A systematic review of inherited retinal dystrophies in Pakistan: updates from 1999 to April 2023

Munir, Asad; Afsar, Salma; Rehman, Atta Ur

doi:10.1186/s12886-024-03319-7

BMC Ophthalmology

Table 2 In-silico predictions of the identified 116 missense variants reported in Pakistani families

From: A systematic review of inherited retinal dystrophies in Pakistan: updates from 1999 to April 2023

Gene	Transcript ID	cDNA	CADD	DANN	LRT	MA	MT	MP	PP-2	PRO	SIFT	ACMG	ClinVar
AIPL1	NM_014336.5	c.465G > T	35	VUS	B	B	VUS	VUS	PD	VUS	VUS	VUS	VUS
SLC6A6	NM_003043.6	c.1196G > T	33	VUS	P	P	VUS	P	PD	n.a	n.a	LP	LP
RLBP1	NM_000326.5	c.346G > C	33	VUS	P	B	VUS	VUS	PD	B	B	P	LP
USH2A	NM_206933.4	c.7334C > T	32	VUS	B	VUS	B	VUS	PD	VUS	VUS	B	B
TULP1	NM_003322.6	c.1561C > T	32	VUS	P	P	VUS	P	PD	P	P	VUS	LP
ADAM9	NM_003816.3	c.1144 T > G	32	VUS	P	P	VUS	P	PD	P	P	VUS	n.a
SNRNP200	NM_014014.5	c.3269G > A	32	P	P	P	VUS	P	PD	VUS	P	LP	P
GUCY2D	NM_000180.4	c.2302C > T	32	P	VUS	P	B	n.a	PD	P	P	P	P
GNAT1	NM_144499.3	c.386A > G	32	VUS	P	P	VUS	P	PD	P	P	LP	P
ARL3	NM_004311.4	c.296G > T	32	VUS	P	P	VUS	P	PD	P	P	LP	P
PDE6A	NM_000440.3	c.1630C > T	32	P	VUS	VUS	B	n.a	PD	P	P	P	P/LP
RPE65	NM_000329.3	c.751G > T	32	VUS	P	P	VUS	P	PD	VUS	P	LP	VUS
PEX6	NM_000287.4	c.2626C > T	32	P	P	P	VUS	n.a	PD	P	VUS	LP	VUS
LRAT	NM_004744.5	c.196G > C	31	VUS	P	P	VUS	P	PD	P	P	LP	n.a
GUCY2D	NM_000180.4	c.2384G > T	31	VUS	VUS	P	B	P	PD	P	P	P	n.a
ARL13B	NM_001174150.2	c.236G > A	31	P	VUS	VUS	VUS	P	PD	VUS	P	LP	P
TULP1	NM_003322.6	c.1445G > A	31	P	P	P	VUS	n.a	PD	VUS	P	P	P
RPE65	NM_000329.3	c.131G > A	31	P	VUS	P	VUS	P	PD	VUS	P	P	P
RDH12	NM_152443.3	c.506G > A	31	P	P	VUS	VUS	P	PD	VUS	P	P	P/LP
GUCY2D	NM_000180.4	c.2384G > A	31	P	VUS	P	B	n.a	PD	VUS	P	LP	VUS
GUCY2D	NM_000180.4	c.582G > C	29.8	VUS	B	VUS	VUS	P	PD	P	P	VUS	n.a
RAX2	NM_001319074.4	c.236G > A	29.7	VUS	B	P	VUS	P	n.a	n.a	n.a	VUS	VUS
USH2A	NM_206933.4	c.12523 T > G	29.5	VUS	B	P	VUS	P	PD	P	P	P	n.a
PRPF3	NM_004698.4	c.1481C > T	29.4	VUS	P	P	VUS	P	PD	P	P	P	CFL
CNGB1	NM_001297.5	c.2284C > T	29.4	P	P	P	VUS	n.a	PD	P	P	P	P
PDE6B	NM_000283.4	c.1655G > A	29.3	P	P	P	VUS	P	PD	VUS	P	P	P/LP
DHX38	NM_014003.4	c.971G > A	29.1	P	VUS	P	VUS	B	PD	VUS	VUS	VUS	LP
CDH23	NM_022124.6	c.8150A > G	29	VUS	P	P	VUS	P	PD	P	P	VUS	n.a
RDH5	NM_002905.5	c.319G > C	28.8	P	P	VUS	VUS	P	PD	P	P	LP	n.a
USH1G/SANS	NM_173477.5	c.1373A > T	28.7	VUS	P	P	VUS	P	PD	n.a	n.a	P	P/LP
RPE65	NM_000329.3	c.179 T > C	28.6	VUS	P	VUS	VUS	P	PD	VUS	P	LP	n.a
RPE65	NM_000329.3	c.782 T > C	28.6	VUS	P	P	VUS	P	PD	P	P	LP	VUS
ABCA4	NM_000350.3	c.5882G > A	28.4	VUS	P	B	VUS	n.a	PD	P	P	P	P
TULP1	NM_003322.6	c.1466A > G	28.2	VUS	P	P	VUS	P	PD	VUS	P	P	P
RPE65	NM_000329.3	c.119G > A	28.1	VUS	P	P	VUS	P	PD	P	P	LP	LP
ABCA4	NM_000350.3	c.91 T > C	27.7	VUS	B	P	VUS	P	PD	P	P	LP	LP
ABCA4	NM_000350.3	c.214G > A	27.6	P	VUS	P	VUS	n.a	PD	P	P	P	P/LP
CNGA3	NM_001298.3	c.991G > C	27.3	P	P	P	VUS	P	PD	P	P	LP	n.a
RDH5	NM_002905.5	c.758 T > G	27.2	B	P	VUS	VUS	VUS	PD	VUS	B	VUS	n.a
RDH12	NM_152443.3	c.609C > A	27.1	VUS	P	P	VUS	P	PD	P	P	P	P
CLRN1	NM_174878.3	c.461 T > G	27	B	P	VUS	VUS	VUS	PD	P	VUS	VUS	LP
CDH23	NM_022124.6	c.7198C > T	27	P	VUS	P	VUS	VUS	PD	P	P	VUS	n.a
ABCA4	NM_000350.3	c.2023G > A	26.9	VUS	P	P	VUS	n.a	PD	B	P	VUS	CFL
CEP290	NM_025114.4	c.148C > T	26.7	VUS	VUS	B	VUS	B	PD	B	VUS	VUS	LP
CNGA3	NM_001298.3	c.955 T > C	26.6	VUS	P	P	VUS	P	PD	P	P	P	P/LP
CERKL	NM_201548.5	c.316C > A	26.5	VUS	VUS	VUS	VUS	P	PD	VUS	B	VUS	CFL
CNGA3	NM_001298.3	c.952G > A	26.5	VUS	P	P	VUS	P	PD	VUS	VUS	VUS	n.a
CNGA3	NM_001298.3	c.847C > T	26.5	VUS	P	P	VUS	P	PD	P	P	P	P/LP
TULP1	NM_003322.6	c.1274 T > C	26.4	VUS	VUS	P	VUS	P	PD	P	P	LP	n.a
SEMA4A	NM_022367.4	c.1049 T > G	26.1	VUS	VUS	P	VUS	P	PD	P	P	LP	P
GUCY2D	NM_000180.4	c.917A > T	26	VUS	VUS	VUS	VUS	P	PD	P	P	VUS	n.a
BBS12	NM_152618.3	c.1589 T > C	26	VUS	VUS	VUS	VUS	P	PD	P	P	VUS	n.a
TMEM67	NM_153704.6	c.1127A > C	26	VUS	VUS	VUS	VUS	VUS	PD	VUS	VUS	P	P
ARL6/BBS3	NM_001278293.3	c.281 T > C	25.8	VUS	P	P	VUS	P	n.a	VUS	P	LP	P
DHX38	NM_014003.4	c.995G > A	25.8	VUS	VUS	VUS	VUS	B	PD	P	B	VUS	VUS
EYS	NM_001142800.2	c.7187G > C	25.7	VUS	VUS	P	B	P	PD	VUS	P	VUS	VUS
ASRGL1	NM_001083926.2	c.532G > A	25.6	P	P	P	VUS	P	PD	P	P	LP	n.a
PDE6B	NM_000283.4	c.1160C > T	25.6	VUS	P	P	VUS	P	PD	P	P	LP	P
IMPDH1	NM_000883.4	c.931G > A	25.6	VUS	P	n.a	VUS	P	PD	P	VUS	P	P
CRB1	NM_201253.3	c.3101G > C	25.5	VUS	n.a	P	VUS	VUS	n.a	P	P	LP	n.a
CRB1	NM_201253.3	c.3962G > C	25.5	P	n.a	P	VUS	P	PD	P	P	P	n.a
RDH12	NM_152443.3	c.619A > G	25.5	VUS	P	P	VUS	P	PD	P	VUS	LP	P
BBS12	NM_152618.3	c.1616G > T	25.4	VUS	VUS	VUS	VUS	P	PD	P	VUS	LP	VUS
RHO	NM_000539.3	c.448G > A	25.3	P	VUS	VUS	VUS	P	PD	B	VUS	P	LP
LCA5	NM_001122769.3	c.652C > G	25.3	VUS	VUS	VUS	B	B	PD	P	P	VUS	n.a
TULP1	NM_003322.6	c.1138A > G	25.2	VUS	P	VUS	VUS	P	B	P	VUS	VUS	n.a
ABCA4	NM_000350.3	c.5243G > A	25.1	VUS	B	VUS	B	VUS	PD	VUS	B	VUS	P
RPGRIP1	NM_020366.4	c.2480G > T	25.1	VUS	VUS	VUS	VUS	P	PD	P	VUS	VUS	P
MKKS	NM_170784.3	c.280 T > C	25	VUS	VUS	P	VUS	P	PD	VUS	B	VUS	n.a
CNGA3	NM_001298.3	c.827A > G	24.8	VUS	P	P	VUS	P	PD	P	P	LP	LP
GUCY2D	NM_000180.4	c.2189 T > C	24.8	VUS	VUS	P	B	P	PD	P	P	LP	n.a
RPGRIP1	NM_020366.4	c.2656C > T	24.7	VUS	VUS	P	VUS	B	PD	VUS	VUS	VUS	n.a
CRB1	NM_201253.3	c.433 T > C	24.6	VUS	n.a	P	VUS	P	PD	P	P	LP	n.a
RDH5	NM_002905.5	c.536A > G	24.5	VUS	P	P	VUS	P	PD	VUS	VUS	LP	P
SEMA4A	NM_022367.4	c.1033G > C	24.4	VUS	VUS	P	VUS	P	PD	VUS	VUS	LP	VUS
PDE6B	NM_001145292.2	c.938C > T	24.3	VUS	P	B	VUS	VUS	B	B	B	VUS	LP
CRB1	NM_201253.3	c.3296C > A	24.3	VUS	n.a	VUS	VUS	VUS	PD	VUS	VUS	VUS	n.a
PRCD	NM_001077620.3	c.2 T > C	24.2	VUS	VUS	n.a	VUS	P	n.a	B	VUS	P	P
BBS5	NM_152384.3	c.2 T > A	24.2	VUS	VUS	n.a	VUS	P	n.a	B	VUS	P	P
CNGA3	NM_001298.3	c.822G > T	24.1	VUS	P	P	VUS	P	PD	P	P	P	CFL
CNGA3	NM_001298.3	c.1306C > T	24	VUS	P	P	VUS	n.a	PD	P	P	P	P
CLRN1	NM_174878.3	c.92C > T	23.9	VUS	VUS	B	VUS	VUS	PD	VUS	VUS	LP	P
BBS2	NM_031885.5	c.443A > T	23.8	VUS	VUS	n.a	B	P	PD	VUS	P	VUS	n.a
ZNF513	NM_144631.6	c.1015 T > C	23.8	VUS	VUS	B	VUS	VUS	PD	P	VUS	B	VUS
GRM6	NM_000843.4	c.824G > A	23.7	VUS	n.a	VUS	VUS	VUS	PD	VUS	B	VUS	VUS
PDE6A	NM_000440.3	c.304C > A	23.6	VUS	P	VUS	B	n.a	PD	VUS	B	P	CFL
IMPDH1	NM_000883.4	c.676G > A	23.6	VUS	P	n.a	VUS	P	B	P	B	VUS	n.a
RDH5	NM_002905.5	c.602C > T	23.6	VUS	VUS	P	B	VUS	PD	VUS	VUS	VUS	n.a
NMNAT1	NM_022787.4	c.25G > A	23.6	VUS	B	P	B	VUS	PD	B	P	P	P
CLCC1	NM_001377458.1	c.75C > A	23.6	VUS	P	P	VUS	P	PD	VUS	P	VUS	P
EYS	NM_001142800.2	c.8299A > T	23.4	VUS	B	VUS	B	VUS	PD	B	B	LB	n.a
TULP1	NM_003322.6	c.1307C > G	23.4	VUS	VUS	B	VUS	P	B	P	VUS	VUS	n.a
AIPL1	NM_014336.5	c.116C > A	23.4	B	P	P	VUS	P	PD	P	P	VUS	n.a
CRB1	NM_201253.3	c.2234C > T	23.1	VUS	n.a	P	VUS	n.a	PD	P	P	P	P/LP
BEST1	NM_004183.4	c.418C > G	22.8	VUS	B	P	VUS	P	PD	B	VUS	LP	CFL
CRB1	NM_201253.3	c.2536G > A	22.8	VUS	n.a	P	VUS	P	PD	P	P	P	P
BBS1	NM_024649.5	c.442G > A	22.7	VUS	n.a	VUS	VUS	n.a	PD	VUS	B	VUS	CFL
GUCY2D	NM_000180.4	c.530G > C	22.7	VUS	B	VUS	VUS	P	PD	VUS	VUS	VUS	n.a
RPE65	NM_000329.3	c.1087C > A	22.7	VUS	VUS	VUS	VUS	P	B	B	B	P	P
NMNAT1	NM_022787.4	c.547C > T	22.7	VUS	B	P	B	VUS	PD	VUS	VUS	VUS	VUS
CRB1	NM_201253.3	c.1459 T > C	22.6	VUS	n.a	VUS	VUS	VUS	PD	P	VUS	VUS	B/LB
IFT43	NM_001102564.3	c.100G > A	22.6	VUS	B	B	B	n.a	PD	VUS	VUS	VUS	CFL
RPGRIP1	NM_020366.4	c.1639G > T	22.5	VUS	B	B	B	n.a	PD	B	B	B	B/LB
GRM6	NM_000843.4	c.2267G > A	22.3	VUS	n.a	VUS	B	P	B	VUS	B	VUS	P
CRB1	NM_201253.3	c.2966 T > C	22.2	VUS	n.a	VUS	VUS	P	PD	VUS	VUS	VUS	n.a
RDH5	NM_002905.5	c.668A > C	22.1	VUS	B	VUS	B	VUS	PD	VUS	B	VUS	n.a
SEMA4A	NM_022367.4	c.2138G > A	21.3	VUS	B	B	B	n.a	B	B	B	B	B/LB
FAM161A	NM_001201543.2	c.1139G > T	18.53	VUS	B	VUS	VUS	P	PD	P	VUS	VUS	VUS
ALMS1	NM_001378454.1	c.5242A > G	17.8	VUS	n.a	n.a	VUS	n.a	n.a	n.a	n.a	B	LB
NR2E3	NM_014249.4	c.227G > A	16.07	B	B	B	n.a	n.a	PD	n.a	n.a	LP	CFL
AIPL1	NM_014336.5	c.773G > C	15.35	B	B	B	VUS	VUS	PD	VUS	B	VUS	LP
CRB1	NM_201253.3	c.3347 T > C	9.398	B	n.a	VUS	VUS	VUS	B	B	B	VUS	n.a
RP1	NM_006269.2	c.1118C > T	9.092	B	B	VUS	B	n.a	B	B	VUS	B	B/LB
RAX2	NM_001319074.4	c.374G > A	1.497	B	B	B	VUS	B	n.a	n.a	n.a	LB	n.a
RP1	NM_006269.2	c.2005G > A	1.173	B	B	B	VUS	n.a	B	B	B	VUS	VUS
GUCY2D	NM_000180.4	c.2384G > A	32	P	VUS	P	B	n.a	PD	VUS	P	P	VUS

MP MutPred, MT Mutation taster, MA Mutation assessor, LRT Likelihood ratio test, PP-2 PolyPhen-2, PRO PROVEAN, SIFT Sorting intolerant from tolerant, ACMG The American college of medical genetics and genomics, B Benign, LB Likely benign, B/LB Benign/Likely benign, P Pathogenic, LP Likely pathogenic, P/LP Pathogenic/Likely pathogenic, PD Probably/Possibly damaging, VUS Variant of uncertain significance, CFL Conflicting, NA Not available

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