Novel Likely Pathogenic Variants Identified by Panel-Based Exome Sequencing in Congenital Cataract Patients

Table 3

Summary of function prediction of three likely pathogenic variants.

Gene symbol	CRYBB2 (family A)	CRYBB2 (family B)	CRYGD (family C)
ID	chr22-25623876	chr22-25623876	chr2-208986446 208986447
Ref_Transcript	NM_000496	NM_000496	NM_006891
Exon	exon4	exon4	exon3
Nucleotide_Changes	c.230G>T	c.230G>A	c.475delG
Amino_Acid_Changes	p.G77V	p.G77D	p.A159Pfs∗9
Gene_Type	het	het	het
Pathogenic_Analysis	Uncertain	Uncertain	Likely pathogenic
clinvar	—	—	—
MutRatio	0.39	0.45	0.55
Mutation_Type	SNV	SNV	deletion
dbsnp	—	—	—
PathSNP	#N/A	#N/A	#N/A
MutInNormal	#N/A	#N/A	#N/A
1000Genome	#N/A	#N/A	#N/A
MutInDatabase	#N/A	#N/A	#N/A
1000g2015aug_all	—	—	—
ESP6500si	—	—	—
Inhouse	—	—	—
gnomAD_exome_ALL	—	—	—
gnomAD_exome_EAS	—	—	—
SIFT	0	0	—
SIFT_Predict	Damaging	Damaging	—
PolyPhen_2	0.999	0.999	—
PolyPhen_2_Predict	Probably_damaging	Probably_damaging	—
MutationTaster	1	1	—
MutationTaster_Predict	Disease_causing	Disease_causing	—
GERP++	5.08	5.08	—
GERP++_Predict	Conserved	Conserved	—
SPIDEX	0.5789	1.3267	—
REVEL_score	0.957	0.968	—
MCAP_score	0.157318302	0.219654258	—
MCAP_pred	P	P	—
InterVar	Likely pathogenic	Likely pathogenic	Uncertain_significance
Highest-MAF	—	—	—
Mygeno_InterACMG	PM2; PP3	PM2; PP3	PVS; PM2
Pathogenic_Analysis (based on ACMG guidlines)	Uncertain	Uncertain	Likely pathogenic

“#N/A” indicates that it does not exist in the database, and “-” indicates the frequency in the database. SIFT predictive value, the smaller the value, the more likely it is to cause disease. PolyPhen prediction value, the larger the value, the more likely it is to cause disease. MutationTaster prediction result, the larger the value, the more likely it is to cause disease. GERP++ indicates the value of predicting conservativeness among various species, and >2 indicates relatively conservative.