Total 44 pathogenic variants reported for X-linked lissencephaly with abnormal genitalia 
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NM_139058.3(ARX):c.1058C>T (p.Pro353Leu) SNV
Germline		 ChrX:25012937 Pathogenic Developmental and epileptic encephalopathy, 1
Corpus callosum agenesis-abnormal genitalia syndrome
X-linked lissencephaly with abnormal genitalia
Developmental and epileptic encephalopathy, 1
Partington syndrome
Intellectual disability, X-linked, with or without seizures, ARX-related
Inborn genetic diseases		 Criteria Provided
Multiple Submitters
No Conflicts
 CA121410 rs_104894743

4 SubmittersRCV000011939RCV004795392RCV004658959
NM_139058.3(ARX):c.995G>A (p.Arg332His) SNV
Germline		 ChrX:25013000 Pathogenic X-linked lissencephaly with abnormal genitalia
Condition: not provided
Developmental and epileptic encephalopathy, 1
Intellectual disability, X-linked, with or without seizures, ARX-related		 Criteria Provided
Multiple Submitters
No Conflicts
 CA213168 rs_111033612

3 SubmittersRCV000011943RCV000145064RCV002512976
NM_139058.3(ARX):c.1117C>T (p.Gln373Ter) SNV
Germline		 ChrX:25010262 Pathogenic X-linked lissencephaly with abnormal genitalia No Assertion Criteria Provided
 CA213169 rs_104894740

1 SubmittersRCV000011944
NM_139058.3(ARX):c.1028T>A (p.Leu343Gln) SNV
Germline		 ChrX:25012967 Pathogenic X-linked lissencephaly with abnormal genitalia No Assertion Criteria Provided
 CA213171 rs_104894741

1 SubmittersRCV000011948
NM_139058.3(ARX):c.232G>T (p.Glu78Ter) SNV
Germline		 ChrX:25013763 Pathogenic X-linked lissencephaly with abnormal genitalia No Assertion Criteria Provided
 CA213174 rs_267606666

1 SubmittersRCV000011956
NM_139058.3(ARX):c.1121T>A (p.Val374Asp) SNV
Germline		 ChrX:25007438 Likely pathogenic X-linked lissencephaly with abnormal genitalia Criteria Provided
Single Submitter
 CA213228 rs_587783183

1 SubmittersRCV000145039
NM_139058.3(ARX):c.1134C>A (p.Asn378Lys) SNV
Germline		 ChrX:25007425 Likely pathogenic X-linked lissencephaly with abnormal genitalia Criteria Provided
Single Submitter
 CA213230 rs_587783184

1 SubmittersRCV000145040
NM_139058.3(ARX):c.1414C>T (p.Arg472Ter) SNV
Germline		 ChrX:25007145 Pathogenic X-linked lissencephaly with abnormal genitalia Criteria Provided
Single Submitter
 CA213233 rs_587783189

1 SubmittersRCV000145045
NM_139058.3(ARX):c.995G>T (p.Arg332Leu) SNV
Germline		 ChrX:25013000 Pathogenic X-linked lissencephaly with abnormal genitalia Criteria Provided
Single Submitter
 CA213238 rs_111033612

1 SubmittersRCV000145065
NM_139058.3(ARX):c.1170C>T (p.Gly390=) SNV
Germline		 ChrX:25007389 Conflicting classifications of pathogenicity Condition: not provided
X-linked lissencephaly with abnormal genitalia
Developmental and epileptic encephalopathy, 1
Partington syndrome
Intellectual disability, X-linked, with or without seizures, ARX-related
Corpus callosum agenesis-abnormal genitalia syndrome
Developmental and epileptic encephalopathy, 1
Intellectual disability, X-linked, with or without seizures, ARX-related
Inborn genetic diseases		 Criteria Provided
Conflicting Classifications
 CA10373824 rs_761632870

4 SubmittersRCV000217574RCV000764873RCV001366501RCV002317744
NM_139058.3(ARX):c.187G>A (p.Ala63Thr) SNV
Germline		 ChrX:25015551 Conflicting classifications of pathogenicity Developmental and epileptic encephalopathy, 1
Intellectual disability, X-linked, with or without seizures, ARX-related
Partington syndrome
Developmental and epileptic encephalopathy, 1
Intellectual disability, X-linked, with or without seizures, ARX-related
Corpus callosum agenesis-abnormal genitalia syndrome
X-linked lissencephaly with abnormal genitalia
not specified
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA10373904 rs_769996976

5 SubmittersRCV000705004RCV000764874RCV000779753RCV001544836
NM_139058.3(ARX):c.525C>G (p.Tyr175Ter) SNV
Germline		 ChrX:25013470 Pathogenic X-linked lissencephaly with abnormal genitalia Criteria Provided
Single Submitter
 CA412612987 rs_1601948603

1 SubmittersRCV001002675
NM_139058.3(ARX):c.956C>A (p.Ser319Ter) SNV
Germline		 ChrX:25013039 Pathogenic/Likely pathogenic Intellectual disability, X-linked, with or without seizures, ARX-related
Developmental and epileptic encephalopathy, 1
X-linked lissencephaly with abnormal genitalia
ARX-related disorder
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA412612079 rs_2048708701

4 SubmittersRCV001215936RCV001375968RCV005250150RCV004794506
NM_139058.3(ARX):c.994C>G (p.Arg332Gly) SNV
Germline		 ChrX:25013001 Pathogenic/Likely pathogenic Developmental and epileptic encephalopathy, 1
Intellectual disability, X-linked, with or without seizures, ARX-related
X-linked lissencephaly with abnormal genitalia
Developmental and epileptic encephalopathy, 1
Intellectual disability, X-linked, with or without seizures, ARX-related
Corpus callosum agenesis-abnormal genitalia syndrome
Partington syndrome		 Criteria Provided
Multiple Submitters
No Conflicts
 CA412611994 rs_2147323593

2 SubmittersRCV001989538RCV002479706
NM_139058.3(ARX):c.880G>T (p.Glu294Ter) SNV
Germline		 ChrX:25013115 Pathogenic X-linked lissencephaly with abnormal genitalia
Intellectual disability, X-linked, with or without seizures, ARX-related
Developmental and epileptic encephalopathy, 1		 Criteria Provided
Multiple Submitters
No Conflicts

2 SubmittersRCV004795482RCV005218334
NM_139058.3(ARX):c.1030G>T (p.Glu344Ter) SNV
Germline		 ChrX:25012965 Pathogenic X-linked lissencephaly with abnormal genitalia Criteria Provided
Single Submitter

1 SubmittersRCV005604014