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Gene

SH2D1A

SH2 domain containing 1A

Summary

Cytogenetic location
Xq25
Coordinates
Chromosome X: 124,346,563–124,373,160 (GRCh38)
Exons
4 exons across 26.6 kb
Protein
128 amino acids
Inheritance
X-linked recessive
Also known as
XLP, MTCP1, DSHP, XLPD, EBVS, SAP
Previous symbols
IMD5, LYP
MANE Select transcript
ENST00000371139.9NM_002351.5
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • X-Linked Lymphoproliferative Disease and XMEN

    • X-linked lymphoproliferative diseaseX-linked recessive

      Severe EBV infection, HLH, low antibodies and lymphoma risk caused by changes in SH2D1A (XLP1) or XIAP (XLP2).

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      Stem cell transplantation can be curative for XLP1; diagnosis also guides HLH treatment, immunoglobulin replacement and testing of relatives.

Broader groupings

  • Other Inborn Errors of Immunity

    • Inborn error of immunity

      One of 114 genes linked to it

      Inherited disorders of the immune system caused by changes in single genes, affecting how the body fights infection or regulates inflammation.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
    • Immunodeficiency Disease

      One of 170 genes linked to it

      Disease in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      HSCT for SCID and severe PIDs; immunoglobulin replacement (IVIG/SCIG) for antibody deficiencies; leniolisib (Joenja, FDA 2023) for APDS; gene therapy for ADA-SCID; abatacept for CTLA4/LRBA deficiency; prophylactic antibiotics; G-CSF for CGD

Inheritance

X-linked recessive
The change is on the X chromosome, so one copy affects males, who have one X, while females with one are usually carriers. A carrier mother passes it on to each child with a one-in-two chance.

How SH2D1A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome X, with a bracket where SH2D1A sits. SH2D1A and 4 genes near it on chromosome X, from 123,859,862 to 124,859,861.Chromosome XXq25p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q28124 Mb124.2 Mb124.4 Mb124.6 Mb124.8 MbXIAP: 123,859,693–123,913,972, forward strandXIAPSTAG2: 123,960,212–124,422,664, forward strandSTAG2TEX13D: 124,246,249–124,336,863, forward strandTEX13DSH2D1A: 124,346,563–124,373,160, forward strandSH2D1ATENM1: 124,375,903–125,204,312, reverse strandTENM1Diagram of SH2D1A: 4 exons on the forward strand of chromosome XExon 1: 6 known disease-causing sitesExon 2: 9 known disease-causing sitesExon 3: 4 known disease-causing sitesExon 4: 1 known disease-causing siteExon 1: 124,346,563–124,346,779, 217 basesExon 2: 124,365,761–124,365,824, 64 basesExon 3: 124,370,176–124,370,320, 145 basesExon 4: 124,371,351–124,373,160, 1,810 bases12345′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 2.2 kb of the gene's 26.6 kb; 387 of those bases code for the protein.

How a genome test reads SH2D1A

26

positions in SH2D1A where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 26.6 kb of SH2D1A, introns included, not only the 2.2 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). SH2D1A gene: SH2 domain containing 1A. Retrieved 17 October 2026, from https://dantelabs.com/genes/sh2d1a

Vancouver

Dante Labs. SH2D1A gene: SH2 domain containing 1A [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/sh2d1a

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