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

Table 1 Clinical characteristics of 24 enrolled Peutz-Jeghers syndrome patients

No.	Gender	Specimen	Time since onset of pigment spots (yr)	Early or late onset	Family history (members)	Number of hospitalizations	Number of operations	Stomach and enteroscopy times	Age at initial diagnosis of polyps	Age at first treatment	Polyp pathology	Load of Gastric polyps/Max. diameter (mm)	Load of small intestinal polyps/Max. diameter (mm)	Load of colorectal polyps/Max. diameter (mm)
1	Male	Paraffin section	20	Late	No	2	1	6	20	15	1	/	20/30	/
2	Male	Paraffin section	6	Late	Yes (mother and sister)	1	2	3	9	9	1	2/16	20/40	1/8
3	Female	Paraffin section	4	Late	No	2	1	4	9	9	1	/	3/28	/
4	Male	Paraffin section	5	Late	No	1	2	1	21	21	3	20/4	6/50	/
5	Male	Paraffin section	1	Early	Yes (mother)	4	2	1	4	4	1	2/12	2/60	/
6	Female	Blood	5	Late	Yes (father)	1	0	1	29	29	1	/	/	/
7	Female	Blood	1	Early	Yes (father and sister)	4	0	11	7	7	1	1/8	2/30	3/40
8	Male	Blood	0	Early	Yes (father and sister)	1	0	1	10	10	1	/	10/50	/
9	Male	Blood	6	Late	Yes (mother and grandmother)	4	1	7	6	7	1	5/12	2/30	3/35
10	Female	Blood	2	Early	No	1	0	3	7	7	1	2/15	/	1/30
11	Male	Blood	3	Late	No	1	4	0	22	32	1	/	1/30	/
12	Male	Blood	2	Early	No	2	1	10	4	4	1	1/6	2/50	/
13	Male	Blood	2	Early	No	1	2	1	25	24	1	/	10/20	/
14	Female	Blood	3	Late	No	8	2	8	6	6	1	1/10	8/80	1/20
15	Male	Blood	5	Late	No	1	2	3	20	19	2	1/6	1/80	2/30
16	Male	Blood	1	Early	Yes (mother)	3	0	2	10	9	1	/	1/25	/
17	Male	Blood	1	Early	No	3	1	4	6	6	1	8/40	10/30	/
18	Female	Blood	1	Early	No	6	2	9	11	10	1	1/15	3/35	1/50
19	Female	Blood	3	Late	Yes (mother)	2	0	4	15	15	1	1/12	2/12	1/25
20	Female	Blood	3	Late	Yes (father, uncle, and grandmother)	2	2	5	7	7	1	/	18/50	/
21	Female	Blood	1	Early	Yes (mother, uncle, and aunt)	2	0	4	31	31	1	/	10/50	10/40
22	Female	Blood	2	Early	Yes (father and brother)	1	0	1	6	6	1	10/10	8/50	/
23	Male	Blood	5	Late	No	1	0	2	11	11	1	1/30	5/70	1/30
24	Male	Blood	2	Early	No	1	0	4	5	4	1	10/15	/	/

(1) STK11 mutation, SLX4 mutation, other gene mutation groups: 0: None 1: Yes; (2) Early onset: Pigment spots appeared at < 3 years of age; Late onset: Pigment spots appeared at ≥ 3 years of age; (3) Polyp pathology: 1 hamartoma, 2 hamartoma with adenoma, 3 hamartoma with cancer; (4) Polyp load is the number of polyps, the largest diameter unit is mm; and (5) 6 was an outpatient, the results of previous endoscopy are unknown.

Table 2 Cancer genetic susceptibility 139 gene panel coverage

AIP	CYLD	FANCL	MLH3	PRSS1	SMARCA4
ALK	DDB2	FANCM	MRE11A	PTCH1	SMARCB1
APC	DICER1	FAS	MSH2	PTCH2	SMARCE1
ATM	DIS3L2	FH	MSH6	PTEN	SOS1
ATR	EGFR	FLCN	MTAP	PTPN11	STAT3
AXIN2	ELANE	GALNT12	MTUS1	RAD50	STK11
BAP1	EPCAM	GATA2	MUTYH	RAD51B	SUFU
BARD1	ERCC1	GEN1	NBN	RAD51C	TERT
BLM	ERCC2	GJB2	NF1	RAD51D	TGFBR1
BMPR1A	ERCC3	GPC3	NF2	RB1	TMEM127
BRCA1	ERCC4	GREM1	NSD1	RECQL	TP53
BRCA2	ERCC5	HMBS	NTRK1	RECQL4	TSC1
BRIP1	EXT1	HNF1A	PALB2	RET	TSC2
BUB1B	EXT2	HOXB13	PALLD	RHBDF2	UROD
CBL	EZH2	HRAS	PDGFRA	RUNX1	USHBP1
CDC73	FANCA	KIT	PHOX2B	SBDS	VEGFA
CDH1	FANCB	LASP1	PMS1	SDHA	VHL
CDK4	FANCC	MAX	PMS2	SDHAF2	WRN
CDKN1B	FANCD2	MC1R	POLD1	SDHB	WT1
CDKN1C	FANCE	MEN1	POLE	SDHC	XPA
CDKN2A	FANCF	MET	POLH	SDHD	XPC
CEBPA	FANCG	MTTF	PPM1D	SLX4	XRCC2
CHEK1	FANCI	MLH1	PRKAR1A	SMAD4	ZMAT3
CHEK2

Table 3 Characteristics of STK11/LKB1 gene mutations

No.	Mutation type	dbSNP RS	Mutation site	Amino acid change	Exon	Variant type
2	Frameshift	rs372511774	c.357delC	p.N119Kfs	2|10	SNV
4	Splice-site variant	rs398123406	c.921-1G>A	/	8|10	SNP
5	Frameshift	rs1060499961	c.131dupA	p.L45Afs	1|10	INS
6	Missense	/	c.869T>C	p.L290P	7|10	SNP
7	Nonsense	/	c.658C>T	p.Q220X	5|10	SNP
8	Frameshift	/	c.548del	p.L183Rfs	4|10	DEL
9	Splice-site variant	rs398123406	c.921-1G>C	/	8|10	SNP
10	Frameshift	/	c.471_472del	p.F157Lfs	4|10	DEL
12	Frameshift	/	c.180del	p.Y60X	1|10	DEL
13	Missense	/	c.869T>A	p.L290H	7|10	SNP
14	Splice-site variant	/	c.598-2A>G	/	5|10	SNP
15	Missense	rs121913315	c.580G>A	p.D194N	4|10	SNP
16	Missense	rs730881978	c.890G>A	p.R297K	7|10	SNP
17	Frameshift	/	c.577_578del	p.S193Rfs	4|10	DEL
18	Splice-site variant	/	c.863-2A>G	/	7|10	SNP
19	Splice-site variant	rs1555735080	c.290+1G>T	/	1|10	SNP
20	Nonsense	/	c.179dup	p.Y60X	1|10	INS
21	Frameshift	rs587782584	c.842dup	p.L282Afs	6|10	INS
23	Frameshift	rs786203886	c.228dup	p.V77Rfs	1|10	INS
24	Nonsense	rs730881970	c.409C>T	p.Q137X	3|10	SNP

DEL; Deletion; INS: Insertion; SNP: Single nucleotide polymorphism; SNV: Single nucleotide variation.

Table 4 Prediction of protein function change caused by STK11/LKB1 mutation

No.	PolyPhen		Mutation Assessor		SIFT
	Score	Prediction	Score	Prediction	Score	Prediction
6	1	Probably damaging	0.98351; 4.21	High	0	Deleterious
13	1	Probably damaging	0.99415; 4.555	High	0	Deleterious
15	1	Probably damaging	0.98178; 4.165	High	0	Deleterious
16	1	Probably damaging	0.98818; 4.34	High	0.01	Deleterious
23	0.022	Benign	0.56769; 1.78	Low	0.26	Tolerated

Table 5 STK11/LKB1 mutation-related databases and pathogenicity analysis

No.	cDNA/protein	Disease database			Pathogenic judgment
		HGMD	ClinVar	OMIM
2	p.N119Kfs	/	(1/1) pathogenic	/	Pathogenic
4	c.921-1G>A	√	/	PJS	Pathogenic
5	p.L45Afs	/	/	/	Pathogenic
6	p.L290P	√	(1/1) pathogenic	PJS	Clinical significance unknown
7	p.Q220X	/	(3/3) pathogenic	PJS	Pathogenic
8	p.L183Rfs	/	/	PJS	Pathogenic
9	c.921-1G>C	√	(2/2) pathogenic	PJS	Pathogenic
10	p.F157Lfs	√	/	PJS	Likely pathogenic
12	p.Y60X	√	√	PJS	Pathogenic
13	p.L290H	/	/	PJS	Clinical significance unknown
14	c.598-2A>G	/	(1/1) pathogenic	PJS	Likely pathogenic
15	p.D194N	√	(4/6) likely pathogenic; (2/6) pathogenic	PJS	Likely pathogenic
16	p.R297K	√	(1/2) pathogenic; (1/2) unknown	PJS	Likely pathogenic
17	p.S193Rfs	/	/	PJS	Likely pathogenic
18	c.863-2A>G	/	(1/1) pathogenic	PJS	Likely pathogenic
19	c.290+1G>T	Pathogenic	/	PJS	Likely pathogenic
20	p.Y60X	Pathogenic	(2/2) pathogenic	PJS	Pathogenic
21	p.L282Afs	Pathogenic	(1/1) pathogenic	PJS	Pathogenic
23	p.V77Rfs	/	/	PJS	Likely pathogenic
24	p.Q137X	Pathogenic	(1/1) pathogenic	PJS	Pathogenic

(4/6) likely pathogenic: A total of six institutions have judged this mutation, four of which are judged as probably pathogenic, the same below. PJS: Peutz-Jeghers syndrome.

Table 6 Characteristics of SLX4 gene mutations

No.	Mutation type	dbSNP RS	Mutation site	Amino acid changes	Exon	Variant type
1	Missense	rs551385115	c.5072A>G	p.N1691S	14|15	SNP
2	Splice-site variant	/	c.1683+1G>A	splice	7|15	SNP
3	Missense	rs774243118	c.2990C>T	p.P997L	12|15	SNP
18	Missense	/	c.2425G>C	p.E809Q	12|15	SNP
22	Non-frameshift	/	c.568_570del	p.P190del	3|15	DEL

DEL: Deletion; SNP: Single nucleotide polymorphism.

Table 7 Prediction of protein function change caused by SLX4 mutation

No.	PolyPhen		Mutation assessor		SIFT
	Score	Prediction	Score	Prediction	Score	Prediction
1	0	Benign	0.08118; 0	Neutral	0.16	Tolerated
3	0.004	Benign	0.05510; -0.035	Neutral	1	Tolerated /
18	0.341	Benign	0.59436; 1.845	Low	0.04	Deleterious

Table 8 SLX4 mutation-related databases and pathogenicity analysis

No.	cDNA/Protein	Disease database			Pathogenic judgment
		HGMD	ClinVar	OMIM
1	p.N1691S	/	(1/1)Uncertain Significance	BTB/POZ domain containing 12\SLX4 structure-specific	Clinical significance unknown
2	c.1683+1G>A	/	/	BTB/POZ domain containing 12\SLX4 structure-specific	Likely pathogenic
3	p.P997L	/	/	BTB/POZ domain containing 12\SLX4 structure-specific	Clinical significance unknown
18	p.E809Q	√	/	BTB (POZ) domain containing 12\SLX4 structure-specific	Clinical significance unknown
22	p.P190del	/	/	BTB (POZ) domain containing 12\SLX4 structure-specific	Clinical significance unknown

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.

Table 10 Prediction of protein function changes caused by other gene mutations

Gene	SIFT		PolyPhen		Mutation Assessor
	Score	Prediction	Score	Prediction	Score	Prediction
BARD1	0	Deleterious	0.144	Benign	0.66939; 2.045	Medium
EGFR	0.4	Tolerated	0.956	Probably damaging	0.33485; 1.01	Low
GEN1	0	Deleterious	0.999	Probably damaging	0.34521; 1.04	Low
BRCA1	0.02	Deleterious	0.775	Probably damaging	0.78223; 2.4	Medium
NTRK1	0.01	Deleterious	0.639	Probably damaging	0.02685; -0.53	Neutral
PDGFRA	0.1	Tolerated	0.05	Benign	0.38838; 1.175	Low
TSC2	0.15	Tolerated	0.327	Benign	0.57536; 1.79	Low
MSH6	0.45	Tolerated	0.176	Benign	0.08118; 0	Neutral
EGFR	0	Deleterious	0.814	Possibly damaging	0.83953; 2.67	Medium
MTUS1	0.09	Tolerated	0.044	Benign	0.27053; 0.805	Low
PTCH1	0	Deleterious	0.7	Possibly damaging	0.88377; 2.95	Medium
SDHA	0.01	Deleterious low confidence	0.078	Benign	0.49699; 1.58	Low
MTUS1	0.01	Deleterious	0.096	Benign	0.29908; 0.895	Low
RECQL4	/	/	/	/	/	/
RECQL4	/	/	/	/	/	/
ATM	0	Deleterious	0.294	Benign	0.67953; 2.075	Medium
TSC2	0.01	Deleterious	0.226	Benign	0.08118; 0	Neutral
FANCG	0.03	Deleterious	0.018	Benign	0.14661; 0.345	Neutral
SBDS	0.12	Tolerated	0.051	Benign	0.71920; 2.185	Medium
VHL	0.06	Tolerated	0.012	Benign	0.19112; 0.55	Neutral
FANCA	0.24	Tolerated	0	Benign	0.02315; -0.6	Neutral
TP53	0.03	Deleterious	0.386	Benign	0.45228; 1.405	Low
FANCA	0.79	Tolerated	0.007	Benign	0.52573; 1.65	Low
PALLD	0.7	Tolerated	0.159	Benign	0.00602; -1.34	Neutral
MLH3	0.47	Tolerated	0	Benign	0.55103; 1.725	Low
SMARCA4	0.05	Deleterious	0.007	Benign	0.29908; 0.895	Low
NF1	0.62	Tolerated	0.015	Benign	0.08118; 0	Neutral
PTCH1	0	Deleterious	0.626	Possibly damaging	0.88377; 2.95	Medium
GALNT12	0.11	Tolerated	0.007	Benign	0.51422; 1.61	Low
ATR	0	Deleterious	0.998	Probably damaging	0.65975; 2.015	Medium
VEGFA	0.25	Tolerated low confidence	0.695	Probably damaging	0.08118; 0	Neutral
DIS3L2	0.05	Tolerated	0.996	Probably damaging	0.87328; 2.875	Medium
TSC1	/	/		/	0.00621; -1.32	Neutral
PTCH1	0.03	Deleterious low confidence	0.259	Benign	0.36672; 1.1	Low
BRIP1	/	/	/	/	/	/
WRN	0.59	Tolerated	0.164	Benign	0.70595; 2.14	Medium
RECQL	0.5	Tolerated	0.005	Benign	0.41079; 1.255	Low
BARD1	0.4	Tolerated	0	Benign	0.08118; 0	Neutral
USHBP1	0.05	Tolerated	0.521	Possibly damaging	0.56769; 1.78	Low
APC	0.16	Tolerated	0.82	Possibly damaging	0.46157; 1.445	Low
DICER1	0.29	Tolerated	0.664	Possibly damaging	0.34521; 1.04	Low
FANCM	1	Tolerated	0	Benign	0.40543; 1.245	Low
APC	0.57	Tolerated low confidence	0.003	Benign	0.14661; 0.345	Neutral
NSD1	0.03	Deleterious	0.684	Possibly damaging	0.66939; 2.045	Medium
SDHA	0.02	Deleterious low confidence	0.02	Benign	0.20574; 0.59	Neutral
MTUS1	0.87	Tolerated	0	Benign	0.12746; 0.255	Neutral
EXT2	0.03	Deleterious	0.993	Possibly damaging	0.82323; 2.585	Medium
ATM	0.58	Tolerated	0.007	Benign	0.56769; 1.78	Low
BRCA2	0.09	Tolerated	0.003	Benign	0.08118; 0	Neutral
TP53	0.94	Tolerated	0	Benign	0.03608; -0.345	Neutral
FLCN	0.03	Deleterious	0	Benign	0.47716; 1.5	Low
MSH2	0.25	Tolerated	0.023	Benign	0.39692;1.235	Low
KIT	0.15	Tolerated	0.472	Possibly damaging	0.03608; -0.345	Neutral
BAP1	0	Deleterious low confidence	0.968	Possibly damaging	0.59436; 1.845	Low
TSC2	0.02	Deleterious	0.446	Possibly damaging	0.75777; 2.31	Medium