Molecular Vision: Verma, Mol Vis 2025; 31:55-67. Table 2

Table 2. In silico analysis of identified LTBP2 variants.

Variant No.	LTBP2 cDNA variant	LTBP2 protein variant	Variant chromosomal location	Variation impact	Franklin prediction	Mutation taster prediction	PhyloP	Phast Cons	Potential target for NMD (Y/N)	Potential effect on splicing (Y/N)	MutPred 2	CADD_ phred Score
1	c.3499C>T	p.Gln1167Ter	14:74508857-74508857	STOPGAIN at 1167 aa	LP	Disease causing	2.241	1	Y	No	0.83405	41
2	c.3183C>A	p.Cys1061Ter	14:74509828-74509828	STOPGAIN at 1061 aa	LP	Disease causing	3.18	1	Y	Y	0.80611	36
3	c.328C>T	p.Gln110Ter	14:74611617-74611617	STOPGAIN at 110 aa	LP	Disease causing	0.237	0.982	Y	Y	0.64702	37
4	c.1921del	p.Arg641GlyfsTer101	14:74532491-74532492	FS at Arg causing PSC at 101 aa downstream	LP	Disease causing	2.643	1	Y	Y	0.683	NA
5	c.1756dupG	p.Val586GlyfsTer17	14:74549896-74549896	FS at Val-586 replaced by Gly causing PSC at 17 aa downstream	LP	Disease causing	3.067	0.418	Y	N	0.537	NA
6	c.985C>T	p.Gln329Ter	14:74555539-74555539	STOPGAIN at 329 aa	LP	Disease causing	0.538	0.305	Y	Y	0.78926	38
7	c.4237T>G	p.Cys1413Gly	14:74505115-74505115	Substitution of Cys with Gly at 1413 aa	VUS	Disease causing	5.65	1	N	N	0.51	26.3
8	c.1201dupC	p.Gln401ProfsTer202	14:74552385-74552385	FS at Gln-401 replaced by Pro causing PSC at 202 aa downstream	LP	Disease causing	2.59	1	Y	N	0.905	NA
9	c.3131C>G	p.Ser1044Ter	14:74510111-74510111	STOPGAIN at 1044 aa	LP	Disease causing	-0.458	0.119	Y	Y	0.80079	36
10	c.4171dupG	p.Ala1391GlyfsTer8	14:74506054-74506054	FS at Ala-1391replaced by Gly causing PSC at 8aa downstream	LP	Disease causing	0.693	0.283	Y	N	0.101	NA
11	c.4545_4552del	p.Gly1516LeufsTer9	14:74503955-74503963	FS at Gly 1516 replaced by Leu causing PSC at 9 aa downstream	LP	Disease causing	0.26	0.999	Y	N	0.956	NA
12	c.2811del	p.Val939CysfsTer71	14:74516918-74516919	FS at Val-939 replaced by Cys causing PSC at 71 aa downstream	LP	Disease causing	0.579	0.001	Y	Y	0.468	NA

PSC: premature stop codon, FS: Frameshift, LP: Likely Pathogenic, Y:Yes, N:No • PhyloP assigns scores between −14 and +6, with positive values indicating conservation and negative values indicating faster-than-expected evolution. • PhastCons assess nucleotide conservation among 46 different species with score range of (0–1) higher scores show higher conservation. • MutPred Indel analyses impact of insertions/deletions (indels) in human protein structure and functions. Scores range from 0 to 1, with higher scores indicating a greater chance of being pathogenic. • CADD Phred-like score based on whole genome CADD raw scores. The larger the score the more likely the SNP has damaging effect.