Table 2.

Selected germline variants in human mucosal melanomas

Gene	Chr.	Position	Ref.	Alt.	Variant effect	Prot. Pos.	AA change	SIFT score	dbSNP ID/ COSMIC ID	ClinVar clinical significance (Variation ID; Alt. name)	Case(s)
BRCA1	17	43124027	ACT	A	Frameshift	23	E/X	—	rs386833395 COSM3190163	Pathogenic (17662; p.Glu23fs; c.68_69 delAG; 185delAG)	PD26992b
BRCA2	13	32338034	CTG	C	Frameshift	1227	L/X	—	rs80359395	Pathogenic (51504)	PD25663b
TP53	17	7676037	CAGACGGAAACC	CTGAAT	Inframe deletion (11 bp del + 5 bp ins	108-111	GFRL/ IQ	—	—	Pathogenic (12381)	PD25652b/e/f
MUTYH	1	45332803	T	C	Missense	176	Y/C	0	rs34612342	Pathogenic (5293; p.Tyr179Cys)	PD26990b
CHEK2	22	28695219	G	A	Missense	471	S/F	0.01	rs137853011 COSM2935967	Conflicting interpretations of pathogenicity; Risk factor (5603; p.Ser428Phe)	PD26997b
MITF	3	69964940	G	A	Missense	419	E/K	0.04	rs149617956	Conflicting interpretations of pathogenicity; Risk factor (29792; p.Glu318Lys)	PD25648b/e
TMEM127	2	96265174	C	T	Missense	70	D/N	0.36	rs121908819	Conflicting interpretations of pathogenicity (126964)	PD26692b
ATM	11	108227849	C	G	Missense	49	S/C	0	rs1800054	Benign/Likely benign; Risk factor (3048)	PD26932b PD26998b
COL6A3	2	237378831	G	A	Missense	768	R/C	0	rs200722892 (G > C)	—	PD26923b
POT1	7	124827283	T	A	Missense	539	Q/H	0.05	rs973319258	—	PD25655b

Shown are germline variants in human mucosal cases from this study that were found in the ClinVar database and classified as a risk factor for cancer, had a clinical significance of either pathogenic or mixed pathogenicity, or had a deleterious SIFT score <= 0.05. “Ref.” and “Alt.” are the reference and alternate bases, respectively, at each position. “AA change” is the amino acid substitution resulting from the alternate base. Identifiers from dbSNP, and the COSMIC and ClinVar databases are shown. Note that variants in the COSMIC database are somatic and ClinVar variants shown were observed previously as germline variants