Table 4 Gene variants identified by network analysis.

From: Using whole-exome sequencing and protein interaction networks to prioritize candidate genes for germline cutaneous melanoma susceptibility

Gene	Chr	Location	SNP ID	REF	VAR	Variant type	Freq in family^a	Family ID	Outgroup count^b	MAF in control dataset			Variant impact	Pathogenecity prediction^c			pVAAST	pVAAST	Prioritization method^f	P-value^g
Gene	Chr	Location	SNP ID	REF	VAR	Variant type	Freq in family^a	Family ID	Outgroup count^b	EXAC	ESP	1 KG	Variant impact	METASVM	METALR	CADD	P-value^d	Rank^e	Prioritization method^f	P-value^g
IL1RN	2	113890242	rs757992723	A	C	Missense	3/5	FF2	0	4.50E−05			Moderate	T	T	24.6	3.03E−04	2	DADA/GM^S/HH^S	0.007
ERCC3	2	128046437	rs200443230	T	A	Missense	3/5	A2	0	l.50E−05			Moderate	T	T	21	ns		DADA/GM^D	0.022
ATR	3	142232392	rs200070057	T	C	Missense	3/5	A2	0	2.55E−04	3.49E−04		Moderate	T	T	25.5	ns		DADA/GM^SD/HH^D	0.024
NGLY1	3	25775422	rs201337954	T	A	Stop_gained	3/4	T	0	2.70E−04	2.33E−04		High				8.00E−06	1	DADA/GM^S	0023
FABP2	4	120241839	Rs367603528	C	T	Missense	3/3	A6	0	l.51E−05			Moderate	T	T	30	2.74E−04	1	DADA/GM^S/HH^S	0.019
CD14	5	140012379	rs151227107	G	C	Missense	3/5	B22	1	3.78E−04	9.30E−04		Moderate	T	D	12.74	ns		DADA/GM^D	0.034
MLLT4	6	168312131	rs769690450	G	A	Missense	3/3	A6	0	4.50E−05			Moderate	T	T	21.9	6.03E−03	98	DADA/GM^D/HH^D	0.037
MLLT4	6	168348545	rs773338292	G	C	Missense	3/5	A2	0	1.50E−05			Moderate	T	T	25.2	ns		DADA/GM^D/HH^D	0.037
ANKS1A	6	34985418	rs748921780	C	T	Missense	4/5	A2	0				Moderate	T	T	24.4	3.03E−04	13	GM^D/HH^D	0.047
PRKDC	8	48840360	rs35938758	C	T	Missense	3/5	FF2	0	2.48E−04	1.19E−04		Moderate	T	T	25.8	ns		DADA/GM^SD	0.007
EIF3A	10	120796765	rs367880512	G	A	Missense	4/4	F10	0	4.50E−05	1.16E−04		Moderate	T	T	21.6	4.50E-04	13	GM^SD	0.017
PLCE1	10	95931182		T	G	Missense	3/3	X	0				Moderate	T	T	26.3	ns		DADA/GM^D	0.011
PROSER2	10	11908784	rs779142603	T	C	Splicing	3/3	D2	0	3.17E−05			High			12.08	4.11E−04	7	DADA/GM^S/HH^S	0.013
CDC42BPG	11	64597710	rs150779995	A	G	Missense	3/3	D2	0				Moderate	T	T	28.4	3.52E−04	2	GM^D/HH^D	0.015
ECI1	16	2294529	rs375300423	C	T	Missense	4/5	FF2	1	2.53E−04	1.16E−04		Moderate	D	D	17.19	5.09E−04	14	DADA/GM^S/HH^S	0.011
CYP4F11	19	16025439	rs200031770	G	C	Stop_gained	3/4	F10	0	8.99E−05	1.16E−04		High			13.01	ns		DADA/GM^S/HH^S	0.008
MAP2K2	19	4101254		G	A	Stop_gained	3/5	FF2	0				High			17.68	ns		DADA/GM^D	0.015

Chr chromosome, REF reference allele, VAR variant allele, Freq frequency, CMM cutaneous malignant melanoma, MAF minor allele frequency, T tolerant, D deleterious, RWR random walk with restart.
^aNumber of cases with the variant/number of cases sequenced in this family.
^bInternal family controls: ~ 2000 exomes from ~ 1000 cancer families (excluding melanoma or pancreatic cancer families).
^cPathogenicity prediction for missense variants based on in silico algorithms, METALR and METASVM, which are ensemble prediction scores that incorporate results from nine algorithms and allele frequency.
^dpVAAST Pedigree Variant Annotation, Analysis, and Search Tool. Gene/variant-based linkage analysis combined with functional prediction and rare variant case–control analysis to evaluate the combined statistical evidence of disease-gene association in each family; ns non-statistically significant.
^epVAAST rank: Candidate genes were ranked based on P-values from the combined pVAAST test.
^fPrioritization method: GM GeneMANIA, HH Hierarchical HotNet; DADA Degree-Aware Disease Gene Prioritization Algorithm; ^Sprotein interacting with susceptibility seed; ^Dprotein interacting with driver seed.
^gPermutation P-values after RWR algorithm and InWeb_IM network.

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