Table 3. Profiles of pathogenic variants in Korean families with ABCA4-associated retinopathies.
| No. exon /intron | Nucleotide change | Protein variant / annotation | No. family† | Disease | Polyphen (score) | SIFT (score) | Mutation taster (ENST00000370225) | CADD Phred score (GRCh37-v1.4)‡ | Allele frequency (%) in gnomAD¶ | Clinical significance (ClinVar) |
|---|---|---|---|---|---|---|---|---|---|---|
| 6 |
c.575C>T |
p.Ala192Val |
1 |
FF |
Benign |
Tolerated (0.58) |
Disease causing |
19.32 |
0.000213 |
Not provided§ |
| -0.353 |
(58/272,116) |
|||||||||
| 8 |
c.880C>T |
p.Gln294Ter |
1 |
RP |
NA |
NA |
Disease causing |
35 |
None |
Pathogenic |
| 12 |
c.1760+2T>G |
Splice site |
1 |
STGD |
NA |
NA |
NA |
23.1 |
None |
Pathogenic |
| 13 |
c.1906C>A |
p.Gln636Lys |
2 |
RP, CRD |
Possibly damaging |
Deleterious |
Disease causing |
26 |
None |
Novel |
| -0.634 |
0 |
|||||||||
| 13 |
c.1933G>A |
p.Asp645Asn |
1 |
STGD |
Probably damaging, (0.954) |
Deleterious (0) |
Disease causing |
28.4 |
1.99E-05 |
Not provided |
| (5/251,094) |
||||||||||
| 23 |
c.3342_3344delCAT |
p.Ile1114del |
1 |
STGD |
NA |
NA |
Disease causing |
NA |
None |
Novel |
| 23 |
c.3349A>G |
p.Thr1117Aal |
1 |
STGD |
Damaging |
Deleterious (0) |
Disease causing |
26.5 |
None |
Novel |
| 23 |
c.3420C>G, |
p.Cys1140Trp, |
1 |
STGD |
Probably damaging, (0.997) |
Deleterious (0) |
Disease causing |
25.8 |
None |
Reported#18 |
| 23 |
c.3470T>G, |
p.Leu1157Ter, |
2 |
STGD |
NA |
NA |
Disease causing |
43 |
None |
Reported12 |
| 33 |
c.4748T>C |
p.Leu1583Pro |
1 |
CRD |
Possibly damaging, (0.878) |
Deleterious (0) |
Disease causing |
25.9 |
7.95E-06 |
Not provided |
| (2/251,468) |
||||||||||
| 33 |
c.4762A>T, |
p.Asn1588Tyr |
2 |
STGD |
Probably damaging, (0.962) |
Deleterious (0.04) |
Disease causing |
26.7 |
None |
Novel |
| 44 | c.6146delA, | p.Lys2049ArgfsTer12 | 2 | STGD | NA | NA | Disease causing | NA | None | Reported12 |
†No. family, the number of families with the same variant; ‡CADD, https://cadd.gs.washington.edu/; ¶gnomAD, https://gnomad.broadinstitute.org/ §Not provided, reported but clinical significance was not determined; #Reported, recently reported but no information in ClinVar or other database.