Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia

Table 1 Pathogenicity predictions for RTEL1 missense VUS from FIP patients

Pos	Ref	Alt	Telomere %	Segregation	PPH2	SIFT	ConSurf	PathProx	Model
55	T	S	3%	Seg	0.00	1.00	−0.56	−0.02	N-terminal
516	V	L	1%	Seg	0.05	0.62	−0.15	0.41	N-terminal
540	S	A	2%	Seg	0.57	0.09	−0.80	0.21	N-terminal
559	F	I	6%	Seg	1.00	0.00	−1.11	0.44	N-terminal
688	S	C	1%	Seg	0.91	0.14	−0.62	0.27	N-terminal
719	D	G	8%	Seg	0.03	0.22	0.21	0.05	N-terminal
512	W	C	Unknown	Unknown	0.17	0.48	0.31	0.47	N-terminal
161	H	Q	Unknown	NonSeg	0.40	0.16	−0.35	−0.13	N-terminal
397	Q	E	94%	NonSeg	0.08	0.20	0.40	−0.09	N-terminal
528	A	E	58%	Unknown	0.62	0.05	−0.75	0.08	N-terminal
574	R	W	45%	NonSeg	0.95	0.00	−0.53	0.07	N-terminal
1107	P	L	6%	NonSeg	0.63	0.01		−0.13	C-terminal
1110	F	L	Unknown	NonSeg	0	1		−0.17	C-terminal

Variants are grouped by evidence for pathogenicity, which is inferred from disease co-segregation and patient telomere lengths. Variants that segregate with disease and short telomeres are treated as pathogenic (Additional file 1: Figure S1). Scores in bold indicate deleterious predictions. All thresholds were applied as recommended by each method

ISSN: 1471-2105