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

Gene ID: 4068, updated on 7-Apr-2019

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

Genomic context

See SH2D1A in Genome Data Viewer
Location:
Xq25
Exon count:
4
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) X NC_000023.11 (124346282..124373160)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (123480132..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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Lymphoproliferative syndrome 1, X-linked Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-04-26)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-26)

ClinGen Genome Curation Page

Pathways from BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Direct p53 effectors, organism-specific biosystem (from Pathway Interaction Database)
    Direct p53 effectors, organism-specific biosystem
    Direct p53 effectors
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystem (from REACTOME)
    Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystemA number of receptors and cell adhesion molecules play a key role in modifying the response of cells of lymphoid origin (such as B-, T- and NK cells) to self and tumor antigens, as well as to pathoge...
  • MAPK Signaling Pathway, organism-specific biosystem (from WikiPathways)
    MAPK Signaling Pathway, organism-specific biosystemThe mitogen-activated protein kinase (MAPK) cascade is a highly conserved module that is involved in various cellular functions, including cell proliferation, differentiation and migration. Mammals e...
  • Measles, organism-specific biosystem (from KEGG)
    Measles, organism-specific biosystemMeasles virus (MV) is highly contagious virus that leads infant death worldwide. Humans are the unique natural reservoir for this virus. It causes severe immunosuppression favouring secondary bacteri...
  • Measles, conserved biosystem (from KEGG)
    Measles, conserved biosystemMeasles virus (MV) is highly contagious virus that leads infant death worldwide. Humans are the unique natural reservoir for this virus. It causes severe immunosuppression favouring secondary bacteri...
  • Natural killer cell mediated cytotoxicity, organism-specific biosystem (from KEGG)
    Natural killer cell mediated cytotoxicity, organism-specific biosystemNatural killer (NK) cells are lymphocytes of the innate immune system that are involved in early defenses against both allogeneic (nonself) cells and autologous cells undergoing various forms of stre...
  • Natural killer cell mediated cytotoxicity, conserved biosystem (from KEGG)
    Natural killer cell mediated cytotoxicity, conserved biosystemNatural killer (NK) cells are lymphocytes of the innate immune system that are involved in early defenses against both allogeneic (nonself) cells and autologous cells undergoing various forms of stre...

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
SH3/SH2 adaptor activity NAS
Non-traceable Author Statement
more info
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
cellular defense response NAS
Non-traceable Author Statement
more info
PubMed 
humoral immune response IEA
Inferred from Electronic Annotation
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
positive regulation of natural killer cell mediated cytotoxicity IEA
Inferred from Electronic Annotation
more info
 
positive regulation of signal transduction IEA
Inferred from Electronic Annotation
more info
 
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)

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_001114937.2NP_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, AL022718, 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_002351.4NP_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, AL022718, 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 Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p12 Primary Assembly

    Range
    124346282..124373160
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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