Total 42 pathogenic variants reported for Congenital primary aphakia 
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NM_012186.3(FOXE3):c.720C>A (p.Cys240Ter) SNV
Germline		 Chr1:47417035 Pathogenic Congenital primary aphakia
Condition: not provided
Anterior segment dysgenesis		 Criteria Provided
Multiple Submitters
No Conflicts
 CA119630 rs_80358194

8 SubmittersRCV000008963RCV000255267RCV001200038
NM_012186.3(FOXE3):c.959G>T (p.Ter320Leu) SNV
Germline		 Chr1:47417274 Pathogenic Congenital primary aphakia No Assertion Criteria Provided
 CA128991 rs_387906793

1 SubmittersRCV000023071
NM_012186.3(FOXE3):c.834C>T (p.Pro278=) SNV
Germline		 Chr1:47417149 Conflicting classifications of pathogenicity Condition: not provided
Anterior segment dysgenesis
Congenital primary aphakia
Cardiovascular phenotype		 Criteria Provided
Conflicting Classifications
 CA10604352 rs_886042525

3 SubmittersRCV000390108RCV001087380RCV002436100
NM_012186.3(FOXE3):c.457G>C (p.Asp153His) SNV
Germline		 Chr1:47416772 Conflicting classifications of pathogenicity Aortic aneurysm, familial thoracic 11, susceptibility to
Congenital aneurysm of ascending aorta
Acute aortic dissection
Congenital primary aphakia
Anterior segment dysgenesis
Cardiovascular phenotype		 Criteria Provided
Conflicting Classifications
 CA16044411 rs_367943249

4 SubmittersRCV000417170RCV000755150RCV001861471RCV002338979
NM_012186.3(FOXE3):c.431A>G (p.Tyr144Cys) SNV
Germline		 Chr1:47416746 Conflicting classifications of pathogenicity Condition: not provided
Congenital primary aphakia
Anterior segment dysgenesis		 Criteria Provided
Conflicting Classifications
 CA842967 rs_747148416

2 SubmittersRCV000439291RCV001861538
NM_012186.3(FOXE3):c.232G>A (p.Ala78Thr) SNV
Germline		 Chr1:47416547 Pathogenic/Likely pathogenic Cardiovascular phenotype
Congenital primary aphakia
Anterior segment dysgenesis
Congenital primary aphakia
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA842917 rs_377669670

6 SubmittersRCV004023273RCV001062090RCV000521849RCV003736793
NM_012186.3(FOXE3):c.310C>T (p.Arg104Cys) SNV
Germline		 Chr1:47416625 Conflicting classifications of pathogenicity Cardiovascular phenotype
Congenital primary aphakia
Anterior segment dysgenesis
Congenital primary aphakia		 Criteria Provided
Conflicting Classifications
 CA340249497 rs_755377651

3 SubmittersRCV005338199RCV003766755RCV000523691
NM_012186.3(FOXE3):c.527C>T (p.Ala176Val) SNV
Germline		 Chr1:47416842 Conflicting classifications of pathogenicity Anterior segment dysgenesis
Congenital primary aphakia
Condition: not provided
Cardiovascular phenotype
FOXE3-related disorder		 Criteria Provided
Conflicting Classifications
 CA842991 rs_201955081

5 SubmittersRCV000797801RCV001172214RCV002345765RCV004751708
NM_012186.3(FOXE3):c.244A>G (p.Met82Val) SNV
Germline		 Chr1:47416559 Conflicting classifications of pathogenicity Congenital primary aphakia
Congenital primary aphakia
Anterior segment dysgenesis
Condition: not provided
FOXE3-related disorder
Cardiovascular phenotype
Cataract 34 multiple types		 Criteria Provided
Conflicting Classifications
 CA842920 rs_746531116

8 SubmittersRCV000826107RCV001386842RCV001092681RCV003413666RCV004994061RCV003492182
NM_012186.3(FOXE3):c.61G>A (p.Ala21Thr) SNV
Germline		 Chr1:47416376 Conflicting classifications of pathogenicity Congenital primary aphakia
Anterior segment dysgenesis
Cardiovascular phenotype		 Criteria Provided
Conflicting Classifications
 CA22068319 rs_886379083

2 SubmittersRCV001068294RCV002365771
NM_012186.3(FOXE3):c.291C>G (p.Ile97Met) SNV
Germline		 Chr1:47416606 Pathogenic Congenital primary aphakia
Anterior segment dysgenesis
Congenital primary aphakia		 Criteria Provided
Single Submitter
 CA842929 rs_762006562

2 SubmittersRCV001203942RCV001391236
NM_012186.3(FOXE3):c.619G>A (p.Gly207Arg) SNV
Germline		 Chr1:47416934 Conflicting classifications of pathogenicity Congenital primary aphakia
Anterior segment dysgenesis
Cardiovascular phenotype
Familial thoracic aortic aneurysm and aortic dissection		 Criteria Provided
Conflicting Classifications
 CA22069157 rs_560327746

3 SubmittersRCV001208683RCV002365937RCV003485688
NM_012186.3(FOXE3):c.289A>G (p.Ile97Val) SNV
Germline		 Chr1:47416604 Likely pathogenic Congenital primary aphakia Criteria Provided
Single Submitter
 CA842928 rs_774505755

3 SubmittersRCV001267882
NM_012186.3(FOXE3):c.166G>A (p.Ala56Thr) SNV
Germline		 Chr1:47416481 Conflicting classifications of pathogenicity Congenital primary aphakia
Anterior segment dysgenesis
Cardiovascular phenotype		 Criteria Provided
Conflicting Classifications
 CA22068413 rs_916755482

2 SubmittersRCV001301227RCV004619608
NM_012186.3(FOXE3):c.286G>A (p.Ala96Thr) SNV
Germline		 Chr1:47416601 Likely pathogenic Congenital primary aphakia No Assertion Criteria Provided
 CA340249402 rs_2124042297

1 SubmittersRCV001391234
NM_012186.3(FOXE3):c.359G>C (p.Arg120Pro) SNV
Germline		 Chr1:47416674 Likely pathogenic Congenital primary aphakia No Assertion Criteria Provided
 CA340249703 rs_772347736

1 SubmittersRCV001391237
NM_012186.3(FOXE3):c.632C>A (p.Ser211Ter) SNV
Germline		 Chr1:47416947 Pathogenic/Likely pathogenic Congenital primary aphakia
Anterior segment dysgenesis
Congenital primary aphakia		 Criteria Provided
Multiple Submitters
No Conflicts
 CA22069181 rs_1035206433

2 SubmittersRCV001930870RCV004017883
NM_012186.3(FOXE3):c.387C>G (p.Phe129Leu) SNV
Germline		 Chr1:47416702 Likely pathogenic Congenital primary aphakia
Anterior segment dysgenesis		 Criteria Provided
Single Submitter
 CA340249821 rs_2124042660

1 SubmittersRCV001921609
NM_012186.3(FOXE3):c.388G>T (p.Val130Phe) SNV
Germline		 Chr1:47416703 Likely pathogenic Congenital primary aphakia No Assertion Criteria Provided
 CA340249827 rs_1646884931

1 SubmittersRCV002291177
NM_012186.3(FOXE3):c.555C>T (p.Pro185=) SNV
Germline		 Chr1:47416870 Conflicting classifications of pathogenicity Cardiovascular phenotype
Congenital primary aphakia
Anterior segment dysgenesis		 Criteria Provided
Conflicting Classifications
 CA417892612 rs_758322369

2 SubmittersRCV002351974RCV005227633
NM_012186.3(FOXE3):c.498C>A (p.Arg166=) SNV
Germline		 Chr1:47416813 Conflicting classifications of pathogenicity Cardiovascular phenotype
Congenital primary aphakia
Anterior segment dysgenesis		 Criteria Provided
Conflicting Classifications
 CA842984 rs_747040897

2 SubmittersRCV002342925RCV003776008
NM_012186.3(FOXE3):c.145G>T (p.Gly49Ter) SNV
Germline		 Chr1:47416460 Pathogenic/Likely pathogenic Congenital primary aphakia
Anterior segment dysgenesis
Congenital primary aphakia		 Criteria Provided
Multiple Submitters
No Conflicts
 CA340249123 rs_958293767

2 SubmittersRCV003005444RCV005255735
NM_012186.3(FOXE3):c.363C>T (p.His121=) SNV
Germline		 Chr1:47416678 Conflicting classifications of pathogenicity Cardiovascular phenotype
Anterior segment dysgenesis
Congenital primary aphakia		 Criteria Provided
Conflicting Classifications
 CA417892330 rs_1646884829

2 SubmittersRCV003181646RCV005227923
NM_012186.3(FOXE3):c.6G>A (p.Ala2=) SNV
Germline		 Chr1:47416321 Conflicting classifications of pathogenicity Anterior segment dysgenesis
Congenital primary aphakia
Cardiovascular phenotype		 Criteria Provided
Conflicting Classifications
 CA417891789 rs_928328635

2 SubmittersRCV005227924RCV003181650
NM_012186.3(FOXE3):c.504G>A (p.Lys168=) SNV
Germline		 Chr1:47416819 Conflicting classifications of pathogenicity Cardiovascular phenotype
Congenital primary aphakia
Anterior segment dysgenesis		 Criteria Provided
Conflicting Classifications
 CA842985 rs_771078208

2 SubmittersRCV003216535RCV005216018
NM_012186.3(FOXE3):c.706G>T (p.Glu236Ter) SNV
Germline		 Chr1:47417021 Pathogenic Anterior segment dysgenesis
Congenital primary aphakia		 Criteria Provided
Single Submitter
 CA340250551 rs_2521321688

1 SubmittersRCV003801268
NM_012186.3(FOXE3):c.222C>G (p.Tyr74Ter) SNV
Germline		 Chr1:47416537 Pathogenic Anterior segment dysgenesis
Congenital primary aphakia		 Criteria Provided
Single Submitter
 CA340249273 rs_1167122307

1 SubmittersRCV003812726
NM_012186.3(FOXE3):c.39C>T (p.Phe13=) SNV
Germline		 Chr1:47416354 Conflicting classifications of pathogenicity Cardiovascular phenotype
Anterior segment dysgenesis
Congenital primary aphakia		 Criteria Provided
Conflicting Classifications
 CA417891825 rs_1350653181

2 SubmittersRCV004519445RCV005220933