268_D273delinsS	GENIE MSK-P-0001890-T01-IM3	Pathogenic	Moderate	Ig-like C2-type D3	Beta-strand and turn structure, folding of D3 domain	Supp. 15	9
Adenoid Cystic Carcinoma	p.V270delinsAEEI	GENIE VICC-349321-unk-1	Non-pathogenic	Moderate	Ig-like C2-type D3	Single position in turn	Supp. 16	10
Uterine Endometrioid Carcinoma	p.G272del	GENIE VICC-580559-unk-1	Non-pathogenic	Moderate	Ig-like C2-type D3	Single position in turn	Supp. 17	11
Intrahepatic Cholangiocarcinoma	p.V280_K292del	GENIE MSK-P-0018110-T01-IM6	Pathogenic	High	Ig-like C2-type D3	Extended recognition of FGF Beta-strand and turn structure, folding of D3 domain	Supp. 18	12
Intrahepatic Cholangiocarcinoma	p.P286_K292del	GENIE MSK-P-0036277-T01-IM6	Pathogenic	High	Ig-like C2-type D3	Recognition of FGF Beta-strand structure, folding of D3 domain	Supp. 19	13
Uterine Endometrioid Carcinoma	p.E369del	GENIE MSK-P-0014582-T01-IM6	Non-pathogenic	Low (not in X-ray)	-	Single position in a non-structured region (not in X-ray), not conserved among FGFRs	-	14

Abbreviations: GENIE, Genomics evidence neoplasia information exchange; NOS, Not otherwise specified.

^aConfidence on the prediction of pathogenicity based on mapping to protein sequence, overlap with reference mutations (see Supplemental Figure 7) (36–51) and structural role in the three-dimensional structure of FGFR2 (see corresponding Figures, last column).

^bAs depicted on the map in Supplemental Figure 7 of the FGFR2 the protein sequence.