Incidental Mutation 'P0016:Slamf6'
ID 7633
Institutional Source Beutler Lab
Gene Symbol Slamf6
Ensembl Gene ENSMUSG00000015314
Gene Name SLAM family member 6
Synonyms KAL1b, NTB-A, KAL1, Ly108, SF2000
MMRRC Submission 038269-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.058) question?
Stock # P0016 (G1)
Quality Score
Status Validated
Chromosome 1
Chromosomal Location 171745002-171776525 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 171764068 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 154 (T154A)
Ref Sequence ENSEMBL: ENSMUSP00000141448 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000171330] [ENSMUST00000194182] [ENSMUST00000194561] [ENSMUST00000195656]
AlphaFold Q9ET39
Predicted Effect probably damaging
Transcript: ENSMUST00000171330
AA Change: T154A

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000130610
Gene: ENSMUSG00000015314
AA Change: T154A

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
low complexity region 28 37 N/A INTRINSIC
IG 39 142 1.49e-2 SMART
low complexity region 145 161 N/A INTRINSIC
Blast:IG_like 162 226 7e-16 BLAST
transmembrane domain 240 262 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000193311
Predicted Effect probably benign
Transcript: ENSMUST00000194182
SMART Domains Protein: ENSMUSP00000142242
Gene: ENSMUSG00000015314

DomainStartEndE-ValueType
low complexity region 22 36 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000194561
AA Change: T154A

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000141944
Gene: ENSMUSG00000015314
AA Change: T154A

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
low complexity region 28 37 N/A INTRINSIC
IG 39 142 1.49e-2 SMART
low complexity region 145 161 N/A INTRINSIC
Blast:IG_like 162 226 5e-16 BLAST
transmembrane domain 240 262 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000195656
AA Change: T154A

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000141448
Gene: ENSMUSG00000015314
AA Change: T154A

DomainStartEndE-ValueType
low complexity region 28 37 N/A INTRINSIC
IG 39 142 5.9e-5 SMART
low complexity region 145 161 N/A INTRINSIC
Blast:IG_like 162 226 8e-16 BLAST
transmembrane domain 240 262 N/A INTRINSIC
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 85.6%
  • 3x: 81.0%
  • 10x: 66.8%
  • 20x: 50.1%
Validation Efficiency 96% (97/101)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] 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]
PHENOTYPE: Mice homozygous for one null allele show no overt phenotype. Mice homozygous for another null allele show impaired IL-4 production by CD4+ T cells, reduced inflammatory response to L. mexicana infection, high susceptibility to S. typhimurium infection, and defective neutrophil bactericidal activity. [provided by MGI curators]
Allele List at MGI

All alleles(3) : Targeted(3)

Other mutations in this stock
Total: 18 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700123K08Rik A T 5: 138,561,200 (GRCm39) L154* probably null Het
4930432E11Rik T C 7: 29,262,537 (GRCm39) noncoding transcript Het
Arap3 T A 18: 38,117,401 (GRCm39) T892S probably benign Het
Ctnnd2 G A 15: 30,967,084 (GRCm39) V987I probably benign Het
Dennd6b T C 15: 89,071,180 (GRCm39) I351V probably benign Het
Kif27 G A 13: 58,451,266 (GRCm39) Q1021* probably null Het
Klb G A 5: 65,537,266 (GRCm39) W865* probably null Het
Mbd1 C T 18: 74,407,609 (GRCm39) R130* probably null Het
Mroh7 T A 4: 106,565,054 (GRCm39) probably null Het
Myo16 C T 8: 10,450,596 (GRCm39) probably benign Het
Rbm22 T A 18: 60,703,842 (GRCm39) probably benign Het
Rnaseh2a C G 8: 85,686,429 (GRCm39) D206H probably damaging Het
Slain1 A G 14: 103,923,110 (GRCm39) T187A probably benign Het
Traip A G 9: 107,845,855 (GRCm39) D316G possibly damaging Het
Ttn T C 2: 76,641,527 (GRCm39) D5196G probably damaging Het
Ubr5 C T 15: 38,000,822 (GRCm39) V1569M probably damaging Het
Zfp750 T A 11: 121,404,804 (GRCm39) K24* probably null Het
Zfp799 T C 17: 33,038,331 (GRCm39) E645G possibly damaging Het
Other mutations in Slamf6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00964:Slamf6 APN 1 171,745,347 (GRCm39) missense probably null 0.27
IGL01011:Slamf6 APN 1 171,765,666 (GRCm39) missense probably benign 0.19
R1565:Slamf6 UTSW 1 171,761,975 (GRCm39) missense possibly damaging 0.53
R1763:Slamf6 UTSW 1 171,770,154 (GRCm39) intron probably benign
R1774:Slamf6 UTSW 1 171,770,154 (GRCm39) intron probably benign
R1993:Slamf6 UTSW 1 171,761,776 (GRCm39) missense possibly damaging 0.74
R2155:Slamf6 UTSW 1 171,765,575 (GRCm39) missense probably damaging 0.99
R2328:Slamf6 UTSW 1 171,761,818 (GRCm39) missense probably benign 0.00
R4693:Slamf6 UTSW 1 171,761,680 (GRCm39) nonsense probably null
R5062:Slamf6 UTSW 1 171,764,100 (GRCm39) missense possibly damaging 0.93
R5172:Slamf6 UTSW 1 171,764,147 (GRCm39) missense probably benign 0.01
R5249:Slamf6 UTSW 1 171,764,249 (GRCm39) missense probably damaging 1.00
R5328:Slamf6 UTSW 1 171,765,662 (GRCm39) missense probably benign 0.04
R5771:Slamf6 UTSW 1 171,745,341 (GRCm39) missense probably damaging 0.98
R6339:Slamf6 UTSW 1 171,775,615 (GRCm39) missense probably null 1.00
R6960:Slamf6 UTSW 1 171,745,320 (GRCm39) missense probably damaging 0.98
R7176:Slamf6 UTSW 1 171,761,858 (GRCm39) missense probably benign 0.13
R7400:Slamf6 UTSW 1 171,747,360 (GRCm39) missense unknown
R7535:Slamf6 UTSW 1 171,747,325 (GRCm39) missense unknown
R7629:Slamf6 UTSW 1 171,764,191 (GRCm39) missense probably damaging 0.97
R8202:Slamf6 UTSW 1 171,761,786 (GRCm39) missense probably benign 0.01
R8934:Slamf6 UTSW 1 171,745,338 (GRCm39) missense possibly damaging 0.76
R9225:Slamf6 UTSW 1 171,764,270 (GRCm39) missense probably benign 0.25
R9338:Slamf6 UTSW 1 171,747,157 (GRCm39) intron probably benign
R9581:Slamf6 UTSW 1 171,761,897 (GRCm39) missense
RF025:Slamf6 UTSW 1 171,769,149 (GRCm39) critical splice acceptor site probably benign
Protein Function and Prediction

Slamf6 (alternatively, NTB-A) is a tyrosine-phosphorylated antigen involved in the lysis of Epstein-Barr virus-infected cells (1).  NTB-A was identified as a member of the CD2 superfamily/CD150 family of receptors and ligands (2).  NTB-A can co-stimulate T cells to induce proliferation and IFN-γ expression (2).  In addition, NTB-A promotes the differentiation of T cells to Th1 cells (2)

Expression/Localization

Slamf6 is expressed on natural killer, T, and B lymphocytes (1;2).

Background

Slamf6tm1Dhow/tm1Dhow; MGI:3581614

involves: 129/Sv * C57BL/6

Homozygous animals have increased circulating IL-12b, IL-16, andTNF levels after infection with Salmonella tymphimurium (3). Also, IL-4 production by CD4+ T cells, reduced inflammatory response to L. mexicana infection, high susceptibility to S. typhimurium infection, and defective neutrophil bactericidal activity (3).

Slamf6tm1Lex/tm1Lex; MGI:3529322

involves: 129S5/SvEvBrd * C57BL/6J

Homozygous mice show no overt phenotype.

References
Posted On 2012-10-05
Science Writer Anne Murray