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SLAMF1 signaling lymphocytic activation molecule family member 1 [ Homo sapiens (human) ]

Gene ID: 6504, updated on 14-Nov-2024

Summary

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Official Symbol
SLAMF1provided by HGNC
Official Full Name
signaling lymphocytic activation molecule family member 1provided by HGNC
Primary source
HGNC:HGNC:10903
See related
Ensembl:ENSG00000117090 MIM:603492; AllianceGenome:HGNC:10903
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SLAM; CD150; CDw150
Summary
Enables several functions, including SH2 domain binding activity; identical protein binding activity; and virus receptor activity. Involved in several processes, including negative regulation of CD40 signaling pathway; negative regulation of cytokine production; and positive regulation of MAPK cascade. Located in extracellular exosome. Is active in plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in lymph node (RPKM 8.7), appendix (RPKM 6.0) and 11 other tissues See more
Orthologs
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Genomic context

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See SLAMF1 in Genome Data Viewer
Location:
1q23.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (160608106..160647044, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159745198..159784140, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160577896..160616834, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1928 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:160460168-160461367 Neighboring gene SLAM family member 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1929 Neighboring gene uncharacterized LOC105371468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1930 Neighboring gene Sharpr-MPRA regulatory region 7182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1931 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1933 Neighboring gene CD84 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1934 Neighboring gene NANOG hESC enhancer GRCh37_chr1:160567464-160567965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1939 Neighboring gene uncharacterized LOC107985220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1940 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:160621837-160622647 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:160622648-160623458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1942 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:160635284-160635845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1943 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:160644012-160644628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1944 Neighboring gene endogenous retrovirus group K member 18 Env polyprotein Neighboring gene SET pseudogene 9 Neighboring gene CD48 molecule

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. Measles virus interacts with human SLAM receptor on dendritic cells to cause immunosuppression. Hahm B, et al. Virology, 2004 Jun 1. PMID 15193925, Free PMC Article
  2. Measles virus infects and suppresses proliferation of T lymphocytes from transgenic mice bearing human signaling lymphocytic activation molecule. Hahm B, et al. J Virol, 2003 Mar. PMID 12610126, Free PMC Article
  3. Absence of SLAM mutations in EBV-associated lymphoproliferative disease patients. Ferrand V, et al. J Med Virol, 2003 May. PMID 12629654
  4. The Measles Virus Receptor SLAMF1 Can Mediate Particle Endocytosis. Gonçalves-Carneiro D, et al. J Virol, 2017 Apr 1. PMID 28100610, Free PMC Article
  5. In vitro allergen-induced mRNA expression of signaling lymphocytic activation molecule by PBMC of patients with allergic rhinitis is increased during specific pollen immunotherapy. Laaksonen K, et al. J Allergy Clin Immunol, 2003 Dec. PMID 14657878

See all (103) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SLAMF1 as a novel molecule mediating the causal association between rheumatoid arthritis and interstitial lung disease: A Mendelian randomization study combined with transcriptomics and in vivo validation.
    Title: SLAMF1 as a novel molecule mediating the causal association between rheumatoid arthritis and interstitial lung disease: A Mendelian randomization study combined with transcriptomics and in vivo validation.
  2. Identification of SLAMF1 as an immune-related key gene associated with rheumatoid arthritis and verified in mice collagen-induced arthritis model.
    Title: Identification of SLAMF1 as an immune-related key gene associated with rheumatoid arthritis and verified in mice collagen-induced arthritis model.
  3. SLAMF1 is expressed and secreted by hepatocytes and the liver in nonalcoholic fatty liver disease.
    Title: SLAMF1 is expressed and secreted by hepatocytes and the liver in nonalcoholic fatty liver disease.
  4. Neutrophil autophagy during human active tuberculosis is modulated by SLAMF1.
    Title: Neutrophil autophagy during human active tuberculosis is modulated by SLAMF1.
  5. SLAMF1/CD150 expression and topology in prostate and breast cancer cell lines.
    Title: SLAMF1/CD150 expression and topology in prostate and breast cancer cell lines.
  6. SLAM/SAP Decreased Follicular Regulatory T Cells in Patients with Graves' Disease.
    Title: SLAM/SAP Decreased Follicular Regulatory T Cells in Patients with Graves' Disease.
  7. CD150 and CD180 are negative regulators of IL-10 expression and secretion in chronic lymphocytic leukemia B cells.
    Title: CD150 and CD180 are negative regulators of IL-10 expression and secretion in chronic lymphocytic leukemia B cells.
  8. In chronic lymphocytic leukaemia, SLAMF1 deregulation is associated with genomic complexity and independently predicts a worse outcome.
    Title: In chronic lymphocytic leukaemia, SLAMF1 deregulation is associated with genomic complexity and independently predicts a worse outcome.
  9. Genome-Wide Association Study Identifies SLAMF1 Affecting the Rate of Memory Decline.
    Title: Genome-Wide Association Study Identifies SLAMF1 Affecting the Rate of Memory Decline.
  10. Increased Plasma Levels of the Co-stimulatory Proteins CDCP1 and SLAMF1 in Patients With Autoimmune Endocrine Diseases.
    Title: Increased Plasma Levels of the Co-stimulatory Proteins CDCP1 and SLAMF1 in Patients With Autoimmune Endocrine Diseases.
Submit: New GeneRIF Correction See all GeneRIFs (60)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of treatment refractory schizophrenia in Han Chinese.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SH2 domain binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables antigen binding TAS
Traceable Author Statement
more info
 PubMed 
enables cell adhesion mediator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables signaling receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables transmembrane signaling receptor activity TAS
Traceable Author Statement
more info
 PubMed 
enables virus receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in adaptive immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in cell adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in leukocyte chemotaxis involved in inflammatory response IEA
Inferred from Electronic Annotation
more info
  
involved_in myeloid dendritic cell activation involved in immune response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in natural killer cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in natural killer cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of CD40 signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of T cell cytokine production IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of interleukin-12 production IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of interleukin-6 production IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of tumor necrosis factor production IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of type II interferon production IEA
Inferred from Electronic Annotation
more info
  
involved_in phagocytosis IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of ERK1 and ERK2 cascade IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of JNK cascade IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of T-helper 1 cell cytokine production IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of activated T cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cell population proliferation TAS
Traceable Author Statement
more info
 PubMed 
involved_in positive regulation of dendritic cell chemotaxis IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of macrophage chemotaxis IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of type II interferon production IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of vesicle fusion IEA
Inferred from Electronic Annotation
more info
  
involved_in symbiont entry into host cell IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular exosome HDA PubMed 
located_in phagocytic vesicle IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
signaling lymphocytic activation molecule
Names
IPO-3
SLAM family member 1

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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.

mRNA and Protein(s)

  1. NM_001330754.2 → NP_001317683.1  signaling lymphocytic activation molecule isoform a precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) represents the longest transcript and encodes the longer isoform (a).
    Source sequence(s)
    AL121985, AL138930, KF471075
    Consensus CDS
    CCDS81389.1
    UniProtKB/Swiss-Prot
    Q13291
    Related
    ENSP00000438406.2, ENST00000538290.2
    Conserved Domains (1) summary
    pfam06214
    Location:1 → 125
    SLAM; Signaling lymphocytic activation molecule (SLAM) protein

  2. NM_003037.5 → NP_003028.1  signaling lymphocytic activation molecule isoform b precursor

    See identical proteins and their annotated locations for NP_003028.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) lacks an alternate coding exon compared to variant 5. The resulting isoform (b) has a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AL121985, AL138930
    Consensus CDS
    CCDS1207.1
    UniProtKB/Swiss-Prot
    Q13291, Q5W172, Q9HBE8, W0HKK7
    UniProtKB/TrEMBL
    Q96QR3
    Related
    ENSP00000306190.6, ENST00000302035.11
    Conserved Domains (1) summary
    pfam06214
    Location:1 → 125
    SLAM; Signaling lymphocytic activation molecule (SLAM) protein

RNA

  1. NR_104399.3 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two internal exons compared to variant 5. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 5, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK304237, AL121985, AL138930

  2. NR_104400.3 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks three alternate internal exons compared to variant 5. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 5, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL121985, AL138930, BC144498

  3. NR_104401.3 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks two alternate internal exons and uses an alternate splice junction compared to variant 5. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 5, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL121985, AL138930, BC144499

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    160608106..160647044 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005245456.5 → XP_005245513.1  signaling lymphocytic activation molecule isoform X2

    See identical proteins and their annotated locations for XP_005245513.1

    UniProtKB/TrEMBL
    B2RAL4, Q96QR3
    Conserved Domains (1) summary
    pfam06214
    Location:1 → 125
    SLAM; Signaling lymphocytic activation molecule (SLAM) protein

  2. XM_017002130.3 → XP_016857619.1  signaling lymphocytic activation molecule isoform X1

    UniProtKB/TrEMBL
    Q96QR3

  3. XM_047428490.1 → XP_047284446.1  signaling lymphocytic activation molecule isoform X6

  4. XM_017002131.3 → XP_016857620.1  signaling lymphocytic activation molecule isoform X5

  5. XM_047428487.1 → XP_047284443.1  signaling lymphocytic activation molecule isoform X4

  6. XM_047428486.1 → XP_047284442.1  signaling lymphocytic activation molecule isoform X3

    UniProtKB/TrEMBL
    B4E2E4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    159745198..159784140 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338391.1 → XP_054194366.1  signaling lymphocytic activation molecule isoform X2

  2. XM_054338390.1 → XP_054194365.1  signaling lymphocytic activation molecule isoform X1

  3. XM_054338395.1 → XP_054194370.1  signaling lymphocytic activation molecule isoform X6

  4. XM_054338394.1 → XP_054194369.1  signaling lymphocytic activation molecule isoform X5

  5. XM_054338393.1 → XP_054194368.1  signaling lymphocytic activation molecule isoform X4

  6. XM_054338392.1 → XP_054194367.1  signaling lymphocytic activation molecule isoform X3

    UniProtKB/TrEMBL
    B4E2E4
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13291.1 GenPept UniProtKB/Swiss-Prot:Q13291

Gene LinkOut

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