Table 2. Open in new tab Germline...

Gene Name

Code

Exonic Function

AA Change

CLINSIG

SIFT

Polyphen

Mutation Taster

Mutation Assessor

CADD

APC

UC35SGR

nsSNP

rs1801155

c.T3920A:p.I1307K

Pathogenic

5.3

UC126SGR

nsSNP

rs876658835

c.C5224T:p.R1742C

VUS

UC1521SGR

nsSNP

rs876660059

c.C5402T:p.A1801V

VUS

14.7

UC169SGR

deletion

rs587778029

c.5501_5506delTCAGAG (p.V1834_R1835del)

VUS

MUTYH

CD4081SGR

nsSNP

rs36053993

c.G1187A:p.G396D

Pathogenic

29.4

UC3964SGR

^ç

nsSNP

rs147480076

c.C1567T:p.R523C

VUS

22.3

MLH1

UC3668SGR

slicing site

rs774073825

c.885-3C>T

Pathogenic

UC393SGR

nsSNP

rs63750361

c.G1166A:p.R389Q

VUS

24.3

UC2766SGR

nsSNP

rs138584384

c.C2173G:p.R725G

VUS

MSH2

UC3964SGR

^ç

nsSNP

rs63750124

c.T435G:p.I145M

VUS

12.7

MSH3

UC3243SGR

^§

nsSNP

rs41545019

c.T2732G:p.L911W

VUS

EPCAM

UC3661SGR

nsSNP

rs115283528

c.A831G:p.I277M

VUS

15.1

POLD1

UC3706SGR

nsSNP

rs145473716

c.G2275A:p.V759I

VUS

POLE

UC3968SGR

^{^}

nsSNP

rs143626223

c.C139T:p.R47W

VUS

BRCA1

UC5172SGR

frameshift

rs886040176

c.3928dupA

Pathogenic

UC126SGR

nsSNP

c.C4754T:p.P1585L

VUS

20.3

UC3243SGR

^§

nsSNP

c.G4908C:p.K1636N

VUS

CHEK2

UC3964SGR

^ç

nsSNP

rs17879961

c.T470C:p.I157T

Pathogenic

21.1

CD5190SGR

frameshift

rs555607708

c.1100delC (p.T367Mfs)

Pathogenic

UC419SGR

nsSNP

rs200050883

G1312T:p.D438Y

VUS

CDKN2A

UC3968SGR

^{^}

nsSNP

rs116150891

c.C430T:p.R144C (OMO MUT)

VUS

10.4

PDGFRA

UC2854SGR

nsSNP

rs150577828

c.G1285A:p.G429R

VUS

9.5

UC3755SGR

nsSNP

c.A2008G:p.I670V

VUS

20.3

Table 2.

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Germline mutation identified in IBD patients with CRC.

Gene Name	Code		Exonic Function		AA Change	CLINSIG	SIFT	Polyphen	Mutation Taster	Mutation Assessor	CADD
APC	UC35SGR		nsSNP	rs1801155	c.T3920A:p.I1307K	Pathogenic	T	B	D	L	5.3
	UC126SGR	*	nsSNP	rs876658835	c.C5224T:p.R1742C	VUS	D	D	D	L	33
	UC1521SGR		nsSNP	rs876660059	c.C5402T:p.A1801V	VUS	T	B	N	N	14.7
	UC169SGR		deletion	rs587778029	c.5501_5506delTCAGAG (p.V1834_R1835del)	VUS	.	.	.	.	.
MUTYH	CD4081SGR		nsSNP	rs36053993	c.G1187A:p.G396D	Pathogenic	D	D	A	H	29.4
	UC3964SGR	^ç	nsSNP	rs147480076	c.C1567T:p.R523C	VUS	T	B	N	N	22.3
MLH1	UC3668SGR		slicing site	rs774073825	c.885-3C>T	Pathogenic	.	.	.	.	.
	UC393SGR		nsSNP	rs63750361	c.G1166A:p.R389Q	VUS	T	P	D	M	24.3
	UC2766SGR		nsSNP	rs138584384	c.C2173G:p.R725G	VUS	D	D	D	M	33
MSH2	UC3964SGR	^ç	nsSNP	rs63750124	c.T435G:p.I145M	VUS	D	B	D	L	12.7
MSH3	UC3243SGR	^§	nsSNP	rs41545019	c.T2732G:p.L911W	VUS	D	D	D	H	25
EPCAM	UC3661SGR		nsSNP	rs115283528	c.A831G:p.I277M	VUS	D	P	N	L	15.1
POLD1	UC3706SGR		nsSNP	rs145473716	c.G2275A:p.V759I	VUS	D	D	D	M	33
POLE	UC3968SGR	^{^}	nsSNP	rs143626223	c.C139T:p.R47W	VUS	D	D	D	M	33
BRCA1	UC5172SGR		frameshift	rs886040176	c.3928dupA	Pathogenic	.	.	.	.
	UC126SGR	*	nsSNP		c.C4754T:p.P1585L	VUS	D	B	N	L	20.3
	UC3243SGR	^§	nsSNP		c.G4908C:p.K1636N	VUS	T	B	N	L	9
CHEK2	UC3964SGR	^ç	nsSNP	rs17879961	c.T470C:p.I157T	Pathogenic	T	P	A	L	21.1
	CD5190SGR		frameshift	rs555607708	c.1100delC (p.T367Mfs)	Pathogenic	.	.	.	.	.
	UC419SGR		nsSNP	rs200050883	G1312T:p.D438Y	VUS	D	D	D	L	33
CDKN2A	UC3968SGR	^{^}	nsSNP	rs116150891	c.C430T:p.R144C (OMO MUT)	VUS	D	B	N	M	10.4
PDGFRA	UC2854SGR		nsSNP	rs150577828	c.G1285A:p.G429R	VUS	T	B	D	L	9.5
	UC3755SGR		nsSNP		c.A2008G:p.I670V	VUS	T	P	N	N	20.3

Gene Name	Code		Exonic Function		AA Change	CLINSIG	SIFT	Polyphen	Mutation Taster	Mutation Assessor	CADD
APC	UC35SGR		nsSNP	rs1801155	c.T3920A:p.I1307K	Pathogenic	T	B	D	L	5.3
	UC126SGR	*	nsSNP	rs876658835	c.C5224T:p.R1742C	VUS	D	D	D	L	33
	UC1521SGR		nsSNP	rs876660059	c.C5402T:p.A1801V	VUS	T	B	N	N	14.7
	UC169SGR		deletion	rs587778029	c.5501_5506delTCAGAG (p.V1834_R1835del)	VUS	.	.	.	.	.
MUTYH	CD4081SGR		nsSNP	rs36053993	c.G1187A:p.G396D	Pathogenic	D	D	A	H	29.4
	UC3964SGR	^ç	nsSNP	rs147480076	c.C1567T:p.R523C	VUS	T	B	N	N	22.3
MLH1	UC3668SGR		slicing site	rs774073825	c.885-3C>T	Pathogenic	.	.	.	.	.
	UC393SGR		nsSNP	rs63750361	c.G1166A:p.R389Q	VUS	T	P	D	M	24.3
	UC2766SGR		nsSNP	rs138584384	c.C2173G:p.R725G	VUS	D	D	D	M	33
MSH2	UC3964SGR	^ç	nsSNP	rs63750124	c.T435G:p.I145M	VUS	D	B	D	L	12.7
MSH3	UC3243SGR	^§	nsSNP	rs41545019	c.T2732G:p.L911W	VUS	D	D	D	H	25
EPCAM	UC3661SGR		nsSNP	rs115283528	c.A831G:p.I277M	VUS	D	P	N	L	15.1
POLD1	UC3706SGR		nsSNP	rs145473716	c.G2275A:p.V759I	VUS	D	D	D	M	33
POLE	UC3968SGR	^{^}	nsSNP	rs143626223	c.C139T:p.R47W	VUS	D	D	D	M	33
BRCA1	UC5172SGR		frameshift	rs886040176	c.3928dupA	Pathogenic	.	.	.	.
	UC126SGR	*	nsSNP		c.C4754T:p.P1585L	VUS	D	B	N	L	20.3
	UC3243SGR	^§	nsSNP		c.G4908C:p.K1636N	VUS	T	B	N	L	9
CHEK2	UC3964SGR	^ç	nsSNP	rs17879961	c.T470C:p.I157T	Pathogenic	T	P	A	L	21.1
	CD5190SGR		frameshift	rs555607708	c.1100delC (p.T367Mfs)	Pathogenic	.	.	.	.	.
	UC419SGR		nsSNP	rs200050883	G1312T:p.D438Y	VUS	D	D	D	L	33
CDKN2A	UC3968SGR	^{^}	nsSNP	rs116150891	c.C430T:p.R144C (OMO MUT)	VUS	D	B	N	M	10.4
PDGFRA	UC2854SGR		nsSNP	rs150577828	c.G1285A:p.G429R	VUS	T	B	D	L	9.5
	UC3755SGR		nsSNP		c.A2008G:p.I670V	VUS	T	P	N	N	20.3

Abbreviations: nsSNP, nonsynonymous SNPs; VUS, variant of uncertain significance; AA change, amino acid change; CLINSIG, clinical significance. SIFT (sorting intolerant from tolerant): D, deleterious; T, tolerated. Polyphen (polymorphism phenotyping): D, probably damaging; P, possibly damaging; B, benign. CADD (combined annotation dependent depletion). Mutation Taster: A, disease causing (predicted as disease causing in ClinVar); D, disease causing; N, polymorphism; P, polymorphism-automatic (predicted as neutral in ClinVar). Mutation Assessor: H, high; M, medium; L, low; N, neutral.

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