Total 35 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_000243.3(MEFV):c.442G>C (p.Glu148Gln) SNV
Germline		 Chr16:3254626 Conflicting classifications of pathogenicity Familial Mediterranean fever
not specified
Condition: not provided
Familial Mediterranean fever, autosomal dominant
Familial Mediterranean fever
Familial Mediterranean fever, autosomal dominant
Inborn genetic diseases
See cases
Autoinflammatory syndrome
Acute febrile neutrophilic dermatosis
Familial Mediterranean fever
Familial Mediterranean fever, autosomal dominant
MEFV-related disorder
Systemic lupus erythematosus		 Criteria Provided
Conflicting Classifications
 CA280097 rs_3743930

37 SubmittersRCV000002651RCV000218652RCV000513398RCV000761446RCV000768024RCV002326658RCV002251861RCV002262542RCV003224086RCV004528067RCV005208118
NM_033629.6(TREX1):c.341G>A (p.Arg114His) SNV
Germline		 Chr3:48466996 Pathogenic/Likely pathogenic Aicardi-Goutieres syndrome 1
Systemic lupus erythematosus, susceptibility to
Condition: not provided
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Aicardi-Goutieres syndrome 1
Chilblain lupus 1
Inborn genetic diseases
Aicardi-Goutieres syndrome 1
Inborn genetic diseases
Chilblain lupus 1
TREX1-related disorder
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Aicardi-Goutieres syndrome 1
Chilblain lupus 1
Systemic lupus erythematosus		 Criteria Provided
Multiple Submitters
No Conflicts
 CA116673 rs_72556554

26 SubmittersRCV000004396RCV000004397RCV000256102RCV000850611RCV001266495RCV002281693RCV004540989RCV005025005
NM_005214.5(CTLA4):c.151C>T (p.Arg51Ter) SNV
Germline		 Chr2:203870627 Pathogenic Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Condition: not provided
Type 1 diabetes mellitus 12
Celiac disease, susceptibility to, 3
Hashimoto thyroiditis
Systemic lupus erythematosus
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Inborn genetic diseases		 Criteria Provided
Multiple Submitters
No Conflicts
 CA173992 rs_606231417

7 SubmittersRCV000148290RCV000788671RCV005016468RCV002515995
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
Chilblain lupus 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Systemic lupus erythematosus
Condition: not provided
Aicardi-Goutieres syndrome 1
Chilblain lupus 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
TREX1-related disorder
Aicardi-Goutieres syndrome 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Systemic lupus erythematosus		 Criteria Provided
Conflicting Classifications
 CA276175 rs_760838030

6 SubmittersRCV000191136RCV000763111RCV001843490RCV001857680RCV004732774RCV005365112
NM_033629.6(TREX1):c.290G>A (p.Arg97His) SNV
Germline		 Chr3:48466945 Pathogenic/Likely pathogenic Aicardi-Goutieres syndrome 1
Condition: not provided
Aicardi-Goutieres syndrome 1
Chilblain lupus 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Systemic lupus erythematosus
Aicardi-Goutieres syndrome 1
Chilblain lupus 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations		 Criteria Provided
Multiple Submitters
No Conflicts
 CA2376620 rs_200773268

8 SubmittersRCV000490435RCV001093075RCV001853392RCV005025345
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
not specified
Condition: not provided
Systemic lupus erythematosus		 Criteria Provided
Conflicting Classifications
 CA4630356 rs_199696853

5 SubmittersRCV000279603RCV001821100RCV001591031RCV002465638
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

5 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
Systemic lupus erythematosus
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA4630031 rs_201252364

6 SubmittersRCV000272839RCV002465634RCV001559550
NM_033629.6(TREX1):c.667G>A (p.Ala223Thr) SNV
Germline		 Chr3:48467322 Conflicting classifications of pathogenicity Condition: not provided
Chilblain lupus 1
Aicardi-Goutieres syndrome 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Aicardi-Goutieres syndrome 1
not specified
Chilblain lupus 1
Aicardi-Goutieres syndrome 1
Systemic lupus erythematosus
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations		 Criteria Provided
Conflicting Classifications
 CA2376707 rs_766785968

9 SubmittersRCV000433529RCV001340342RCV001330236RCV004701472RCV005027489
NM_005214.5(CTLA4):c.118G>A (p.Val40Met) SNV
Germline		 Chr2:203870594 Conflicting classifications of pathogenicity Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Condition: not provided
Celiac disease, susceptibility to, 3
Hashimoto thyroiditis
Systemic lupus erythematosus
Type 1 diabetes mellitus 12
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Inborn genetic diseases		 Criteria Provided
Conflicting Classifications
 CA350138101 rs_1553657378

7 SubmittersRCV000604644RCV000788529RCV005018832RCV005549976
NM_005214.5(CTLA4):c.410C>T (p.Pro137Leu) SNV
Germline		 Chr2:203870886 Pathogenic/Likely pathogenic Condition: not provided
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Type 1 diabetes mellitus 12
Celiac disease, susceptibility to, 3
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Systemic lupus erythematosus
Hashimoto thyroiditis		 Criteria Provided
Multiple Submitters
No Conflicts
 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
Chilblain lupus 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Systemic lupus erythematosus
Aicardi-Goutieres syndrome 1
Condition: not provided
Chilblain lupus 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Aicardi-Goutieres syndrome 1		 Criteria Provided
Conflicting Classifications
 CA2376601 rs_755919767

8 SubmittersRCV000626116RCV000764509RCV000656254RCV001219467
NM_005214.5(CTLA4):c.410C>A (p.Pro137Gln) SNV
Germline		 Chr2:203870886 Conflicting classifications of pathogenicity Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Type 1 diabetes mellitus 12
Celiac disease, susceptibility to, 3
Hashimoto thyroiditis
Systemic lupus erythematosus
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency		 Criteria Provided
Conflicting Classifications
 CA350138739 rs_1553657429

2 SubmittersRCV000695947RCV005021075
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
 CA4629867 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
 CA370315074 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
 CA4630353 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
Condition: not provided
BLK-related disorder
Monogenic diabetes		 Criteria Provided
Conflicting Classifications
 CA4630364 rs_146505280

9 SubmittersRCV000758186RCV001162886RCV002249457RCV002305535RCV003938143RCV005357984
NM_005214.5(CTLA4):c.457G>A (p.Asp153Asn) SNV
Germline		 Chr2:203870933 Conflicting classifications of pathogenicity Hashimoto thyroiditis
Systemic lupus erythematosus
Type 1 diabetes mellitus 12
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Celiac disease, susceptibility to, 3
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA350138843 rs_1581573970

2 SubmittersRCV002061137RCV000788196
NM_033629.6(TREX1):c.1A>G (p.Met1Val) SNV
Germline		 Chr3:48466656 Conflicting classifications of pathogenicity Systemic lupus erythematosus
Condition: not provided
Chilblain lupus 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Aicardi-Goutieres syndrome 1		 Criteria Provided
Conflicting Classifications
 CA2376541 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
 CA394739994 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
 CA394740825 rs_2069586831

2 SubmittersRCV001254900RCV001526872
NM_016562.4(TLR7):c.1521T>G (p.Phe507Leu) SNV
Germline		 ChrX:12887029 Pathogenic Systemic lupus erythematosus
Systemic lupus erythematosus 17		 No Assertion Criteria Provided
 CA412407850 rs_2147245859

2 SubmittersRCV002259554RCV002251771
NM_016562.4(TLR7):c.82A>G (p.Arg28Gly) SNV
Germline		 ChrX:12885590 Pathogenic Systemic lupus erythematosus 17 No Assertion Criteria Provided
 CA412403934 rs_2147245261

1 SubmittersRCV002248405