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. 2021 Dec 23;13(1):27. doi: 10.3390/genes13010027

Table 1.

Disease-associated variants identified in 86 patients with definite diagnosis.

No. Initial
Clinical
Diagnosis		 Gene Mutations Zygosity Segregation Analysis gnomAD (MAF) CADD Previous Literature
(PMID)		 ACMG
Classification		 Accession ID
for Transcript
1 Cone-rod dystrophy ABCA4 c.1958G>A:p.(Arg653His)
c.3470T>G:p.(Leu1157*)		 Compound heterozygous NA 10/280000
None		 25.9
43		 10711710
29975949		 LP
P		 NM_000350.2
2 d LCA AHI1 c.2174G>A:p.(Trp725*) Homozygous NA 4/248916 43 25445212 P NM_001134831.1
3 d Laurence-Moon
syndrome		 BBS1 c.908delT:p.(Val303Glyfs*29)
c.1285C>T:p.(Arg429*)		 Compound heterozygous Paternal
Maternal		 None
3/251446		 34
40		 32165824 e
12677556		 P
P		 NM_024649.4
4 d IIN CACNA1F Exon 13-23 deletion Hemizygous NA None NA 34064005 e P NM_005183.2
5 d LCA CACNA1F c.2175_2179delins CATCATGTATGATGGTATCATGGCATT:p.(Gly726Ilefs*61) Hemizygous Maternal None 28.3 34064005 e P NM_005183.2
6 d IIN CACNA1F c.1910+1G>A Hemizygous NA None 21 34064005 e P NM_005183.2
LPR5 c.3833G>A:p.(Trp1278*) Heterozygous NA None 45 Novel LP NM_002335.2
7 d IIN CACNA1F c.1301C>T:p.(Ala434Val) Hemizygous Maternal None 17.47 28002560 LP NM_005183.2
8 d IIN CACNA1F c.1910+1G>A Hemizygous NA None 21 34064005 e P NM_005183.2
9 d LCA CEP290 c.1666delA:p.(Ile556Phefs*17)
c.3904C>T:p.(Gln1302*)		 Compound
heterozygous		 Maternal
Paternal		 245/174532
None		 31
37		 16909394
25445212		 P
P		 NM_025114.3
10 Achromatopsia CNGA3 c.1190G>T:p.(Glu397Val) a
c.1279C>T:p.(Arg427Cys) a
c.553C>G:p.(Leu185Val)		 Compound
heterozygous		 Paternal
Paternal
Maternal		 None
110/281878
1/251394		 25.5
33
20.5		 18636117
11536077
31144483		 LP
LP
LP		 NM_001298.2
11 d Stickler syndrome COL2A1 c.3165+1G>A Heterozygous NA None 25.5 34680973 e P NM_001844.4
12 d Pierre-Robin
sequence		 COL2A1 c.2680-3C>G Heterozygous NA None 23.7 34680973 e P NM_001844.4
13 d LCA CRX c.101-1G>A b
c.122G>A:p.(Arg41Gln) b 		Compound
heterozygous		 Trans by IGV None
1/31396		 32
25.1		 32165824 e
9427255		 P
P		 NM_000554.4
14 Congenital cataract CRYGC c.173T>C:p.(Leu58Pro) Heterozygous NA None 26 Novel LP NM_020989.3
15 RP EYS c.8805C>G:p.(Tyr2935*)
Exon 42-43 duplication		 Compound
heterozygous		 NA None
None		 35
NA		 22363543
Novel		 LP
US		 NM_001142800.1
16 IIN FRMD7 c.368C>A:p.(Ser123Tyr) Hemizygous NA None 23.8 Novel LP NM_194277.2
17 IIN FRMD7 c.575A>C:p.(His192Pro) Hemizygous NA 25/182271 25.6 30025138 LP NM_194277.2
18 IIN FRMD7 c.637G>A:p.(Val213Met) Heterozygous NA None 32 Novel LP NM_194277.2
19 IIN FRMD7 c.685C>T:p.(Arg229Cys) Hemizygous NA None 34 17768376 P NM_194277.2
20 IIN FRMD7 c.772A>G:p.(Lys241Arg) Hemizygous NA None 27.4 31106028 LP NM_194277.2
21 IIN FRMD7 c.875T>C:p.(Leu292Pro) Heterozygous NA 4/183318 27.5 25678693 P NM_194277.2
22 IIN FRMD7 c.875T>C:p.(Leu292Pro) Hemizygous NA 4/183318 27.5 25678693 P NM_194277.2
23 IIN FRMD7 c.875T>C:p.(Leu292Pro) Heterozygous NA 4/183318 27.5 25678693 P NM_194277.2
24 IIN FRMD7 c.875T>C:p.(Leu292Pro) Heterozygous NA 4/183318 27.5 25678693 P NM_194277.2
25 IIN FRMD7 c.875T>C:p.(Leu292Pro) Hemizygous NA 4/183318 27.5 25678693 P NM_194277.2
26 IIN FRMD7 c.875T>C:p.(Leu292Pro) Hemizygous NA 4/183318 27.5 25678693 P NM_194277.2
27 IIN FRMD7 c.875T>C:p.(Leu292Pro) Hemizygous NA 4/183318 27.5 25678693 P NM_194277.2
28 IIN FRMD7 c.875T>C:p.(Leu292Pro) Hemizygous NA 4/183318 27.5 25678693 P NM_194277.2
29 IIN FRMD7 c.875T>C:p.(Leu292Pro) Hemizygous NA 4/183318 27.5 25678693 P NM_194277.2
30 IIN FRMD7 c.875T>C:p.(Leu292Pro) Hemizygous NA 4/183318 27.5 25678693 P NM_194277.2
31 IIN FRMD7 c.875T>C:p.(Leu292Pro) Hemizygous NA 4/183318 27.5 25678693 P NM_194277.2
32 IIN FRMD7 c.875T>C:p.(Leu292Pro) Hemizygous NA 4/183318 27.5 25678693 P NM_194277.2
33 IIN FRMD7 c.886G>T:p.(Gly296Cys) Hemizygous NA None 34 30015830 LP NM_194277.2
34 IIN FRMD7 c.901T>C:p.(Tyr301His) Hemizygous NA None 26.7 29145603 e LP NM_194277.2
35 IIN FRMD7 c.1016C>G:p.(Ser339Cys) Hemizygous NA None 34 Novel LP NM_194277.2
36 IIN FRMD7 c.1023_1030AGACCTCC:
p.(Asp342Leufs*2)		 Hemizygous NA None 35 Novel P NM_194277.2
37 IIN FRMD7 Exon 5 deletion Hemizygous NA None NA Novel P NM_194277.2
38 Congenital cataract FTL c.-168G>T Heterozygous Maternal None 20.8 9414300 P NM_000146.3
39 FEVR FZD4 c.752C>G:p.(Pro251Arg) Heterozygous Maternal None 25.1 Novel LP NM_012193.3
40 FEVR FZD4 c.205C>T:p.(His69Tyr) Heterozygous NA 138/277634 24.2 15370539 P NM_012193.3
41 FEVR FZD4 c.470T>C:p.(Met157Thr) Heterozygous NA None 21.8 21097938 P NM_012193.3
42 Congenital cataract GJA3 c.290T>G:p.(Leu97Arg) Heterozygous NA None 29 Novel US NM_021954.3
OPA1 c.449-2A>C Heterozygous NA None 23.6 Novel P NM_130832.2
43 Ocular albinism GPR143 c.248T>C:p.(Leu83Pro) Hemizygous NA None 25.9 31106028 LP NM_000273.2
44 Ocular albinism GPR143 c.360+2T>C Hemizygous NA None 23 Novel P NM_000273.2
45 Ocular albinism GPR143 c.925delG:p.(Ala309Profs*24) Hemizygous NA None 34 Novel P NM_000273.2
46 Ocular albinism GPR143 c.518C>G:p.(Ala173Asp) Hemizygous NA None 24.2 Novel LP NM_000273.2
47 Ocular albinism GPR143 Xp22.3 deletion Hemizygous NA None - Novel P -
48 Ocular albinism GPR143 c.223_228dupGCTGCC:
p.(Ala75_Ala76dup)		 Hemizygous NA None 8.758 28339057 LP NM_000273.2
49 d LCA GUCY2D c.1991A>C:p.(His664Pro)
c.2984G>A:p.(Arg995Gln)		 Compound heterozygous Maternal
Paternal		 None
1/244998		 27
35		 28966547
32165824 e 		P
LP		 NM_000180.3
50 d LCA GUCY2D c.2649del:p.(Phe883Leufs*13) Homozygous NA None 33 28966547 P NM_000180.3
51 d LCA GUCY2D c.1790G>A:p.(Gly597Glu)
exon 4-5 duplication		 Compound heterozygous Paternal
De novo		 None
None		 27.4
-		 29068479
32165824 e 		LP
LP		 NM_000180.3
52 d IIN GUCY2D c.1978C>T:p.(Arg660*)
c.2947C>A:p.(Pro983Thr) a
c.2960G>C:p.(Gly987Ala) a 		Compound heterozygous Paternal
Maternal		 1/251328
None
None		 40
25.3
28.4		 10766140
32165824 e
32165824 e 		P
LP
LP		 NM_000180.3
53 CCDD KIF21A c.1067T>C:p.(Met356Thr) Heterozygous Maternal None 25.4 14595441 LP NM_001173464.1
54 FEVR LRP5 c.607G>A:p.(Asp203Asn) Heterozygous Paternal None 32 16252235 P NM_002335.2
55 Congenital cataract NHS c.1117C>T:p.(Arg373*) Heterozygous NA None 38 14564667 P NM_198270.2
56 d LCA NMNAT1 c.275G>A:p.(Trp92*)
c.709C>T:p.(Arg237Cys)		 Compound heterozygous Paternal
Maternal		 None
14/282780		 38
35		 32165824 e
22842227		 LP
P		 NM_022787.3
57 d LCA NMNAT1 c.196C>T:p.(Arg66Trp)
c.709C>T:p.(Arg237Cys)		 Compound heterozygous Paternal
Maternal		 22/282832
14/282780		 35
35		 22842227
22842227		 P
P		 NM_022787.3
58 d Optic atrophy NR2F1 c.91_93dupCGC:p.(Arg31dup) Heterozygous NA None 19.92 34466801 e LP NM_005654.4
59 d Optic atrophy NR2F1 c.513C>G:p.(Tyr171*) Heterozygous NA None 37 34466801 e LP NM_005654.4
60 d IIN NYX c.182_183insT:
p.(Cys62Valfs*53)		 Hemizygous Maternal None 32 34064005 e P NM_022567.2
61 Unexplained visual loss NYX c.38-1_38delGCinsTT:
p.(Ala13Vafs*102)		 Hemizygous Maternal None 14.49 ClinVar P NM_022567.2
62 Optic atrophy OPA1 c.1240A>C:p.(Thr414Pro) Heterozygous NA None 26.5 26905822 LP NM_015560.2
63 Optic atrophy OPA1 c.795_798delTGAC:
p.(Asp266Cysfs*41)		 Heterozygous NA None 35 Novel P NM_015560.2
64 PAX6 phenotype PAX6 c.383G>A:p.(Arg128His) Heterozygous NA None 34 30167917 LP NM_000280.4
65 PAX6 phenotype PAX6 c.607C>T:p.(Arg203*) Heterozygous NA None 36 7550230 P NM_000280.4
66 PAX6 phenotype PAX6 c.397G>T:p.(Glu133*) Heterozygous NA None 38 16712695 P NM_000280.4
67 PAX6 phenotype PAX6 c.702T>A:p.(Tyr234*) Heterozygous NA None 36 Novel P NM_000280.4
68 PAX6 phenotype PAX6 c.362C>T:p.(Ser121Leu) Heterozygous NA None 25.9 23734086 LP NM_000280.4
69 PAX6 phenotype PAX6 c.607C>T:p.(Arg203*) Heterozygous NA None 37 7550230 P NM_000280.4
70 PAX6 phenotype PAX6 c.702T>A:p.(Tyr234*) Heterozygous NA None 36 Novel P NM_000280.4
71 Achromatopsia PDE6C c.1771G>A:p.(Glu591Lys)
c.2269C>T:p.(Gln757*)		 Compound heterozygous Paternal
Maternal		 2/251120
None		 33
49		 26992781
Novel		 P
P		 NM_006204.3
72 Achromatopsia PDE6C c.85C>T:p.(Arg29Trp)
c.712C>T:p.(Arg238*)		 Compound heterozygous Maternal
Paternal		 6/282886
2/251376		 29.3
38		 19615668
27124789		 P
P		 NM_006204.3
73 Optic atrophy PDHA1 c.232G>A:p.(Ala78Thr) Hemizygous Maternal None 24.8 Novel LP NM_000284.3
74 RP PRPH2 c.708C>G:p.(Tyr236*) Heterozygous Paternal None 37 22863181 P NM_000322.4
75 CSNB RHO c.302G>A:p.(Gly101Glu) Heterozygous NA 2/250994 25.5 26161267 LP NM_000539.3
76 Cone dystrophy RP1 c.4196delG:p.(Cys1399Leufs*5)
c.6181delA:p.(Ile2061Serfs*12)		 Compound heterozygous NA None
None		 23.7
23		 25097241
29425069		 P
P		 NM_006269.1
77 LCA RPGRIP1 c.3565_3571delCGAAGGC:
p.(Arg1189Glyfs*7)		 Homozygous NA 4/249114 35 18682808 P NM_020366.3
78 d PAX6 phenotype SLC38A8 c.692G>A:p.(Cys231Tyr)
c.964C>T:p.(Gln322*)		 Compound heterozygous Paternal
Maternal		 None
2/248656		 27.2
37		 32744312 e
32744312 e 		LP
P		 NM_001080442.1
79 d Ocular albinism SLC38A8 c.995dupG:p.(Trp333Metfs*35)
c.1214+5G>C		 Compound heterozygous Paternal
Maternal		 None
None		 22.9
23.2		 32744312 e
32744312 e 		P
LP		 NM_001080442.1
80 d PAX6 phenotype SLC38A8 c.558C>A:p.(Tyr186*)
c.1078_1104del:
p.(Ala360_leu368del)		 Compound heterozygous Maternal
Paternal		 None
None		 58
16.29		 32744312 e
32744312 e 		P
LP		 NM_001080442.1
81 Oculocutaneous
albinism		 SLC45A2 c.220T>C:p.(Trp74Arg) Heterozygous Maternal None 26.7 Novel US NM_016180.3
82 d LCA SPATA7 c.388C>T:p.(Gln130*)
c.1160+1G>A		 Compound heterozygous Maternal
Paternal		 2/249908
None		 35
33		 32165824 e
32165824 e 		P
P		 NM_018418.4
83 d LCA TUBB3 c.967A>G:p.(Met323Val) Heterozygous De novo None 25.3 33921132 e LP NM_006086.4
84 Oculocutaneous
albinism		 TYR c.929dupC:p.(Arg311Lysfs*7)
c.1037-7T>A		 Compound heterozygous NA 11/251178
242/280983		 22.9
18.81		 2511845
8217557		 P
P		 NM_000372.4
85 Usher syndrome USH2A c.2802T>G:p.(Cys934Trp)
c.11389+3A>T		 Compound heterozygous Son c 57/282482
2/250762		 26.6
22.7		 21686329
28714225		 P
LP		 NM_206933.2
86 Usher syndrome USH2A c.8559-2A>G Homozygous NA 8/251134 34 32093671 P NM_206933.2
87 X-linked
retinoschisis		 VPS13B c.6200T>A:p.(Leu2067*)
c.9530_9531del:
p.(Ala3177Valfs*18)		 Compound heterozygous NA 3/250746
None		 39
27.5		 15141358
Novel		 P
P		 NM_017890.4
88 Corneal dystrophy ZEB1 c.2034_2035delAA:
p.(Pro680Phefs*5)		 Heterozygous NA None 23.8 Novel P NM_030751.5
89 Corneal dystrophy ZEB1 c.1576delG:p.(Val526*) Heterozygous NA None 23.9 Novel P NM_030751.5
90 Optic atrophy SOX5 12p12.2p12.1 deletion Heterozygous De novo None NA Novel P NM_006940.4

ACMG: American College of Medical Genetics, CADD: combined annotation-dependent depletion, CCDD: congenital cranial dys-innervational disorder, FEVR: familial exudative vitreoretinopathy, IGV: integrative genomic viewer, IIN: idiopathic infantile nystagmus, gnomAD: genome aggregation dataset, LCA: Leber congenital amaurosis, LP: likely pathogenic, MAF: minor allele frequency, NA: not available, P: pathogenic, RP: retinitis pigmentosa, US: uncertain significance. a These two variants were existed in cis, confirmed by manual inspection through integrative genomic viewer. b These two variants were existed in trans, confirmed by manual inspection through integrative genomic viewer. c Segregation was confirmed by proband’s children. d Previously reported patients by the authors. e Novel, but previously reported by the authors.