GENE REFERENCE / HGNC:10820

SH2D1A

SH2 domain containing 1A

protein-coding geneXq25Gene information

What does this gene do?

The SH2D1A gene provides instructions for making a protein called signaling lymphocyte activation molecule (SLAM) associated protein (SAP). SAP interacts with other proteins called SLAM family receptors to activate signaling pathways that are involved in the control of immune cells (lymphocytes). In particular, it helps regulate lymphocytes that destroy other cells (cytotoxic lymphocytes) and is necessary for the development of specialized lymphocytes called natural killer T cells. SAP also helps control immune reactions by triggering self-destruction (apoptosis) of lymphocytes when they are no longer needed.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-28. Source review: 2010-08.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
X-linked lymphoproliferative disease due to SH2D1A deficiencyMONDO:0024551 · Evaluated 2025-10-14	X-linked	DefinitivePrimary Immune Regulatory Disorders Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 384
Submissions for variants in or overlapping this gene: 489
Submissions explicitly reporting this gene: 295
Alleles reported pathogenic / likely pathogenic: 56
VariationIDs with uncertain significance: 65
VariationIDs with conflicting classifications: 13

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about SH2D1A?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 56 alleles in SH2D1A reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in SH2D1A.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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