A novel stop-gain pathogenic variant in FLT4 and a nonsynonymous pathogenic variant in PTPN11 associated with congenital heart defects

Tabib, Avisa; Talebi, Taravat; Ghasemi, Serwa; Pourirahim, Maryam; Naderi, Niloofar; Maleki, Majid; Kalayinia, Samira

doi:10.1186/s40001-022-00920-8

Table 1 Bioinformatics analysis of pathogenic reported variants in FLT4 (NM_182925.5) related to congenital heart defects

From: A novel stop-gain pathogenic variant in FLT4 and a nonsynonymous pathogenic variant in PTPN11 associated with congenital heart defects

No.	Exon	HGVS DNA	HGVS Protein	Chromosome 5 Position (hg19)	dbSNP	CADD	SIFT	Polyphen-2	PROVEAN	Mutation taster	ClinVar	Condition	Refs.
1	18	c.2554G > A	p. G852S	180,046,758	NA	26.8	D	PD	D	DC	NA	MD	[24]
2	18	c.2554G > C	p. G852R	180,046,758	NA	26.7	D	PD	D	DC	NA	MD	[24]
3	18	c.2555G > T	p. G852V	180,046,757	NA	26.1	D	PD	D	DC	NA	MD	[24]
4	18	c.2560G > C	p. G854R	180,046,752	rs144045237	29.2	D	PD	D	DC	NA	MD	[24,25]
5	18	c.2569G > A	p. G857R	180,046,743	rs267606818	27.9	D	PD	D	DC	P	MD	[24,26]
6	26	c.3433C > T	p.R1145C	180,039,610	rs202140363	25.9	D	PD	N	DC	NA	MD	[24]
7	19	c.2740G > C	p. G914R	180,046,274	NA	32	D	PD	D	DC	NA	MD	[24]
8	19	c.2744C > A	p. A915E	180,046,270	NA	32	D	PD	D	DC	NA	MD	[24]
9	19	c.2749A > C	p. T917P	180,046,265	NA	29.4	D	PD	D	DC	NA	MD	[24]
10	20	c.2797G > C	p. G933R	180,046,074	NA	32	D	PD	D	DC	NA	MD	[24,25]
11	20	c.2800A > T	p. N934Y	180,046,071	NA	32	D	PD	D	DC	NA	MD	[24]
12	20	c.2828G > C	p. R943P	180,046,043	NA	31	D	PD	D	DC	NA	MD	[24]
13	22	c.3054C > A	p. S1018R	180,043,942	NA	25.4	D	PD	D	DC	NA	MD	[24]
14	22	c.3056 T > C	p. F1019S	180,043,940	NA	30	D	PD	D	DC	UVS	MD	[24]
15	22	c.3075G > A	p. M1025I	180,043,921	NA	29.8	D	PD	D	DC	NA	MD	[24]
16	23	c.3097 T > G	p. C1033G	180,043,489	NA	27.9	D	PD	D	DC	NA	MD	[24]
17	23	c.3104A > G	p. H1035R	180,043,482	rs121909653	25.4	D	PD	D	DC	P	MD	[24]
18	23	c.3109G > C	p. D1037H	180,043,477	NA	28.9	D	PD	D	DC	NA	MD	[24]
19	23	c.3111C > A	p. D1037E	180,043,475	NA	24.5	D	PD	D	DC	NA	MD	[24]
20	23	c.3119C > A	p. A1040D	180,043,467	NA	27.6	D	PD	D	DC	NA	MD	[24]
21	23	c.3122G > A	p. R1041Q	180,043,464	NA	29.8	D	PD	D	DC	NA	MD	[24]
22	23	c.3122G > C	p. R1041P	180,043,464	rs121909650	28.9	D	PD	D	DC	P	MD	[24,26,27]
23	23	c.3157A > T	p. I1053F	180,043,429	NA	27.1	D	PD	D	DC	NA	MD	[24]
24	23	c.3170G > A	p. G1057D	180,043,416	NA	26.7	D	PD	D	DC	NA	MD	[24]
25	24	c.3250G > A	p. E1084K	180,041,149	NA	31	D	PD	D	DC	NA	MD	[24]
26	24	c.3308 T > C	p. L1103P	180,041,091	NA	26.1	D	PD	D	DC	NA	MD	[24]
27	24	c.3310C > T	p. L1104F	180,041,089	NA	25.3	D	PD	D	DC	NA	MD	[24]
28	24	c.3318G > T	p. E1106D	180,041,081	rs201431522	25.3	D	PD	D	DC	NA	MD	[24]
29	24	c.3323 T > C	p. F1108S	180,041,076	NA	29.1	D	PD	D	DC	NA	MD	[24]
30	25	c.3391G > C	p. G1131R	180,040,051	NA	27.5	D	PD	D	DC	P	MD	[24]
31	17	c.2531G > C	p. R844P	180,047,184	NA	29.5	D	PD	D	DC	NA	MD	[24]
32	18	c.2560G > A	p. G854S	180,046,752	NA	28.5	D	PD	D	DC	NA	MD	[24]
33	18	c.2563G > A	p. A855T	180,046,749	rs121909657	24.6	D	PD	D	DC	P	MD	[24,27,74]
34	18	c.2629G > A	p. A877T	180,046,683	NA	25.9	D	PD	D	DC	NA	MD	[24]
35	18	c.2632G > A	p. V878M	180,046,680	rs121909654	25.6	D	PD	D	DC	P	MD	[24,27,29]
36	19	c.2677C > G	p. L893V	180,046,337	NA	25.0	D	PD	D	DC	NA	MD	[24,30,31]
37	19	c.2737_2739del	p.Leu913del	180,046,275	NA	22.5	NA	NA	NA	DC	NA	MD	[24]
38	19	c.2743G > C	p.A915P	180,046,271	NA	32	D	PD	D	DC	NA	MD	[24,25]
39	19	c.2748C > G	p.C916W	180,046,266	NA	27.3	D	PD	D	DC	NA	MD	[24,25]
40	22	c.3059A > T	p.Q1020L	180,043,937	NA	27.4	D	PD	D	DC	NA	MD	[24,32]
41	22	c.3070G > A	p.G1024R	180,043,926	NA	29.6	D	PD	D	DC	NA	MD	[24]
42	22	c.3071G > A	p.G1024E	180,043,925	NA	28.2	D	PD	D	DC	NA	MD	[24]
43	23	c.3105C > G	p.H1035Q	180,043,481	NA	25.1	D	PD	D	DC	NA	MD	[24,29,30]
44	23	c.3109G > T	p.D1037Y	180,043,477	NA	31	D	PD	D	DC	NA	MD	[24]
45	23	c.3121C > T	p.R1041W	180,043,465	rs1451816005	27.9	D	PD	D	DC	LP	MD	[24,25]
46	23	c.3125A > G	p.N1042S	180,043,461	NA	25.0	D	PD	D	DC	NA	MD	[24]
47	23	c.3131 T > C	p.L1044P	180,043,455	rs121909651	27.2	D	PD	D	DC	P	MD	[24,26]
48	23	c.3151G > A	p.V1051M	180,043,435	NA	25.1	D	PD	D	DC	NA	MD	[24]
49	23	c.3164A > C	p.D1055A	180,043,422	NA	26.9	D	PD	D	DC	NA	MD	[24]
50	23	c.3164A > T	p.D1055V	180,043,422	NA	27.7	D	PD	D	DC	NA	MD	[24]
51	24	c.3257 T > C	p.I1086T	180,041,142	rs121909655	26.4	D	PD	D	DC	P	MD	[24,29]
52	24	c.3316G > A	p.E1106K	180,041,083	rs121909656	27.2	D	PD	D	DC	P	MD	[24,33]
53	25	c.3341C > T	p.P1114L	180,040,101	rs121909652	29.8	D	PD	D	DC	P	MD	[24,26,27,30]
54	25	c.3344A > G	p.Y1115C	180,040,098	NA	28.3	D	PD	D	DC	NA	MD	[24]
55	25	c.3410C > T	p.P1137L	180,040,032	rs1762335528	27.6	D	PD	D	DC	LP	MD	[24,25,30,31]
56	3	c.244C > T	p.R82X	180,057,711	NA	34	NA	NA	NA	DC	P	TOF	[24]
57	8	c.1083C > A	p.Y361X	180,055,902	NA	36	NA	NA	NA	DC	NA	TOF	[24]
58	15	c.2206C > T	p.Q736X	180,047,969	NA	42	NA	NA	NA	DC	NA	TOF	[24]
59	21	c.2995C > T	p.Q999X	180,045,776	NA	35	NA	NA	NA	DC	NA	TOF	[24]
60	21	c.2860C > T	p.P954S	180,045,911	rs34255532	21.3	D	B	N	DC	NA	MD	[24]
61	18	c.2587 T > C	p.S863P	180,046,725	NA	25.6	T	PD	D	DC	NA	Lymphedema	[24]
62	20	c.2819G > C	p.R940P	180,046,052	NA	32	D	PD	D	DC	NA	Lymphedema	[30]
63	25	c.3391G > A	p.G1131S	180,040,051	rs1554109707	27.7	D	PD	D	DC	LP	Lymphedema	[30]
64	13	c.1921C > T	p.P641S	180,048,641	rs55667289	22.1	T	B	N	DC	NA	PCL	[26]
65	20	c.2777 T > C	p.I926T	180,046,094	NA	32	D	PD	D	DC	NA	PCL	[34]
66	19	c.2740G > T	p.G914W	180,046,274	NA	32	D	PD	D	DC	NA	PCL	[34]
67	18	c.2575G > A	p.V859M	180,046,737	NA	26.2	D	PD	D	DC	NA	PCL	[34]
68	19	c.2650G > A	p.G884S	180,046,364	NA	29.9	D	PD	D	DC	NA	MD	[35]
69	28	c.3704C > G	p.S1235C	180,037,008	NA	29.9	T	PD	N	DC	NA	MD	[36]
70	23	c.3163G > C	p.D1055H	180,043,423	NA	27.7	D	PD	D	DC	NA	MD	[37]
71	24	c.3315G > C	p.W1105C	180,041,084	NA	28.7	D	PD	D	DC	NA	MD	[37]
72	24	c.3295 T > C	p.S1099P	180,041,104	NA	27.2	D	PD	D	DC	NA	MD	[37]
73	18	c.2515G > C	p.E839Q	180,047,200	NA	27.5	D	PD	D	DC	NA	MD	[37]
74	10	c.1289C > T	p.S430F	180,053,001	NA	23.6	T	PD	D	DC	NA	MD	[37]
75	20	c.2771 T > C	p.M924T	180,046,100	NA	29.5	D	PD	D	DC	NA	MD	[37]
76	24	c.3296C > T	p.S1099F	180,041,103	NA	29.2	D	PD	D	DC	NA	MD	[37]
77	24	c.3230C > T	p.P1077L	180,041,169	NA	28.6	D	PD	D	DC	NA	MD	[37]
78	18	c.2615G > A	p.S872N	180,046,697	NA	22.6	D	PD	N	DC	NA	MD	[37]
79	24	c.3233 T > A	p.L1078Q	180,041,166	NA	28.0	D	PD	D	DC	NA	MD	[37]
80	23	c.3175G > C	p.A1059P	180,043,411	NA	26.8	D	PD	D	DC	P	MD	[37]
81	24	c.3316G > C	p.E1106Q	180,041,083	NA	26.2	D	PD	D	DC	NA	MD	[37]
82	18	c.2546G > A	p.R849K	180,046,766	NA	14.84	T	B	N	DC	NA	MD	[37]
83	18	c.2554G > T	p.G852C	180,046,758	NA	27.8	D	PD	D	DC	NA	MD	[37]
84	2	c.137G > A	p.S46N	180,058,700	NA	22.3	D	B	N	DC	NA	MD	[37]
85	22	c.3073A > T	p.M1025L	180,043,923	NA	26.5	D	B	D	DC	NA	MD	[37]
86	23	c.3111 C > G	p.D1037E	180,043,475	NA	24.5	D	PD	D	DC	NA	MD	[38]
87	24	c.3323_3325delTCT	p.F1108del	180,041,074	rs587776833	21.1	NA	NA	NA	DC	P	MD	[24,25,29]
88	17	c.2542 + 2delT	NA	180,047,171	NA	24.3	NA	NA	NA		NA	MD	[24,35]
89	24	c.3243G > T	M1081I	180,041,156	NA	26.9	D	PD	D	DC	NA	MD	[39]
90	9	c.1258 + 6_1258 + 10 delTCAGG	NA	180,053,101	rs1247895470	3.209	NA	NA	NA	DC	NA	MD	[37]
91	12	c.1622dupG	p. Q542PTer3	180,049,766	rs1581655293	33	NA	NA	NA	DC	NA	TOF	[37]
92	2	c.89delC	p. P30R Ter3	180,058,748	rs755445139	29.1	NA	NA	NA	DC	NA	TOF	[37]

CHD congenital heart disease, MD Milroy disease, TOF tetralogy of Fallot, PCL primary congenital lymphedema, DC disease causing, D deleterious, T tolerated, N neutral, B benign, PD probably damaging, P pathogenic, NA not available/not applicable
CADD, Phred ≤ 20: damaging; Phred > 20: natural
SIFT, score ≤ 0.05: deleterious; score > 0.05: tolerable
Polyphen-2, score = 0–0.15: benign; score = 0.15–0.85: possibly damaging; score = 0.85–1: probably damaging
PROVEAN, score ≤ − 2.5: deleterious; score > − 2.5: natural

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