Total 22 pathogenic variants reported for Systemic lupus erythematosus 
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NM_001098629.3(IRF5):c.-12+198= SNV
Germline		 Chr7:128938247 Pathogenic; risk factor Systemic lupus erythematosus, susceptibility to, 10
Rheumatoid arthritis		 No Assertion Criteria Provided
 CA116178 rs_2004640

1 SubmittersRCV000003564RCV000003565
NM_033629.6(TREX1):c.341G>A (p.Arg114His) SNV
Germline		 Chr3:48466996 Conflicting classifications of pathogenicity Aicardi-Goutieres syndrome 1
Systemic lupus erythematosus, susceptibility to
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Condition: not provided
Chilblain lupus 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Aicardi-Goutieres syndrome 1
Inborn genetic diseases
Chilblain lupus 1
Aicardi-Goutieres syndrome 1
Inborn genetic diseases
TREX1-related disorder		 Criteria Provided
Conflicting Classifications
 CA116673 rs_72556554

21 SubmittersRCV000004396RCV000004397RCV000388382RCV000256102RCV000850611RCV001266495RCV002281693RCV004540989
NM_033629.6(TREX1):c.340C>T (p.Arg114Cys) SNV
Germline		 Chr3:48466995 Conflicting classifications of pathogenicity Aicardi-Goutieres syndrome 1
Aicardi-Goutieres syndrome 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Systemic lupus erythematosus
Chilblain lupus 1
Condition: not provided
Aicardi-Goutieres syndrome 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Chilblain lupus 1		 Criteria Provided
Conflicting Classifications
 CA276175 rs_760838030

4 SubmittersRCV000191136RCV000763111RCV001843490RCV001857680
NM_001715.3(BLK):c.1057C>T (p.Arg353Cys) SNV
Germline		 Chr8:11561329 Conflicting classifications of pathogenicity Maturity-onset diabetes of the young type 11
Condition: not provided
not specified
Systemic lupus erythematosus		 Criteria Provided
Conflicting Classifications
 CA4630356 rs_199696853

5 SubmittersRCV000279603RCV001591031RCV001821100RCV002465638
NM_001715.3(BLK):c.187G>A (p.Val63Met) SNV
Germline		 Chr8:11548043 Conflicting classifications of pathogenicity Maturity-onset diabetes of the young type 11
Condition: not provided
Systemic lupus erythematosus		 Criteria Provided
Conflicting Classifications
 CA4629750 rs_138972988

4 SubmittersRCV000343718RCV001584087RCV002464191
NM_001715.3(BLK):c.672C>T (p.Ala224=) SNV
Germline		 Chr8:11555384 Conflicting classifications of pathogenicity Maturity-onset diabetes of the young type 11
Condition: not provided
Systemic lupus erythematosus		 Criteria Provided
Conflicting Classifications
 CA4630031 rs_201252364

6 SubmittersRCV000272839RCV001559550RCV002465634
NM_005214.5(CTLA4):c.410C>T (p.Pro137Leu) SNV
Germline		 Chr2:203870886 Conflicting classifications of pathogenicity Condition: not provided
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Hashimoto thyroiditis
Celiac disease, susceptibility to, 3
Type 1 diabetes mellitus 12
Systemic lupus erythematosus
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency		 Criteria Provided
Conflicting Classifications
 CA350138741 rs_1553657429

5 SubmittersRCV000498929RCV000652446RCV000768197
NM_033629.6(TREX1):c.218C>T (p.Pro73Leu) SNV
Germline		 Chr3:48466873 Conflicting classifications of pathogenicity Aicardi-Goutieres syndrome 1
Condition: not provided
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Chilblain lupus 1
Systemic lupus erythematosus
Aicardi-Goutieres syndrome 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Chilblain lupus 1
Aicardi-Goutieres syndrome 1		 Criteria Provided
Conflicting Classifications
 CA2376601 rs_755919767

8 SubmittersRCV000626116RCV000656254RCV000764509RCV001219467
NM_001715.3(BLK):c.391C>T (p.Arg131Trp) SNV
Germline		 Chr8:11550181 Conflicting classifications of pathogenicity Systemic lupus erythematosus
Maturity-onset diabetes of the young type 11
Condition: not provided
not specified		 Criteria Provided
Conflicting Classifications
 rs_73663163

7 SubmittersRCV000758181RCV001164841RCV001796205RCV002249456
NM_001715.3(BLK):c.919C>G (p.Pro307Ala) SNV
Germline		 Chr8:11556804 Pathogenic Systemic lupus erythematosus No Assertion Criteria Provided
 rs_1307379746

1 SubmittersRCV000758184
NM_001715.3(BLK):c.1048T>C (p.Tyr350His) SNV
Germline		 Chr8:11561320 Pathogenic Systemic lupus erythematosus No Assertion Criteria Provided
 rs_758750492

1 SubmittersRCV000758185
NM_001715.3(BLK):c.1075C>T (p.Arg359Cys) SNV
Germline		 Chr8:11561347 Conflicting classifications of pathogenicity Systemic lupus erythematosus
Maturity-onset diabetes of the young type 11
not specified
BLK-related disorder
Condition: not provided		 Criteria Provided
Conflicting Classifications
 rs_146505280

8 SubmittersRCV000758186RCV001162886RCV002249457RCV003938143RCV002305535
NM_005214.5(CTLA4):c.457G>A (p.Asp153Asn) SNV
Germline		 Chr2:203870933 Conflicting classifications of pathogenicity Condition: not provided
Hashimoto thyroiditis
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Celiac disease, susceptibility to, 3
Systemic lupus erythematosus
Type 1 diabetes mellitus 12		 Criteria Provided
Conflicting Classifications
 rs_1581573970

2 SubmittersRCV000788196RCV002061137
NM_033629.6(TREX1):c.1A>G (p.Met1Val) SNV
Germline		 Chr3:48466656 Conflicting classifications of pathogenicity Systemic lupus erythematosus
Condition: not provided
Aicardi-Goutieres syndrome 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Chilblain lupus 1		 Criteria Provided
Conflicting Classifications
 rs_761165865

3 SubmittersRCV001198990RCV001839030RCV001863135
NM_003745.2(SOCS1):c.460T>C (p.Tyr154His) SNV
Germline		 Chr16:11255019 Pathogenic/Likely pathogenic Systemic lupus erythematosus
AUTOINFLAMMATORY SYNDROME, FAMILIAL, WITHOUT IMMUNODEFICIENCY		 No Assertion Criteria Provided
 rs_2069578995

2 SubmittersRCV001254901RCV001526873
NM_003745.2(SOCS1):c.64C>T (p.Arg22Trp) SNV
Germline		 Chr16:11255415 Pathogenic/Likely pathogenic Systemic lupus erythematosus
AUTOINFLAMMATORY SYNDROME, FAMILIAL, WITHOUT IMMUNODEFICIENCY		 No Assertion Criteria Provided
 rs_2069586831

2 SubmittersRCV001254900RCV001526872
NM_016562.4(TLR7):c.1521T>G (p.Phe507Leu) SNV
Germline		 ChrX:12887029 Pathogenic Systemic lupus erythematosus 17
Systemic lupus erythematosus		 No Assertion Criteria Provided
 rs_2147245859

2 SubmittersRCV002251771RCV002259554
NM_016562.4(TLR7):c.82A>G (p.Arg28Gly) SNV
Germline		 ChrX:12885590 Pathogenic Systemic lupus erythematosus 17 No Assertion Criteria Provided
 rs_2147245261

1 SubmittersRCV002248405