Total 36 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
Familial Mediterranean fever, autosomal dominant
Condition: not provided
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

41 SubmittersRCV000002651RCV000218652RCV000761446RCV000513398RCV000768024RCV002326658RCV002251861RCV002262542RCV003224086RCV004528067RCV005208118
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
Chilblain lupus 1
Aicardi-Goutieres syndrome 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Inborn genetic diseases
Chilblain lupus 1
Aicardi-Goutieres syndrome 1
Inborn genetic diseases
TREX1-related disorder
Chilblain lupus 1
Aicardi-Goutieres syndrome 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Systemic lupus erythematosus
Adult onset neurodegenerative disorder		 Criteria Provided
Multiple Submitters
No Conflicts
 CA116673 rs_72556554

30 SubmittersRCV000004396RCV000004397RCV000256102RCV000850611RCV001266495RCV002281693RCV004540989RCV005025005RCV006629049
NM_005214.5(CTLA4):c.151C>T (p.Arg51Ter) SNV
Germline		 Chr2:203870627 Pathogenic Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Condition: not provided
Inborn genetic diseases
Type 1 diabetes mellitus 12
Systemic lupus erythematosus
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Celiac disease, susceptibility to, 3
Hashimoto thyroiditis		 Reviewed By Expert Panel
 CA173992 rs_606231417

10 SubmittersRCV000148290RCV000788671RCV002515995RCV005016468
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
Systemic lupus erythematosus
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
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
Systemic lupus erythematosus
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations		 Criteria Provided
Conflicting Classifications
 CA276175 rs_760838030

6 SubmittersRCV000191136RCV000763111RCV001843490RCV001857680RCV004732774RCV005365112
NM_033629.6(TREX1):c.290G>A (p.Arg97His) SNV
Germline		 Chr3:48466945 Conflicting classifications of pathogenicity Aicardi-Goutieres syndrome 1
Condition: not provided
Aicardi-Goutieres syndrome 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Chilblain lupus 1
Aicardi-Goutieres syndrome 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Chilblain lupus 1
Systemic lupus erythematosus		 Criteria Provided
Conflicting Classifications
 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
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

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
Aicardi-Goutieres syndrome 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Chilblain lupus 1
Aicardi-Goutieres syndrome 1
not specified
Aicardi-Goutieres syndrome 1
Systemic lupus erythematosus
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Chilblain lupus 1		 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 Condition: not provided
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Inborn genetic diseases
Celiac disease, susceptibility to, 3
Hashimoto thyroiditis
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Systemic lupus erythematosus
Type 1 diabetes mellitus 12		 Criteria Provided
Conflicting Classifications
 CA350138101 rs_1553657378

8 SubmittersRCV000788529RCV000604644RCV005549976RCV005018832
NM_005214.5(CTLA4):c.410C>T (p.Pro137Leu) SNV
Germline		 Chr2:203870886 Likely pathogenic Condition: not provided
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Celiac disease, susceptibility to, 3
Type 1 diabetes mellitus 12
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Hashimoto thyroiditis
Systemic lupus erythematosus		 Reviewed By Expert Panel
 CA350138741 rs_1553657429

6 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
Aicardi-Goutieres syndrome 1
Chilblain lupus 1
Systemic lupus erythematosus
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
Aicardi-Goutieres syndrome 1
Chilblain lupus 1		 Criteria Provided
Conflicting Classifications
 CA2376601 rs_755919767

8 SubmittersRCV000626116RCV000656254RCV000764509RCV001219467
NM_005214.5(CTLA4):c.410C>A (p.Pro137Gln) SNV
Germline		 Chr2:203870886 Conflicting classifications of pathogenicity Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Systemic lupus erythematosus
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Celiac disease, susceptibility to, 3
Hashimoto thyroiditis
Type 1 diabetes mellitus 12		 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
Condition: not provided
not specified
BLK-related disorder
Monogenic diabetes		 Criteria Provided
Conflicting Classifications
 CA4630364 rs_146505280

9 SubmittersRCV000758186RCV001162886RCV002305535RCV002249457RCV003938143RCV005357984
NM_005214.5(CTLA4):c.457G>A (p.Asp153Asn) SNV
Germline		 Chr2:203870933 Pathogenic Condition: not provided
Celiac disease, susceptibility to, 3
Hashimoto thyroiditis
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency
Type 1 diabetes mellitus 12
Systemic lupus erythematosus
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency		 Reviewed By Expert Panel
 CA350138843 rs_1581573970

3 SubmittersRCV000788196RCV002061137RCV006436900
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
Chilblain lupus 1
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations		 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 17
Systemic lupus erythematosus		 No Assertion Criteria Provided
 CA412407850 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
 CA412403934 rs_2147245261

1 SubmittersRCV002248405
NM_016562.4(TLR7):c.1520T>C (p.Phe507Ser) SNV
Germline		 ChrX:12887028 Pathogenic Systemic lupus erythematosus No Assertion Criteria Provided

1 SubmittersRCV005646084