Phenotypic Mutation 'goodnow' (pdf version)
Allele | goodnow |
Mutation Type |
splice site
|
Chromosome | 11 |
Coordinate | 46,228,926 bp (GRCm39) |
Base Change | A ⇒ C (forward strand) |
Gene |
Itk
|
Gene Name | IL2 inducible T cell kinase |
Synonym(s) | Tcsk, Tsk, Emt |
Chromosomal Location |
46,215,977-46,280,342 bp (-) (GRCm39)
|
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an intracellular tyrosine kinase expressed in T-cells. The protein contains both SH2 and SH3 domains which are often found in intracellular kinases. It is thought to play a role in T-cell proliferation and differentiation. [provided by RefSeq, Jul 2008] PHENOTYPE: Mice homozygous for disruptions in this gene display decreased percentages of CD4 and CD8 cells, increased percentage of B cells, impaired T cell receptor signaling, and increased susceptibility to Toxoplasma gondii infection. [provided by MGI curators]
|
Accession Number | NCBI RefSeq: NM_001281965 (variant 1), NM_010583 (variant 2), NM_001281966 (variant 3), NM_001281967 (variant 4), NM_001281968 (variant 5); MGI:96621
|
Mapped | Yes |
Amino Acid Change |
|
Institutional Source | Beutler Lab |
Gene Model |
predicted gene model for protein(s):
[ENSMUSP00000020664 †]
[ENSMUSP00000104860 †]
† probably from a misspliced transcript
|
AlphaFold |
Q03526 |
SMART Domains |
Protein: ENSMUSP00000020664 Gene: ENSMUSG00000020395
Domain | Start | End | E-Value | Type |
PH
|
5 |
113 |
2.3e-13 |
SMART |
BTK
|
113 |
149 |
1.1e-21 |
SMART |
SH3
|
174 |
230 |
5.87e-14 |
SMART |
SH2
|
237 |
328 |
9.44e-29 |
SMART |
TyrKc
|
362 |
611 |
3.28e-133 |
SMART |
|
Predicted Effect |
probably null
|
SMART Domains |
Protein: ENSMUSP00000104860 Gene: ENSMUSG00000020395
Domain | Start | End | E-Value | Type |
PH
|
5 |
119 |
3.94e-12 |
SMART |
BTK
|
119 |
155 |
1.1e-21 |
SMART |
SH3
|
180 |
236 |
5.87e-14 |
SMART |
SH2
|
243 |
334 |
9.44e-29 |
SMART |
TyrKc
|
368 |
617 |
3.28e-133 |
SMART |
|
Predicted Effect |
probably null
|
Meta Mutation Damage Score |
0.9755 |
Is this an essential gene? |
Probably nonessential (E-score: 0.116) |
Phenotypic Category |
Autosomal Recessive |
Candidate Explorer Status |
loading ... |
Single pedigree Linkage Analysis Data
|
|
Penetrance | |
Alleles Listed at MGI | All Mutations and Alleles(10) : Chemically induced (ENU)(1) Chemically induced (other)(1) Targeted(8)
|
Lab Alleles |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00950:Itk
|
APN |
11 |
46258723 |
missense |
probably damaging |
1.00 |
IGL01349:Itk
|
APN |
11 |
46232027 |
missense |
possibly damaging |
0.84 |
IGL03290:Itk
|
APN |
11 |
46225764 |
missense |
probably damaging |
1.00 |
IGL03385:Itk
|
APN |
11 |
46222688 |
nonsense |
probably null |
|
Calame
|
UTSW |
11 |
46233222 |
splice site |
probably null |
|
carbone
|
UTSW |
11 |
46222776 |
nonsense |
probably null |
|
demon
|
UTSW |
11 |
46231539 |
missense |
probably damaging |
1.00 |
itxaro
|
UTSW |
11 |
46229044 |
missense |
probably damaging |
1.00 |
Segun
|
UTSW |
11 |
46235710 |
intron |
probably benign |
|
BB009:Itk
|
UTSW |
11 |
46231519 |
missense |
probably benign |
|
BB019:Itk
|
UTSW |
11 |
46231519 |
missense |
probably benign |
|
R0095:Itk
|
UTSW |
11 |
46233279 |
missense |
probably damaging |
0.99 |
R0265:Itk
|
UTSW |
11 |
46280285 |
start gained |
probably benign |
|
R0281:Itk
|
UTSW |
11 |
46244743 |
missense |
probably damaging |
1.00 |
R0463:Itk
|
UTSW |
11 |
46222816 |
missense |
probably damaging |
1.00 |
R0518:Itk
|
UTSW |
11 |
46251115 |
missense |
probably damaging |
0.98 |
R0521:Itk
|
UTSW |
11 |
46251115 |
missense |
probably damaging |
0.98 |
R1121:Itk
|
UTSW |
11 |
46222721 |
missense |
possibly damaging |
0.93 |
R1550:Itk
|
UTSW |
11 |
46280153 |
missense |
probably damaging |
1.00 |
R1762:Itk
|
UTSW |
11 |
46227309 |
missense |
probably damaging |
0.98 |
R2418:Itk
|
UTSW |
11 |
46229044 |
missense |
probably damaging |
1.00 |
R2419:Itk
|
UTSW |
11 |
46229044 |
missense |
probably damaging |
1.00 |
R2859:Itk
|
UTSW |
11 |
46235662 |
intron |
probably benign |
|
R3107:Itk
|
UTSW |
11 |
46218291 |
missense |
probably benign |
0.15 |
R3546:Itk
|
UTSW |
11 |
46246675 |
missense |
probably benign |
0.00 |
R4601:Itk
|
UTSW |
11 |
46227342 |
missense |
probably benign |
0.17 |
R4610:Itk
|
UTSW |
11 |
46227342 |
missense |
probably benign |
0.17 |
R4792:Itk
|
UTSW |
11 |
46235658 |
intron |
probably benign |
|
R4885:Itk
|
UTSW |
11 |
46227171 |
splice site |
probably null |
|
R4934:Itk
|
UTSW |
11 |
46280152 |
missense |
probably damaging |
1.00 |
R5286:Itk
|
UTSW |
11 |
46228926 |
splice site |
probably null |
|
R5328:Itk
|
UTSW |
11 |
46222703 |
missense |
probably benign |
0.04 |
R5399:Itk
|
UTSW |
11 |
46228938 |
missense |
probably benign |
0.44 |
R5958:Itk
|
UTSW |
11 |
46235682 |
intron |
probably benign |
|
R6235:Itk
|
UTSW |
11 |
46227255 |
missense |
probably benign |
0.16 |
R6828:Itk
|
UTSW |
11 |
46232045 |
missense |
probably damaging |
1.00 |
R6849:Itk
|
UTSW |
11 |
46222762 |
missense |
probably damaging |
1.00 |
R7356:Itk
|
UTSW |
11 |
46258659 |
missense |
possibly damaging |
0.72 |
R7753:Itk
|
UTSW |
11 |
46222722 |
missense |
probably damaging |
1.00 |
R7932:Itk
|
UTSW |
11 |
46231519 |
missense |
probably benign |
|
R7988:Itk
|
UTSW |
11 |
46246661 |
missense |
probably damaging |
0.99 |
R8188:Itk
|
UTSW |
11 |
46222776 |
nonsense |
probably null |
|
R8337:Itk
|
UTSW |
11 |
46233222 |
splice site |
probably null |
|
R8738:Itk
|
UTSW |
11 |
46231539 |
missense |
probably damaging |
1.00 |
R8993:Itk
|
UTSW |
11 |
46225735 |
missense |
probably damaging |
1.00 |
R9028:Itk
|
UTSW |
11 |
46235710 |
intron |
probably benign |
|
R9650:Itk
|
UTSW |
11 |
46222778 |
missense |
probably damaging |
1.00 |
U24488:Itk
|
UTSW |
11 |
46228971 |
missense |
probably damaging |
1.00 |
X0062:Itk
|
UTSW |
11 |
46256871 |
missense |
probably benign |
0.15 |
Z1088:Itk
|
UTSW |
11 |
46244689 |
splice site |
probably null |
|
|
Mode of Inheritance |
Autosomal Recessive |
Local Stock | |
Repository | |
Last Updated |
2018-01-30 8:38 AM
by Anne Murray
|
Record Created |
2017-06-20 11:49 AM
by Bruce Beutler
|
Record Posted |
2017-08-18 |
Phenotypic Description |
The goodnow phenotype was identified among N-ethyl-N-nitrosourea (ENU)-mutagenized G3 mice of the pedigree R5286, some of which showed an increase in the B:T cell ratio (Figure 1) due to a decrease in the frequencies of T cells (Figure 2), CD4+ T cells (Figure 3), CD4+ T cells in CD3+ T cells (Figure 4), CD8+ T cells (Figure 5), naive CD4 T cells in CD4 T cells (Figure 6), and naive CD8 T cells in CD8 T cells (Figure 7) with concomitant increased frequencies of B cells (Figure 8), IgD+ B cells (Figure 9), IgM+ B cells (Figure 10), CD44+ T cells (Figure 11), CD44+ CD8 T cells (Figure 12), central memory CD4 T cells in CD4 T cells (Figure 13), effector memory CD4 T cells in CD4 T cells (Figure 14), and central memory CD8 T cells in CD8 T cells (Figure 15), all in the peripheral blood. CD44 expression on T cells (Figure 16), CD4 T cells (Figure 17), and CD8 T cells (Figure 18) was increased.
|
Nature of Mutation |
Whole exome HiSeq sequencing of the G1 grandsire identified 56 mutations. All of the above anomalies were linked by continuous variable mapping to a mutation in Itk: a T to G transversion at base pair 46,338,099 (v38) on chromosome 11, or base pair 51,417 in the GenBank genomic region NC_000076 within the donor splice site of intron 12. The strongest association was found with a recessive model of inheritance to the normalized frequency of central memory CD8 T cells in CD8 T cells, wherein three variant homozygotes departed phenotypically from nine homozygous reference mice and 14 heterozygous mice with a P value of 5.285 x 10-20 (Figure 19). The effect of the mutation at the cDNA and protein levels have not examined, but the mutation is predicted to result in the use of a cryptic site in intron 12. The resulting transcript would have a 5-base pair insertion of intron 12, causing a frame shifted protein product beginning after amino acid 410 of the protein, which is normally 619 amino acids in length.
C57BL/6J:
<--exon 12 intron 12--> exon 13--> <--exon 17
51401 ……GAAGTCATGAT gtgagttagagcagg…… GAAACTCTCTCAC…… ……GCTGGGCTTTAG……
407 ……-E--V--M--M --K--L--S--H-…… ……-A--G--L--*- 619
|
Genomic numbering corresponds to NC_000076. The donor splice site of intron 12, which is destroyed by the goodnow mutation, is indicated in blue lettering and the mutated nucleotide is indicated in red.
|
Illustration of Mutations in
Gene & Protein |
|
---|
Protein Prediction |
ITK is one of five members of the Tec family of tyrosine kinases, which includes ITK, Btk, Tec, Bmx, and Rlk (also called Txk). ITK is a 72 kD protein with similarity to Csk and the Src and Abl family tyrosine kinases in the organization of its SH3-SH2-kinase domain cassette. However, ITK lacks the N-terminal myristoylation consensus sequence and the C-terminal negative regulatory tyrosine residue present in Src kinases, indicating a distinct regulatory mechanism. The N-terminus of ITK contains a pleckstrin homology (PH) domain that binds to the membrane phospholipid phosphatidylinositol 3,4,5-trisphosphate (PIP3), thereby recruiting ITK to the plasma membrane to interact with the activated T cell receptor (1-3). The ITK N-terminus also contains a Tec homology domain consisting of a Btk homology (BH) motif that binds to zinc and a proline-rich region that binds to SH3 domains (4). Please see the entry itxaro for more information about Itk.
|
Putative Mechanism | Mice with the goodnow mutation of Itk displayed key phenotypes characteristic of ITK deficiency, including a reduced frequency of CD4 T cells, increased activated/memory CD4 and CD8 T cells, and elevated CD44 expression on CD4 and CD8 T cells.
|
Primers |
PCR Primer
goodnow_pcr_F: CTTCCCATCCAGCTTCTTCTTCT
goodnow_pcr_R: AAAGCATTCCCTCTTCCTCTGTT
Sequencing Primer
goodnow_seq_F: CTGCAGATTTGAACTTGGTC
goodnow_seq_R: TTCCAGGGAAGTGGGTGATC
|
Genotyping | 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 10:00 7) 4°C hold
The following sequence of 463 nucleotides is amplified (chromosome 11, - strand):
1 aagcattccc tcttcctctg ttccagggaa gtgggtgatc caaccctcag agctaacgtt 61 cgtgcaggag attggcagcg ggcagtttgg gctggtgcat ctcggctact ggctcaacaa 121 ggacaaggtg gccatcaaga ccattcagga aggggcgatg tcagaagaag actttatcga 181 ggaggcggaa gtcatgatgt gagttagagc agggatgtgc aggcatgctg ggaaggaggg 241 tcccggctgt gcttgtaaaa ttccactctg atgtattgtc atgccccagt agtagacgcc 301 tactacatac acaaggaaaa cacaaaaaga gccttgttag ggcctaggag atggagatgg 361 ctcccgtggt gaagtgcttg ctgcacggcc actaagacca agttcaaatc tgcagaaatc 421 atgctattaa gaaagaagaa gaagaagaag ctggatggga agg
Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red. |
References |
3. Huang, Y. H., Grasis, J. A., Miller, A. T., Xu, R., Soonthornvacharin, S., Andreotti, A. H., Tsoukas, C. D., Cooke, M. P., and Sauer, K. (2007) Positive Regulation of Itk PH Domain Function by Soluble IP4. Science. 316, 886-889.
|
Science Writers | Anne Murray |
Illustrators | Diantha La Vine |
Authors | Xue Zhong, Aijie Liu, Bruce Beutler |