X-linked lymphoproliferative disease due to SH2D1A deficiency: genes and variants
X-linked lymphoproliferative disease due to SH2D1A deficiency is linked to 1 analyzed protein (SH2D1A). 7 DNA variants are known to cause it; 24 more are uncertain, and 1 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to X-linked lymphoproliferative disease due to SH2D1A deficiency
SH2D1A: SH2 domain-containing protein 1A
It coordinates signaling through SLAM-family immune receptors and is essential for normal T-cell and natural-killer-cell responses to Epstein-Barr virus. Loss-of-function variants cause X-linked lymphoproliferative disease type 1, with fulminant EBV-associated immune dysregulation.
7 disease-causing and 24 uncertain variants in SH2D1A are linked to X-linked lymphoproliferative disease due to SH2D1A deficiency.
Known disease-causing variants in X-linked lymphoproliferative disease due to SH2D1A deficiency
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| SH2D1A M1T | 1 | Disease-causing (★★) | |
| SH2D1A D2G | 2 | Disease-causing (★★) | |
| SH2D1A M1V | 1 | Disease-causing (★) | |
| SH2D1A I84T | 84 | SH2 | Disease-causing (★) |
| SH2D1A Y54N | 54 | SH2 | Disease-causing (★) |
| SH2D1A R32T | 32 | SH2 | Disease-causing |
| SH2D1A R55L | 55 | SH2 | Disease-causing |
Uncertain variants in X-linked lymphoproliferative disease due to SH2D1A deficiency that look disease-causing
| Variant | Position | Protein part | Clinical label | Evidence |
|---|---|---|---|---|
| SH2D1A R55Q | 55 | SH2 | Conflicting reports (★) | +7: 2 other pathogenic changes within 3 positions; R55L at the same position is pathogenic; seen in 0 of gnomAD DNA copies; REVEL 0.869 |
Diseases related to X-linked lymphoproliferative disease due to SH2D1A deficiency
- Autoinflammatory syndrome, also linked to SH2D1A
Frequently asked questions
Which genes are linked to X-linked lymphoproliferative disease due to SH2D1A deficiency?
In CATVariant, X-linked lymphoproliferative disease due to SH2D1A deficiency is linked to 1 analyzed protein: SH2D1A (SH2 domain-containing protein 1A).
How many genetic variants are linked to X-linked lymphoproliferative disease due to SH2D1A deficiency?
31 variants: 7 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 24 are of uncertain significance or have conflicting reports.
Which uncertain variants in X-linked lymphoproliferative disease due to SH2D1A deficiency look disease-causing?
1 uncertain variants reach the likely-pathogenic range of the ACMG/AMP points scale on computable evidence, for example SH2D1A R55Q. These are leads for expert review, not diagnoses.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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