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SLAMF6 SLAM family member 6 [ Homo sapiens (human) ]

Gene ID: 114836, updated on 13-Mar-2020

Summary

Official Symbol
SLAMF6provided by HGNC
Official Full Name
SLAM family member 6provided by HGNC
Primary source
HGNC:HGNC:21392
See related
Ensembl:ENSG00000162739 MIM:606446
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
KALI; NTBA; CD352; KALIb; Ly108; NTB-A; SF2000
Summary
The protein encoded by this gene is a type I transmembrane protein, belonging to the CD2 subfamily of the immunoglobulin superfamily. This encoded protein is expressed on Natural killer (NK), T, and B lymphocytes. It undergoes tyrosine phosphorylation and associates with the Src homology 2 domain-containing protein (SH2D1A) as well as with SH2 domain-containing phosphatases (SHPs). It functions as a coreceptor in the process of NK cell activation. It can also mediate inhibitory signals in NK cells from X-linked lymphoproliferative patients. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, May 2010]
Expression
Biased expression in lymph node (RPKM 29.2), spleen (RPKM 15.5) and 7 other tissues See more
Orthologs

Genomic context

See SLAMF6 in Genome Data Viewer
Location:
1q23.2-q23.3
Exon count:
8
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (160485030..160523263, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160454820..160493052, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371466 Neighboring gene VANGL planar cell polarity protein 2 Neighboring gene uncharacterized LOC105371467 Neighboring gene uncharacterized LOC105371468 Neighboring gene Sharpr-MPRA regulatory region 7182 Neighboring gene CD84 molecule

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

NHGRI GWAS Catalog

Description
Robust evidence for five new Graves' disease risk loci from a staged genome-wide association analysis.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef HIV-1 (SF2) Nef downregulates SLAMF6 (NTB-A); downregulation is dependent upon a proline rich SH3 binding domain in Nef as shown in A3.01 T cells and HeLa TZM-bl cells PubMed
Vpu vpu HIV-1 (NL4-3) Vpu downregulates SLAMF6 (NTB-A); downregulation is dependent upon serines at positions 52 and 56 in Vpu as shown in A3.01 T cells and HeLa TZM-bl cells PubMed
vpu HIV-1 Vpu downregulates NTB-A on infected T cells. Vpu does not increase NTB-A endocytosis or degradation within lysosomes. Vpu-mediated downregulation of NTB-A protects the HIV infected cell from lysis by NK cells PubMed
vpu HIV-1 (NL4-3) Vpu downregulates SLAMF6 via a cullin-RING E3 ubiquitin ligase complex- independent mechanism PubMed
vpu The second alpha-helix of Vpu is critical to affect the glycosylation and surface expression of NTB-A. Vpu delta-23, Vpu A18H, and Vpu-KKDQ mutants exhibit an attenuated activity on NTB-A glycosylation PubMed
vpu HIV-1 Vpu modulates the glycosylation pattern of NTB-A, which correlates with re-localization of NTB-A from the cell surface to the Golgi-compartment PubMed
vpu HIV-1 Vpu proteins from Cameroonian group N viruses are largely unable to downregulate NTB-A PubMed
vpu A combination of molecular dynamics simulations and docking approaches shows the lowest energy structure of Vpu-NTB-A, indicating that the residues C-235, F-238, I-242, and L-243/245/246 in NTB-A interact with the alanine rim (A-8/11/15/19) of Vpu PubMed
vpu HIV-1 Vpu binds to NK-T- and -B cell antigen (NTB-A) through its transmembrane region (residues 4-28) PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ50657, MGC104953

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
extracellular exosome HDA PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
SLAM family member 6
Names
NK-T-B-antigen
NTBA receptor
activating NK receptor
natural killer-, T- and B-cell antigen

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.

mRNA and Protein(s)

  1. NM_001184714.2NP_001171643.1  SLAM family member 6 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001171643.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK125624, AY358159, DB197632
    Consensus CDS
    CCDS53394.1
    UniProtKB/Swiss-Prot
    Q96DU3
    Related
    ENSP00000357036.3, ENST00000368057.8
    Conserved Domains (1) summary
    cd16842
    Location:32126
    Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family
  2. NM_001184715.2NP_001171644.1  SLAM family member 6 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses multiple alternate splice sites in the coding region, compared to variant 1, which result in an isoform (3) with a shorter extracellular domain than isoform 1.
    Source sequence(s)
    AJ277141, AK125624, AK303990
    UniProtKB/Swiss-Prot
    Q96DU3
    UniProtKB/TrEMBL
    B4E1U5
    Conserved Domains (2) summary
    pfam13927
    Location:102150
    Ig_3; Immunoglobulin domain
    cl11960
    Location:378
    Ig; Immunoglobulin domain
  3. NM_001184716.2NP_001171645.1  SLAM family member 6 isoform 4 precursor

    See identical proteins and their annotated locations for NP_001171645.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate exon in the 5' coding region, compared to variant 1, which result in an isoform (4) with a shorter extracellular domain than isoform 1.
    Source sequence(s)
    AK125624, AK301026, AW402723, DB197632
    Consensus CDS
    CCDS53393.1
    UniProtKB/Swiss-Prot
    Q96DU3
    Related
    ENSP00000357034.1, ENST00000368055.1
  4. NM_052931.5NP_443163.1  SLAM family member 6 isoform 2 precursor

    See identical proteins and their annotated locations for NP_443163.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, compared to variant 1, which results in an isoform (2) that is one amino acid shorter than isoform 1.
    Source sequence(s)
    AK125624, BC113893, DB197632
    Consensus CDS
    CCDS1205.1
    UniProtKB/Swiss-Prot
    Q96DU3
    Related
    ENSP00000357038.3, ENST00000368059.7
    Conserved Domains (3) summary
    cd05775
    Location:32127
    Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
    smart00410
    Location:34126
    IG_like; Immunoglobulin like
    pfam13927
    Location:151199
    Ig_3; Immunoglobulin domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    160485030..160523263 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000217.1XP_016855706.1  SLAM family member 6 isoform X3

  2. XM_017000216.1XP_016855705.1  SLAM family member 6 isoform X2

  3. XM_017000215.2XP_016855704.1  SLAM family member 6 isoform X1

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