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SH2D1A SH2 domain containing 1A [ Homo sapiens (human) ]

Gene ID: 4068, updated on 10-Apr-2021

Summary

Official Symbol
SH2D1Aprovided by HGNC
Official Full Name
SH2 domain containing 1Aprovided by HGNC
Primary source
HGNC:HGNC:10820
See related
Ensembl:ENSG00000183918 MIM:300490
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LYP; SAP; XLP; DSHP; EBVS; IMD5; XLPD; MTCP1; XLPD1; SAP/SH2D1A
Summary
This gene encodes a protein that plays a major role in the bidirectional stimulation of T and B cells. This protein contains an SH2 domain and a short tail. It associates with the signaling lymphocyte-activation molecule, thereby acting as an inhibitor of this transmembrane protein by blocking the recruitment of the SH2-domain-containing signal-transduction molecule SHP-2 to its docking site. This protein can also bind to other related surface molecules that are expressed on activated T, B and NK cells, thereby modifying signal transduction pathways in these cells. Mutations in this gene cause lymphoproliferative syndrome X-linked type 1 or Duncan disease, a rare immunodeficiency characterized by extreme susceptibility to infection with Epstein-Barr virus, with symptoms including severe mononucleosis and malignant lymphoma. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Biased expression in lymph node (RPKM 17.0), spleen (RPKM 6.1) and 7 other tissues See more
Orthologs
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Genomic context

See SH2D1A in Genome Data Viewer
Location:
Xq25
Exon count:
4
Annotation release Status Assembly Chr Location
109.20210226 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (124346563..124373160)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (123480413..123507010)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene nucleophosmin 1 pseudogene 34 Neighboring gene uncharacterized LOC105373331 Neighboring gene TEX13 family member D Neighboring gene teneurin transmembrane protein 1 Neighboring gene ribosomal protein S26 pseudogene 57

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Lymphoproliferative syndrome 1, X-linked
MedGen: CN034206 OMIM: 308240
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2021-01-27)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2021-01-27)

ClinGen Genome Curation PagePubMed

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ18687, FLJ92177

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
cell-cell signaling IEA
Inferred from Electronic Annotation
more info
 
cellular defense response IEA
Inferred from Electronic Annotation
more info
 
humoral immune response IEA
Inferred from Electronic Annotation
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
negative regulation of T cell receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of natural killer cell mediated cytotoxicity IEA
Inferred from Electronic Annotation
more info
 
regulation of immune response IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of immune response TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
SH2 domain-containing protein 1A
Names
Duncan disease SH2-protein
SLAM associated protein/SH2 domain protein 1A
SLAM-associated protein
T cell signal transduction molecule SAP
signaling lymphocyte activation molecule-associated protein
signaling lymphocytic activation molecule-associated protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007464.1 RefSeqGene

    Range
    4983..31861
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_106

mRNA and Protein(s)

  1. NM_001114937.3NP_001108409.1  SH2 domain-containing protein 1A isoform 2

    See identical proteins and their annotated locations for NP_001108409.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AA190204, AF100541, AL023657, DA007747
    Consensus CDS
    CCDS48162.1
    UniProtKB/Swiss-Prot
    O60880
    Related
    ENSP00000353126.4, ENST00000360027.4
    Conserved Domains (1) summary
    cd10400
    Location:2104
    SH2_SAP1a; Src homology 2 (SH2) domain found in SLAM-associated protein (SAP) 1a
  2. NM_002351.5NP_002342.1  SH2 domain-containing protein 1A isoform 1

    See identical proteins and their annotated locations for NP_002342.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AA190204, AL023657
    Consensus CDS
    CCDS14608.1
    UniProtKB/Swiss-Prot
    O60880
    Related
    ENSP00000360181.4, ENST00000371139.8
    Conserved Domains (1) summary
    cd10400
    Location:2104
    SH2_SAP1a; Src homology 2 (SH2) domain found in SLAM-associated protein (SAP) 1a

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210226

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    124346563..124373160
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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