Detection and analysis of common pathogenic germline mutations in Peutz-Jeghers syndrome

Table 9 Other gene mutations and inclusion in relevant database

No.	Gene	Type	Mutation site	Amino acid changes	Exon	Disease database
						HGMD	ClinVar	OMIM
1	BARD1	TSG	c.556A>G	p.S186G	4|11	/	(6/6)Uncertain Significance	/
	EGFR	/	c.61G>A	p.A21T	1|28	/	/	Epidermal growth factor receptor
2	GEN1	/	c.181T>A	p.S61T	3|14	/	/	Gen endonuclease homolog 1
	BRCA1	TSG	c.2387C>T	p.T796I	10|23	/	(8/8)Uncertain Significance	/
4	NTRK1	/	c.1604A>G	p.E535G	13|17	/	/	/
	PDGFRA	/	c.1423G>A	p.E475K	10|23	/	/	/
	TSC2	TSG	c.521C>T	p.S174L	6|42	/	(2/2)Uncertain Significance	/
	MSH6	/	c.1063G>A	p.G355S	4|10		(4/7)Uncertain Significance(3/7)likely benign	/
5	EGFR	/	c.3040G>A	p.D1014N	25|28	/	/	Epidermal growth factor receptor
	MTUS1	TSG	c.2282G>A	p.S761N	3|15	/	/	Mitochondrial tumor suppressor 1
	PTCH1	TSG	c.2222C>T	p.A741V	14|24	/	(3/4)benign, (1/4)likely benign	/
6	SDHA	TSG	c.715A>G	p.I239V	6|15	√	(2/2)Uncertain significance	/
	MTUS1	TSG	c.1866C>G	p.N622K	2|15	√	√	Mitochondrial tumor suppressor 1
7	RECQL4	/	c.1048A>G	p.R350G	5|21	/	(1/1)Uncertain Significance	/
	RECQL4	/	c.236G>A	p.G79E	4|21	/	/	/
8	ATM	TSG	c.6503C>T	p.S2168L	45|63	/	(7/7)Uncertain Significance	Ataxia telangiectasia mutated
10	TSC2	TSG	c.3475C>T	p.R1159W	30|42	/	(2/4)benign, (2/4)likely benign	/
	FANCG	TSG	c.458C>G	p.A153G	4|14	/	(1/1)Uncertain Significance	/
11	SBDS	/	c.98A>G	p.K33R	1|5	/	/	/
12	VHL	TSG	c.134C>T	p.P45L	1|3	/	/	Von Hippel-Lindau syndrome
	FANCA	/	c.3031C>T	p.R1011C	31|43	/	(1/1)likely benign	/
	TP53	TSG	c.620A>G	p.D207G	6|11	√	/	/
13	FANCA	/	c.2944A>G	p.T982A	30|43	/	(2/2)Uncertain Significance	/
14	PALLD	/	c.1011C>A	p.D337E	3|21	/	/	/
	MLH3	TSG	c.1519A>G	p.M507V	2|13	/	(1/1)Uncertain Significance	Mutl (E. Coli) homolog 3
	SMARCA4	TSG	c.3791C>T	p.T1264M	28|36	/	(3/3)Uncertain Significance	/
	NF1	TSG	c.3940T>C	p.W1314R	29|58	/	(1/1)Uncertain Significance	/
15	PTCH1	TSG	c.2222C>T	p.A741V	14|24	/	(1/1)likely benign	/
	GALNT12	/	c.148C>A	p.P50T	1|10	/	/	/
16	ATR	TSG	c.325C>T	p.R109W	4|47	/	(1/1)Uncertain Significance	Ataxia telangiectasia and Rad3 related
	VEGFA	TSG	c.1039G>A	p.V347I	6|8	/	/	Vascular endothelial growth factor
	DIS3L2	/	c.1642G>A	p.A548T	13|21	/	/	/
17	TSC1	TSG	c.2693C>G	p.T898S	21|23	√	(3/5)likely benign, (1/5)benign, (1/5)Uncertain significance	/
18	PTCH1	TSG	c.109G>T	p.G37W	1|24	√	(1/1)Uncertain Significance	/
	BRIP1	/	c.3072del	p.S1025Hfs	20|20	√	(1/2)likely pathogenic, (1/2)Uncertain significance	/
	WRN	/	c.3778G>A	p.A1260T	32|35	/	(2/2)Uncertain significance	werner syndrome
	RECQL	/	c.166G>A	p.G56R	4|16	/	/	/
19	BARD1	TSG	c.1148T>G	p.M383R	4|11	/	/	/
	USHBP1	/	c.1358C>T	p.P453L	9|13	/	/	/
	APC	TSG	c.2882A>G	p.N961S	16|16	/	(1/1)Uncertain Significance	Adenomatosis polyposis coli
20	DICER1	TSG	c.2113A>G	p.I705V	13|27	/	/	Multinodular goiter
	FANCM	/	c.2762G>A	p.C921Y	14|23	/	/	/
	APC	TSG	c.5257G>C	p.A1753P	16|16	/	(3/3)Uncertain Significance	Adenomatosis polyposis coli
	NSD1	/	c.5493T>G	p.D1831E	16|23	/	/	Sotos syndrome
	SDHA	TSG	c.739A>G	p.I247V	6|15	/	(4/4)Uncertain Significance	/
	MTUS1	TSG	c.908A>G	p.N303S	2|15	/	/	Mitochondrial tumor suppressor 1
22	EXT2	TSG	c.896G>A	p.R299H	5|14	√	(1/2)likely benign, (1/2)uncategorized	/
	ATM	TSG	c.1555G>A	p.V519I	10|63	√	(3/3)Uncertain Significance	Ataxia telangiectasia mutated
	BRCA2	TSG	c.1568A>G	p.H523R	10|27	√	(1/12)benign, (9/12)likely benign, (2/12)Uncertain Significance	Fanconi anemia
	TP53	TSG	c.214C>G	p.P72A	4|11	√	(5/5)Uncertain Significance	/
23	FLCN	TSG	c.1366G>C	p.D456H	12|14	/	/
	MSH2	TSG	c.1789G>A	p.D597N	12|16	/	(1/1)Uncertain Significance	Colon cancer, nonpolyposis type 1
	KIT	/	c.2263G>A	p.A755T	16|21	/	(1/2)Uncertain Significance,(1/2)uncategorized	Piebald trait
24	BAP1	TSG	c.1154G>A	p.R385Q	12|17	/	(2/2)Uncertain Significance	/
	TSC2	TSG	c.1609C>T	p.R537C	16|42	√	(1/5)benign, (2/5)likely benign; (1/5)Uncertain Significance; (1/5)uncategorized	/

HGMD: Human Gene Mutation Database; OMIM: Online Mendelian Inheritance in Man; TSG: Tumor suppressor gene.