Table 2 Pathogenicity assesment of novel rare missense and splicing variants.

From: Panel-based NGS Reveals Novel Pathogenic Mutations in Autosomal Recessive Retinitis Pigmentosa

Missense Variants

Family

Gene

cDNA

Protein

SIFT

Polyphen

Align GVGD

Mut.Taster

phyloP

SPV

EVS

ExAC

RP-1147

CNGA1

c.1037G > A

p.Arg346Gln

D(0)

Pos. D(0.852)

Class C35

D

5.39

–

0.0001

0.00001

RP-1201

RP2

c.708C > G

p.Cys236Trp

D(0)

Pr. D(0.997)

Class C65

D

-0.149

–

–

–

RP-0456

USH2A

c.10709G > T

p.Cys3570Phe

D(0)

Pr. D(0.996)

Class C65

D

5.21

–

–

–

RP-0338

USH2A

c.9433C > T

p.Leu3145Phe

D(0.02)

Pos. D(0.598)

Class C15

P

0.70

–

0.0001

–

RP-2113

USH2A

c.5462A > G

p.Lys1821Arg

T(0.1)

B(0.096)

Class C25

P

2.00

–

–

–

Splice Variants

Family

Gene

cDNA

Protein

HSF

BDGP

AST

NetGene 2

ESEFinder

SPV

EVS

ExAC

RP-2066

PDE6A

c.1620 + 1G > T

splicing defect

95.1/-

0.99/-

86.85/69.73

0.82/-

loss SF2/ASF

–

–

0.00001

RP-0040

PRCD

c.74 + 1G > A

splicing defect

79.8/-

0.45/-

67.08/49.96

0.7/-

loss SF2/ASF

–

–

0.00002

  1. Abbreviations: SIFT ( D: deleterious; T: tolerated); Polyphen (Pos.D: possibly damaging; Pr.D: probably damaging; B: benign); Align GVGD (Class C15 less likely pathogenic and Class C65 most likely pathogenic); Mutation taster (D: disease causing; P: polymorphism). PhyloP (From negative values to 1: fast-evolving sites and positive values above 1: conserved sites). Splicing prediction software: wild-type/mutant score. Human Splice finder (HSF), Berkeley Drosophila Genome Project (BDGP), Analyzer Splice Tool (AST). – means the depletion of the 5’ splice site. SPV: Spanish Population Variation Database. EVS: Exome Variant Server. ExAC: Exome Aggregation Consortium.
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