Phenotypic Mutation 'Cpg3' (pdf version)
AlleleCpg3
Mutation Type missense
Chromosome9
Coordinate106,101,351 bp (GRCm39)
Base Change T ⇒ A (forward strand)
Gene Tlr9
Gene Name toll-like receptor 9
Chromosomal Location 106,099,797-106,104,075 bp (+) (GRCm39)
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 member of the Toll-like receptor (TLR) family which plays a fundamental role in pathogen recognition and activation of innate immunity. TLRs are highly conserved from Drosophila to humans and share structural and functional similarities. They recognize pathogen-associated molecular patterns (PAMPs) that are expressed on infectious agents, and mediate the production of cytokines necessary for the development of effective immunity. The various TLRs exhibit different patterns of expression. This gene is preferentially expressed in immune cell rich tissues, such as spleen, lymph node, bone marrow and peripheral blood leukocytes. Studies in mice and human indicate that this receptor mediates cellular response to unmethylated CpG dinucleotides in bacterial DNA to mount an innate immune response. [provided by RefSeq, Jul 2008]
PHENOTYPE: Nullizygous mice exhibit impaired immune responses to CpG DNA and altered susceptibility to EAE and parasitic infection. ENU-induced mutants may exhibit altered susceptibility to viral infection or induced colitis and impaired immune response to unmethylated CpG oligonucleotides. [provided by MGI curators]
Accession Number
NCBI RefSeq: NM_031178; MGI: 1932389
MappedYes 
Amino Acid Change Valine changed to Glutamic Acid
Institutional SourceBeutler Lab
Gene Model not available
AlphaFold Q9EQU3
PDB Structure Crystal structure of mouse TLR9 (unliganded form) [X-RAY DIFFRACTION]
Crystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 1) [X-RAY DIFFRACTION]
Crystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 2) [X-RAY DIFFRACTION]
Crystal structure of mouse TLR9 in complex with inhibitory DNA_super [X-RAY DIFFRACTION]
Crystal Structure of the C-terminal Domain of Mouse TLR9 [X-RAY DIFFRACTION]
SMART Domains Protein: ENSMUSP00000082207
Gene: ENSMUSG00000045322
AA Change: V214E

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
LRR 62 85 1.49e2 SMART
LRR 122 144 1.41e1 SMART
LRR 198 221 4.98e-1 SMART
LRR 283 306 6.59e1 SMART
LRR 307 332 1.62e1 SMART
Blast:LRR 333 361 8e-6 BLAST
LRR 390 413 7.38e1 SMART
LRR 414 440 1.86e2 SMART
LRR 496 520 1.81e2 SMART
LRR 521 544 6.05e0 SMART
LRR 545 568 2.27e2 SMART
LRR 575 599 4.58e1 SMART
LRR 628 651 3.87e1 SMART
LRR_TYP 677 700 3.39e-3 SMART
LRR 702 724 2.27e2 SMART
LRR 726 748 3.09e2 SMART
Blast:LRRCT 761 810 4e-11 BLAST
Pfam:TIR 870 1029 7.4e-11 PFAM
Predicted Effect probably damaging

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000062241)
Meta Mutation Damage Score Not available question?
Is this an essential gene? Probably nonessential (E-score: 0.078) question?
Phenotypic Category Autosomal Semidominant
Candidate Explorer Status loading ...
Single pedigree
Linkage Analysis Data
Penetrance 100% 
Alleles Listed at MGI

All alleles(9) : Targeted, knock-out(1) Gene trapped(1) Chemically induced(7)

Lab Alleles
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00864:Tlr9 APN 9 106102206 missense probably damaging 1.00
IGL01764:Tlr9 APN 9 106103004 missense probably damaging 1.00
IGL02077:Tlr9 APN 9 106102704 missense possibly damaging 0.90
IGL02232:Tlr9 APN 9 106102136 missense probably damaging 1.00
IGL02851:Tlr9 APN 9 106101929 nonsense probably null
Asura UTSW 9 106101846 missense probably damaging 1.00
Cpg1 UTSW 9 106102206 missense probably damaging 1.00
Cpg11 UTSW 9 106101785 missense probably damaging 1.00
Cpg2 UTSW 9 106103664 missense probably damaging 1.00
Cpg5 UTSW 9 106101888 missense probably damaging 1.00
Cpg6 UTSW 9 106103792 missense probably damaging 1.00
cpg7 UTSW 9 106102548 missense probably benign 0.00
Meager UTSW 9 106101338 missense probably damaging 1.00
PIT4498001:Tlr9 UTSW 9 106100721 missense probably benign 0.00
R0058:Tlr9 UTSW 9 106102164 missense possibly damaging 0.90
R0058:Tlr9 UTSW 9 106102164 missense possibly damaging 0.90
R0071:Tlr9 UTSW 9 106100777 missense probably benign
R0071:Tlr9 UTSW 9 106100777 missense probably benign
R0126:Tlr9 UTSW 9 106102881 missense probably benign 0.01
R0165:Tlr9 UTSW 9 106103286 missense probably benign 0.10
R0534:Tlr9 UTSW 9 106102086 missense probably benign 0.01
R0585:Tlr9 UTSW 9 106102275 missense probably benign 0.01
R1527:Tlr9 UTSW 9 106100949 missense probably benign 0.09
R1712:Tlr9 UTSW 9 106101248 missense probably damaging 1.00
R1817:Tlr9 UTSW 9 106102142 missense probably benign
R1940:Tlr9 UTSW 9 106101846 missense probably damaging 1.00
R2117:Tlr9 UTSW 9 106102536 missense probably damaging 1.00
R2656:Tlr9 UTSW 9 106101140 missense probably benign 0.05
R3700:Tlr9 UTSW 9 106101278 missense probably damaging 1.00
R4600:Tlr9 UTSW 9 106101732 missense probably damaging 1.00
R4608:Tlr9 UTSW 9 106102173 missense probably damaging 0.99
R4612:Tlr9 UTSW 9 106101006 missense probably damaging 1.00
R4959:Tlr9 UTSW 9 106101876 missense probably benign
R5173:Tlr9 UTSW 9 106103151 missense possibly damaging 0.49
R5472:Tlr9 UTSW 9 106101512 missense probably damaging 1.00
R5572:Tlr9 UTSW 9 106102836 missense possibly damaging 0.47
R5618:Tlr9 UTSW 9 106101938 missense possibly damaging 0.47
R5820:Tlr9 UTSW 9 106099906 critical splice donor site probably null
R6393:Tlr9 UTSW 9 106102136 missense probably damaging 1.00
R6397:Tlr9 UTSW 9 106102305 missense probably damaging 1.00
R6455:Tlr9 UTSW 9 106101198 missense probably damaging 1.00
R7385:Tlr9 UTSW 9 106102463 missense probably damaging 1.00
R7455:Tlr9 UTSW 9 106101729 missense probably benign 0.00
R7561:Tlr9 UTSW 9 106103148 missense probably benign 0.00
R8889:Tlr9 UTSW 9 106099834 start gained probably benign
R8892:Tlr9 UTSW 9 106099834 start gained probably benign
R8926:Tlr9 UTSW 9 106103213 missense probably benign
R9221:Tlr9 UTSW 9 106101972 missense probably damaging 1.00
R9228:Tlr9 UTSW 9 106102752 missense possibly damaging 0.49
R9581:Tlr9 UTSW 9 106101510 missense probably damaging 1.00
R9689:Tlr9 UTSW 9 106100721 missense probably benign 0.00
R9697:Tlr9 UTSW 9 106100723 nonsense probably null
R9788:Tlr9 UTSW 9 106101006 missense probably damaging 1.00
Z1176:Tlr9 UTSW 9 106100862 missense probably benign 0.03
Mode of Inheritance Autosomal Semidominant
Local Stock Live Mice, Sperm, gDNA
MMRRC Submission 030343-UCD
Last Updated 2016-05-13 3:09 PM by Peter Jurek
Record Created unknown
Record Posted 2007-12-05
Phenotypic Description
The CpG3 phenotype was identified in a G3 screen for mutants with impaired response to Toll-like receptor (TLR) ligands (TLR Signaling Screen). Peritoneal macrophages from CpG3 mice produce normal amounts of tumor necrosis factor (TNF)-α in response to all TLR ligands tested, except oligodeoxynucleotides containing CpG motifs (CpG ODNs). In response to CpG ODN treatment, homozygous CpG3 macrophages produce no TNF-α. In addition, naïve B cells from whole blood of homozygous CpG3 mice fail to proliferate upon stimulation with CpG ODN in vitro, a response recently demonstrated to be specific for CpG ODN among other TLR agonists (1) (Figure 1).
 
Although not all of the same phenotypes have been examined, those tested are identical between CpG1, CpG2, CpG3 and CpG5 mice. (CpG3 heterozygote phenotypes have not been tested; CpG3 is tentatively classified as semidominant).  Sequence analysis revealed that all four strains contain mutations in Tlr9. However, the positions of the mutations differ, with the CpG1, CpG3 and CpG5 mutations located in the sixteenth, sixth and ­­fourteenth extracellular leucine-rich repeats (LRR), respectively, and the CpG2 mutation located in the cytoplasmic Toll/IL-1R (TIR) domain. In addition to CpG1, CpG2, CpG3 and CpG5, another strain of mice, designated effete, also exhibits impaired TNF-α responses to CpG ODN treatment. The mutant has no TLR9 mutation; the causative mutation is under investigation.
Nature of Mutation
The CpG3 mutation corresponds to a T to A transversion at position 747 of the Tlr9 transcript, in exon 2 of 2 total exons.
 
731 AACAACCTCACAAAGGTGCCCCGCCAACTGCCC
209 -N--N--L--T--K--V--P--R--Q--L--P-
 
The mutated nucleotide is indicated in red lettering, and causes a valine to glutamic acid substitution at residue 214 of the TLR9 protein.
Illustration of Mutations in
Gene & Protein
Protein Prediction
Figure 2. Protein and domain structure of TLR9. (A) Schematic representation of TLR9 based on crystalized structures of mouse TLR9 LRR (PBD 3WPF) and human TLR2 TIR (1FYW) domains. The residue affected by the CpG3 mutation is highlighted. 3D image was created using UCSF Chimera. (B) TLR9 is a 1032 amino acid protein with an extracellur domain (pink) of leucine rich repeats (LRR), a short transmembrane (TM) domain (blue) and a cytoplasmic Toll/Interleukin-1 receptor (TIR) domain (green). The CpG3 mutation (red asterisk) results in a valine to glutamic acid change at position 214 of the TLR9 protein in the predicted sixth LRR. This image is interactive. Click on the image to view other mutations found in TLR9. Click on each mutation for more specific information.
The CpG3 mutation results in a valine to glutamic acid change at position 214 of the TLR9 protein, which lies in the predicted sixth LRR module of the TLR9 ectodomain (Figure 3).
 
Please see the record for CpG1 for information about Tlr9.
Putative Mechanism
The CpG3 mutation substitutes glutamic acid for valine at position 214 of the TLR9 protein, which lies in the predicted sixth LRR module of the TLR9 ectodomain and is conserved in human TLR9. No tertiary structural data presently exist for TLR9, making it difficult to hypothesize how the CpG3 mutation could affect either ligand binding or receptor dimerization.  Recently, the crystal structure of the related TLR3 heterodimer bound to double-stranded (ds) RNA has been elucidated (see record for CpG1).  The ligand-bound TLR3 heterodimer forms an M-shape with the dsRNA binding to the concave surfaces of the TLR3 heterodimer at two locations on each ectodomain (2). It has been hypothesized that TLR7, 8 and 9 ligands may also bind to the concave surface of the ectodomain at a site made up by insertions at LRR 2, 5, 8 and 11 (3).  The CpG3 mutation might somehow disrupt ligand binding and/or receptor dimerization, or destroy proper folding or localization of the receptor.  The CpG3 phenotype supports any and all of these possibilities.
Primers Primers cannot be located by automatic search.
Genotyping
CpG3 genotyping is performed by amplifying the region containing the mutation using PCR, followed by sequencing of the amplified region to detect the single nucleotide change.
 
Primers for PCR amplification
CpG3(F): 5’- GGACGGGAACTGCTACTACAAGAAC-3’
CpG3(R): 5’- ATTGTGTGCCAGGCTAAGGCTC-3’
 
PCR program
1) 94°C             2:00
2) 94°C             0:30
3) 55°C             0:30
4) 72°C             1:00
5) repeat steps (2-4) 40X
6) 72°C             7:00
7) 4°C               ∞
 
Primers for sequencing
CpG3_seq(F): 5’- TGAGCAATCTCACCCATCTG -3’
CpG3_seq(R):5' - GCAAAGGATACCTTCTTGCG -3'
 
NOTE: The forward PCR primer works better for forward sequencing:
CpG3(F): 5’- GGACGGGAACTGCTACTACAAGAAC-3’
 
The following sequence of 1237 nucleotides (from Genbank genomic region NC_000075 for linear DNA sequence of Tlr9) is amplified:
 
1436                                                             ggacg
1441 ggaactgcta ctacaagaac ccctgcacag gagcggtgaa ggtgacccca ggcgccctcc
1501 tgggcctgag caatctcacc catctgtctc tgaagtataa caacctcaca aaggtgcccc
1561 gccaactgcc ccccagcctg gagtacctcc tggtgtccta taacctcatt gtcaagctgg
1621 ggcctgaaga cctggccaat ctgacctccc ttcgagtact tgatgtgggt gggaattgcc
1681 gtcgctgtga ccatgccccc aatccctgta tagaatgtgg ccaaaagtcc ctccacctgc
1741 accctgagac cttccatcac ctgagccatc tggaaggcct ggtgctgaag gacagctctc
1801 tccatacact gaactcttcc tggttccaag gtctggtcaa cctctcggtg ctggacctaa
1861 gcgagaactt tctctatgaa agcatcaccc acaccaatgc ctttcagaac ctaacccgcc
1921 tgcgcaagct caacctgtcc ttcaattacc gcaagaaggt atcctttgcc cgcctccacc
1981 tggcaagttc ctttaagaac ctggtgtcac tgcaggagct gaacatgaac ggcatcttct
2041 tccgcttgct caacaagtac acgctcagat ggctggccga tctgcccaaa ctccacactc
2101 tgcatcttca aatgaacttc atcaaccagg cacagctcag catctttggt accttccgag
2161 cccttcgctt tgtggacttg tcagacaatc gcatcagtgg gccttcaacg ctgtcagaag
2221 ccacccctga agaggcagat gatgcagagc aggaggagct gttgtctgcg gatcctcacc
2281 cagctccgct gagcacccct gcttctaaga acttcatgga caggtgtaag aacttcaagt
2341 tcaccatgga cctgtctcgg aacaacctgg tgactatcaa gccagagatg tttgtcaatc
2401 tctcacgcct ccagtgtctt agcctgagcc acaactccat tgcacaggct gtcaatggct
2461 ctcagttcct gccgctgact aatctgcagg tgctggacct gtcccataac aaactggact
2521 tgtaccactg gaaatcgttc agtgagctac cacagttgca ggccctggac ctgagctaca
2581 acagccagcc ctttagcatg aagggtatag gccacaattt cagttttgtg acccatctgt
2641 ccatgctaca gagccttagc ctggcacaca at
 
PCR primer binding sites are underlined; sequencing primer binding sites are highlighted in gray; the mutated T is shown in red text.
References
Science Writers Eva Marie Y. Moresco
Illustrators Diantha La Vine
AuthorsMichael Berger, Bruce Beutler
Edit History
2010-12-08 3:31 PM (current)
2010-08-06 10:07 AM
2010-06-23 11:04 AM
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2010-04-29 11:18 AM
2010-02-25 2:59 PM