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.