Total 49 pathogenic variants reported for X-linked lymphoproliferative disease due to SH2D1A deficiency 
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NM_002351.5(SH2D1A):c.163C>T (p.Arg55Ter) SNV
Germline		 ChrX:124365786 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency
Condition: not provided
X-linked lymphoproliferative syndrome		 Criteria Provided
Multiple Submitters
No Conflicts
 CA255589 rs_111033623

5 SubmittersRCV000011645RCV001091713RCV001270156
NM_002351.5(SH2D1A):c.172C>T (p.Gln58Ter) SNV
Germline		 ChrX:124365795 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency No Assertion Criteria Provided
 CA255592 rs_111033628

1 SubmittersRCV000011646
NM_002351.5(SH2D1A):c.95G>C (p.Arg32Thr) SNV
Germline		 ChrX:124346737 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency No Assertion Criteria Provided
 CA255595 rs_111033624

1 SubmittersRCV000011648
NM_002351.5(SH2D1A):c.138-1G>T SNV
Germline		 ChrX:124365760 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency
Thyroid cancer, nonmedullary, 1		 No Assertion Criteria Provided
 CA414123359 rs_1603238847

2 SubmittersRCV000011649RCV005887430
NM_002351.5(SH2D1A):c.385T>A (p.Ter129Arg) SNV
Germline		 ChrX:124371389 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency No Assertion Criteria Provided
 CA255597 rs_111033625

1 SubmittersRCV000011650
NM_002351.5(SH2D1A):c.302C>T (p.Pro101Leu) SNV
Germline		 ChrX:124370276 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency No Assertion Criteria Provided
 CA255600 rs_111033626

1 SubmittersRCV000011651
NM_002351.5(SH2D1A):c.-10C>T SNV
Germline		 ChrX:124346633 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency No Assertion Criteria Provided
 CA913185017 rs_1603236465

1 SubmittersRCV000011653
NM_002351.5(SH2D1A):c.3G>T (p.Met1Ile) SNV
Germline		 ChrX:124346645 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency No Assertion Criteria Provided
 CA255604 rs_111033629

1 SubmittersRCV000011655
NM_002351.5(SH2D1A):c.164G>T (p.Arg55Leu) SNV
Germline		 ChrX:124365787 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency No Assertion Criteria Provided
 CA255607 rs_111033630

1 SubmittersRCV000011657
NM_002351.5(SH2D1A):c.137+5G>C SNV
Germline		 ChrX:124346784 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency No Assertion Criteria Provided
 CA270627 rs_587777612

1 SubmittersRCV000133459
NM_002351.4(SH2D1A):c.-124T>A SNV
Germline		 ChrX:124346519 Conflicting classifications of pathogenicity X-linked lymphoproliferative disease due to SH2D1A deficiency
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA10645911 rs_148700291

2 SubmittersRCV000312775RCV003221963
NM_002351.5(SH2D1A):c.*862T>A SNV
Germline		 ChrX:124372253 Conflicting classifications of pathogenicity X-linked lymphoproliferative disease due to SH2D1A deficiency
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA10645918 rs_774701387

2 SubmittersRCV000350702RCV003437148
NM_002351.5(SH2D1A):c.53A>G (p.Lys18Arg) SNV
Germline		 ChrX:124346695 Conflicting classifications of pathogenicity Condition: not provided
X-linked lymphoproliferative disease due to SH2D1A deficiency		 Criteria Provided
Conflicting Classifications
 CA414122278 rs_1303880423

3 SubmittersRCV000727009RCV003509560
NM_002351.5(SH2D1A):c.5A>G (p.Asp2Gly) SNV
Germline		 ChrX:124346647 Likely pathogenic Condition: not provided
X-linked lymphoproliferative disease due to SH2D1A deficiency		 Criteria Provided
Multiple Submitters
No Conflicts
 CA414122169 rs_1556619319

2 SubmittersRCV000788711RCV000660264
NM_002351.5(SH2D1A):c.192G>A (p.Trp64Ter) SNV
Germline		 ChrX:124365815 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Single Submitter
 CA414123674 rs_1556620706

2 SubmittersRCV000660265
NM_002351.5(SH2D1A):c.385T>C (p.Ter129Arg) SNV
Germline		 ChrX:124371389 Likely pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Single Submitter
 CA414125202 rs_111033625

1 SubmittersRCV000660266
NM_002351.5(SH2D1A):c.138-3C>G SNV
Germline		 ChrX:124365758 Likely pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency No Assertion Criteria Provided
 CA658824028 rs_1556620697

1 SubmittersRCV000663341
NM_002351.5(SH2D1A):c.164G>A (p.Arg55Gln) SNV
Germline		 ChrX:124365787 Conflicting classifications of pathogenicity Condition: not provided
X-linked lymphoproliferative disease due to SH2D1A deficiency
Lymphoproliferative disorder		 Criteria Provided
Conflicting Classifications
 CA414123516 rs_111033630

4 SubmittersRCV001091714RCV001327374RCV004798886
NM_002351.5(SH2D1A):c.219T>A (p.His73Gln) SNV
Germline		 ChrX:124370193 Conflicting classifications of pathogenicity X-linked lymphoproliferative disease due to SH2D1A deficiency
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA414124395 rs_954824608

2 SubmittersRCV001237812RCV002069308
NM_002351.5(SH2D1A):c.7G>T (p.Ala3Ser) SNV
Germline		 ChrX:124346649 Conflicting classifications of pathogenicity X-linked lymphoproliferative disease due to SH2D1A deficiency
not specified
Autoinflammatory syndrome		 Criteria Provided
Conflicting Classifications
 CA10509240 rs_148554414

3 SubmittersRCV001520732RCV002246403RCV002264372
NM_002351.5(SH2D1A):c.225A>G (p.Arg75=) SNV
Germline		 ChrX:124370199 Conflicting classifications of pathogenicity Condition: not provided
X-linked lymphoproliferative disease due to SH2D1A deficiency		 Criteria Provided
Conflicting Classifications
 CA10509280 rs_371553659

2 SubmittersRCV001769384RCV005095036
NM_002351.5(SH2D1A):c.2T>C (p.Met1Thr) SNV
Germline		 ChrX:124346644 Pathogenic/Likely pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency
Autoinflammatory syndrome		 Criteria Provided
Multiple Submitters
No Conflicts
 CA414122161 rs_2147519353

3 SubmittersRCV001946671RCV002264437
NM_002351.5(SH2D1A):c.191G>A (p.Trp64Ter) SNV
Germline		 ChrX:124365814 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Single Submitter
 CA10509271 rs_746035909

1 SubmittersRCV001949632
NM_002351.5(SH2D1A):c.201+2T>C SNV
Germline		 ChrX:124365826 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Single Submitter
 CA414123730 rs_2147531379

1 SubmittersRCV002021792
NM_002351.5(SH2D1A):c.160T>A (p.Tyr54Asn) SNV
Germline		 ChrX:124365783 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Single Submitter
 CA414123488 rs_2147531326

1 SubmittersRCV002250349
NM_002351.5(SH2D1A):c.202-1G>C SNV
Germline		 ChrX:124370175 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Single Submitter
 CA414124319 rs_2147534019

1 SubmittersRCV002250350
NM_002351.5(SH2D1A):c.273T>C (p.Asp91=) SNV
Germline		 ChrX:124370247 Conflicting classifications of pathogenicity Autoinflammatory syndrome
X-linked lymphoproliferative disease due to SH2D1A deficiency		 Criteria Provided
Conflicting Classifications
 CA10509282 rs_775759946

2 SubmittersRCV002264509RCV003621617
NM_002351.5(SH2D1A):c.251T>C (p.Ile84Thr) SNV
Germline		 ChrX:124370225 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Single Submitter
 CA414124554 rs_2522819003

1 SubmittersRCV002471422
NM_002351.5(SH2D1A):c.102C>A (p.Ser34Arg) SNV
Germline		 ChrX:124346744 Conflicting classifications of pathogenicity X-linked lymphoproliferative disease due to SH2D1A deficiency
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA414122383 rs_1484311033

2 SubmittersRCV003041478RCV003236948
NM_002351.5(SH2D1A):c.295C>T (p.Gln99Ter) SNV
Germline		 ChrX:124370269 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Single Submitter
 CA414124815 rs_2522819045

1 SubmittersRCV003041480
NM_002351.5(SH2D1A):c.1A>G (p.Met1Val) SNV
Germline		 ChrX:124346643 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Single Submitter
 CA414122158 rs_2522797198

1 SubmittersRCV003150604
NM_002351.5(SH2D1A):c.23A>C (p.His8Pro) SNV
Germline		 ChrX:124346665 Conflicting classifications of pathogenicity X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Conflicting Classifications
 CA414122208 rs_2522797252

3 SubmittersRCV003228222
NM_002351.5(SH2D1A):c.126C>A (p.Cys42Ter) SNV
Germline		 ChrX:124346768 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Single Submitter
 CA414122441 rs_2522797441

1 SubmittersRCV003510656
NM_002351.5(SH2D1A):c.138-1G>A SNV
Germline		 ChrX:124365760 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency
Condition: not provided
Thyroid cancer, nonmedullary, 1		 Criteria Provided
Multiple Submitters
No Conflicts
 CA414123363 rs_1603238847

4 SubmittersRCV003509078RCV004701744RCV005931462
NM_002351.5(SH2D1A):c.201+1G>A SNV
Germline		 ChrX:124365825 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Single Submitter
 CA414123723 rs_2522815020

1 SubmittersRCV003509079
NM_002351.5(SH2D1A):c.162C>A (p.Tyr54Ter) SNV
Unknown		 ChrX:124365785 Likely pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Single Submitter
 rs_2522814914

1 SubmittersRCV004560455
NM_002351.5(SH2D1A):c.138-2A>G SNV
Germline		 ChrX:124365759 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency
Thyroid cancer, nonmedullary, 1
Nonpapillary renal cell carcinoma		 Criteria Provided
Single Submitter

2 SubmittersRCV005199259RCV005938039RCV005938038
NM_002351.5(SH2D1A):c.137+1G>A SNV
Germline		 ChrX:124346780 Likely pathogenic Thyroid cancer, nonmedullary, 1
X-linked lymphoproliferative disease due to SH2D1A deficiency		 Criteria Provided
Single Submitter

2 SubmittersRCV006174042RCV006475289
NM_002351.5(SH2D1A):c.201+1G>C SNV
Germline		 ChrX:124365825 Pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency Criteria Provided
Single Submitter

1 SubmittersRCV006516225