Phenotypic Mutation 'Meteor' (pdf version)
Allele | Meteor |
Mutation Type |
missense
|
Chromosome | 10 |
Coordinate | 28,657,828 bp (GRCm39) |
Base Change | T ⇒ A (forward strand) |
Gene |
Themis
|
Gene Name | thymocyte selection associated |
Synonym(s) | Tsepa, Gasp, E430004N04Rik |
Chromosomal Location |
28,544,356-28,759,814 bp (+) (GRCm39)
|
MGI Phenotype |
FUNCTION: This gene encodes a protein that plays a regulatory role in both positive and negative T-cell selection during late thymocyte development. The protein functions through T-cell antigen receptor signaling, and is necessary for proper lineage commitment and maturation of T-cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2015] PHENOTYPE: Homozygous null mice have defects in T cell positive selection that leads to very few alpha-beta T cells being found in the periphery. [provided by MGI curators]
|
Accession Number | NCBI RefSeq: NM_178666; MGI:2443552
|
Mapped | Yes |
Amino Acid Change |
Valine changed to Glutamic Acid
|
Institutional Source | Beutler Lab |
Gene Model |
predicted gene model for protein(s):
[ENSMUSP00000060129]
[ENSMUSP00000055315]
[ENSMUSP00000101155]
[ENSMUSP00000123919 †]
[ENSMUSP00000123894]
† probably from a misspliced transcript
|
AlphaFold |
Q8BGW0 |
SMART Domains |
Protein: ENSMUSP00000060129 Gene: ENSMUSG00000049109 AA Change: V285E
Domain | Start | End | E-Value | Type |
Pfam:CABIT
|
17 |
266 |
5.2e-59 |
PFAM |
Pfam:CABIT
|
282 |
530 |
3.7e-48 |
PFAM |
low complexity region
|
550 |
564 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
PolyPhen 2
Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)
(Using ENSMUST00000056097)
|
SMART Domains |
Protein: ENSMUSP00000055315 Gene: ENSMUSG00000049109 AA Change: V285E
Domain | Start | End | E-Value | Type |
Pfam:CABIT
|
17 |
272 |
9.3e-52 |
PFAM |
Pfam:CABIT
|
282 |
532 |
5e-62 |
PFAM |
low complexity region
|
550 |
564 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
PolyPhen 2
Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)
(Using ENSMUST00000060409)
|
SMART Domains |
Protein: ENSMUSP00000101155 Gene: ENSMUSG00000049109 AA Change: V285E
Domain | Start | End | E-Value | Type |
Pfam:CABIT
|
17 |
272 |
9e-52 |
PFAM |
Pfam:CABIT
|
282 |
532 |
4.9e-62 |
PFAM |
low complexity region
|
550 |
564 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
PolyPhen 2
Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)
(Using ENSMUST00000105516)
|
SMART Domains |
Protein: ENSMUSP00000123919 Gene: ENSMUSG00000049109
Domain | Start | End | E-Value | Type |
Pfam:CABIT
|
17 |
91 |
1.9e-10 |
PFAM |
|
Predicted Effect |
probably benign
|
SMART Domains |
Protein: ENSMUSP00000123894 Gene: ENSMUSG00000049109 AA Change: V132E
Domain | Start | End | E-Value | Type |
Pfam:CABIT
|
17 |
86 |
1.9e-9 |
PFAM |
Pfam:CABIT
|
129 |
203 |
5.1e-18 |
PFAM |
|
Predicted Effect |
possibly damaging
PolyPhen 2
Score 0.903 (Sensitivity: 0.82; Specificity: 0.94)
(Using ENSMUST00000161345)
|
Meta Mutation Damage Score |
0.1152 |
Is this an essential gene? |
Probably nonessential (E-score: 0.169) |
Phenotypic Category |
Unknown |
Candidate Explorer Status |
loading ... |
Single pedigree Linkage Analysis Data
|
|
Penetrance | |
Alleles Listed at MGI | All Mutations and Alleles(15) : Chemically induced (ENU)(6) Chemically induce (other) (1) Gene trapped(2) Targeted(6)
|
Lab Alleles |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL01609:Themis
|
APN |
10 |
28544749 |
splice site |
probably benign |
|
IGL01729:Themis
|
APN |
10 |
28637587 |
nonsense |
probably null |
|
IGL01833:Themis
|
APN |
10 |
28658307 |
nonsense |
probably null |
|
IGL02582:Themis
|
APN |
10 |
28637543 |
missense |
probably benign |
0.00 |
IGL02835:Themis
|
APN |
10 |
28637616 |
intron |
probably benign |
|
cloudies
|
UTSW |
10 |
28637195 |
nonsense |
probably null |
|
currant
|
UTSW |
10 |
28658007 |
missense |
probably damaging |
1.00 |
death_valley
|
UTSW |
10 |
28544723 |
missense |
probably damaging |
1.00 |
six_flags
|
UTSW |
10 |
28657903 |
missense |
probably damaging |
1.00 |
R0445:Themis
|
UTSW |
10 |
28658007 |
missense |
probably damaging |
1.00 |
R0507:Themis
|
UTSW |
10 |
28657828 |
missense |
possibly damaging |
0.90 |
R0709:Themis
|
UTSW |
10 |
28637570 |
missense |
probably benign |
0.00 |
R1170:Themis
|
UTSW |
10 |
28544744 |
missense |
possibly damaging |
0.80 |
R1442:Themis
|
UTSW |
10 |
28658131 |
missense |
probably damaging |
0.96 |
R1844:Themis
|
UTSW |
10 |
28657753 |
missense |
probably damaging |
1.00 |
R2004:Themis
|
UTSW |
10 |
28658720 |
missense |
probably benign |
0.28 |
R2150:Themis
|
UTSW |
10 |
28544723 |
missense |
probably damaging |
1.00 |
R2358:Themis
|
UTSW |
10 |
28739376 |
missense |
possibly damaging |
0.57 |
R4529:Themis
|
UTSW |
10 |
28658331 |
missense |
possibly damaging |
0.92 |
R4693:Themis
|
UTSW |
10 |
28658647 |
missense |
probably damaging |
1.00 |
R4717:Themis
|
UTSW |
10 |
28665748 |
missense |
probably benign |
|
R4801:Themis
|
UTSW |
10 |
28637507 |
missense |
probably benign |
0.21 |
R4802:Themis
|
UTSW |
10 |
28637507 |
missense |
probably benign |
0.21 |
R5249:Themis
|
UTSW |
10 |
28637195 |
nonsense |
probably null |
|
R5557:Themis
|
UTSW |
10 |
28657882 |
missense |
possibly damaging |
0.90 |
R5569:Themis
|
UTSW |
10 |
28657887 |
missense |
possibly damaging |
0.95 |
R5640:Themis
|
UTSW |
10 |
28739372 |
missense |
probably damaging |
0.99 |
R5735:Themis
|
UTSW |
10 |
28598530 |
missense |
probably benign |
0.09 |
R6467:Themis
|
UTSW |
10 |
28657762 |
missense |
possibly damaging |
0.47 |
R6523:Themis
|
UTSW |
10 |
28657894 |
missense |
possibly damaging |
0.65 |
R6727:Themis
|
UTSW |
10 |
28657903 |
missense |
probably damaging |
1.00 |
R7014:Themis
|
UTSW |
10 |
28665703 |
missense |
probably benign |
|
R7101:Themis
|
UTSW |
10 |
28637422 |
nonsense |
probably null |
|
R7185:Themis
|
UTSW |
10 |
28657873 |
missense |
probably benign |
0.00 |
R7323:Themis
|
UTSW |
10 |
28609497 |
missense |
probably benign |
|
R7386:Themis
|
UTSW |
10 |
28665743 |
missense |
probably benign |
0.00 |
R7472:Themis
|
UTSW |
10 |
28637415 |
missense |
possibly damaging |
0.69 |
R7555:Themis
|
UTSW |
10 |
28657698 |
missense |
possibly damaging |
0.67 |
R7715:Themis
|
UTSW |
10 |
28739305 |
missense |
probably benign |
0.02 |
R7825:Themis
|
UTSW |
10 |
28658470 |
missense |
probably benign |
0.11 |
R7992:Themis
|
UTSW |
10 |
28637342 |
missense |
probably benign |
0.02 |
R8112:Themis
|
UTSW |
10 |
28673502 |
makesense |
probably null |
|
R8850:Themis
|
UTSW |
10 |
28673492 |
missense |
possibly damaging |
0.83 |
R8954:Themis
|
UTSW |
10 |
28665709 |
missense |
probably benign |
0.00 |
R9038:Themis
|
UTSW |
10 |
28657749 |
missense |
probably damaging |
0.99 |
R9081:Themis
|
UTSW |
10 |
28544582 |
unclassified |
probably benign |
|
R9168:Themis
|
UTSW |
10 |
28658233 |
missense |
probably benign |
0.01 |
R9169:Themis
|
UTSW |
10 |
28658233 |
missense |
probably benign |
0.01 |
R9170:Themis
|
UTSW |
10 |
28658233 |
missense |
probably benign |
0.01 |
R9171:Themis
|
UTSW |
10 |
28658233 |
missense |
probably benign |
0.01 |
R9269:Themis
|
UTSW |
10 |
28739390 |
missense |
probably benign |
0.10 |
R9404:Themis
|
UTSW |
10 |
28665743 |
missense |
probably benign |
0.00 |
R9518:Themis
|
UTSW |
10 |
28544748 |
critical splice donor site |
probably null |
|
|
Mode of Inheritance |
Unknown |
Local Stock | |
Repository | |
Last Updated |
2019-09-04 9:30 PM
by Diantha La Vine
|
Record Created |
2019-01-23 10:40 AM
by Bruce Beutler
|
Record Posted |
2019-02-14 |
Phenotypic Description |
The Meteor phenotype was identified among G3 mice of the pedigree R0507, some of which showed reduced frequencies of CD4+ T cells in the peripheral blood (Figure 1).
|
Nature of Mutation |
Whole exome HiSeq sequencing of the G1 grandsire identified 70 mutations. The CD4+ T cell phenotype was linked by continuous variable mapping to a mutation in Themis: a T to A transversion at base pair 28,781,832 (v38) on chromosome 10, or base pair 113,506 in the GenBank genomic region NC_000076 encoding Themis. Linkage was found with a dominant model of inheritance, wherein six variant homozygotes and five heterozygous mice departed phenotypically from three homozygous reference mice with a P value of 0.000183 (Figure 2). The mutation corresponds to residue 1,154 in the mRNA sequence NM_178666 within exon 4 of 6 total exons.
1138 AAAGAGTTTCCTGTAGTAGCTGAAGTTGTCGAA
280 -K--E--F--P--V--V--A--E--V--V--E-
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The mutated nucleotide is indicated in red. The mutation results in a valine to glutamic acid substitution at position 285 (V285E) in the Themis protein, and is strongly predicted by PolyPhen-2 to be benign (score = 0.122).
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Illustration of Mutations in
Gene & Protein |
|
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Protein Prediction |
Themis encodes Thymocyte expressed molecule involved in selection [Themis; alternatively, Grb2-associating protein (Gasp)]. Themis contains two CABIT (cysteine-containing all beta in Themis) domains (amino acids 1-261 (CABIT1) and 262-521 (CABIT2) in Themis), a bipartite nuclear localization signal (NLS; amino acids 345-349 in Themis), and a proline-rich region (PRR; PPPRPPKHP; amino acids 555-563 in Themis) [Figure 3; (1-3)]. The Meteor mutation (V285E) is within the CABIT2 domain. For more information about Themis, please see the record for currant.
|
Putative Mechanism | Themis functions at the positive selection checkpoint in thymocyte development; its mode of action is not known (1-5). Several Themis mutant mouse strains exhibited a block in positive selection, resulting in a block in the developmental progression from DP to SP cells (1-6). As a result, the mutant mice exhibited reduced numbers of thymic and peripheral CD4 and CD8 SP cells; the CD4 SP cells were more affected than the CD8 SP cell population (1-6). The role of Themis in negative selection is unclear. In several mutant mouse studies, minor defects in negative selection were observed along with defects in positive selection (1;4). The function of Themis in TCR signaling has not been resolved. Studies have reported a constitutive association of Themis with TCR signaling proteins including Vav1 (1), Itk, and PLCγ1 (4;6;7). In addition, several studies determined that, upon TCR stimulation, Themis associated with PLCγ1, LAT, and SLP-76 indicating that Themis may be a component of the SLP-76/LAT signalosome (1;4;6-8). Mutations in the noncoding region between THEMIS and PTPRK have been linked to susceptibility to celiac disease in humans (9). In addition, patients with celiac disease exhibit elevated THEMIS levels in the duodenal mucosa compared to unaffected individuals (10). Mice with mutations or deficiency in Themis phenocopy the Meteor mice in that all of the models exhibit reduced frequencies of peripheral CD4 SP cells compared to wild-type mice (1-4;10), suggesting that the Meteor mutation is hypomorphic. Thymocyte positive selection is likely defective in Meteor mice, as shown for other Themis mutants.
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Primers |
PCR Primer
Meteor_pcr_F: GCATTTAAGTCAGGAGAGTGCTTACCA
Meteor_pcr_R: GACAGCTCCTTGTGAAGTGTATGGAAA
Sequencing Primer
Meteor_seq_F: TTGGAAGATTATCTCTACCCAGACAC
Meteor_seq_R: TCATAGGCCGTGGGGAAC
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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 750 nucleotides is amplified (chromosome 10, + strand):
1 gcatttaagt caggagagtg cttaccattt gtagtagtaa gaaagaagtg atatttgctg 61 agttttacat aaatataagg gttgggtaac ctctgtttct tgagttgagc atgttggtat 121 atatatcatt ttgttttcat caaaaagttt caaaactgaa aagtctaaca taaggaaaat 181 tatattatga ttatttgaat tcttttctcc ctcctaaatg aaaattatct atggtattgg 241 aagattatct ctacccagac accatctctt gagagctctt taaacaaaat gtcagttgtc 301 ttctctttca ttttcagttc aaaaggacat agtccggatt ctcccaagtt tagacgttga 361 agtcaaagat attactgatt cttatgatgc taactggttt cttcagttgc tgtctacgga 421 cgaccttttt gaaatgacca gcaaagagtt tcctgtagta gctgaagttg tcgaaatatc 481 tcaagggaac cacctgcccc aaagtatttt gcagcgagag aaaaccattg tcatccacaa 541 aaagtaccag gcttcgagga tcttagcttc agaaattcgc agcaatttcc ctaaaagaca 601 cttcttgatc cctattagct acaaaggcaa gttcaaaaga agaccacggg agttccccac 661 ggcctatgac ctgcagatag ctaagagcag gaaagaaact ctccacgtgg tggccaccaa 721 agctttccat acacttcaca aggagctgtc
Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red. |
References | 1. Lesourne, R., Uehara, S., Lee, J., Song, K. D., Li, L., Pinkhasov, J., Zhang, Y., Weng, N. P., Wildt, K. F., Wang, L., Bosselut, R., and Love, P. E. (2009) Themis, a T Cell-Specific Protein Important for Late Thymocyte Development. Nat Immunol. 10, 840-847.
2. Patrick, M. S., Oda, H., Hayakawa, K., Sato, Y., Eshima, K., Kirikae, T., Iemura, S., Shirai, M., Abe, T., Natsume, T., Sasazuki, T., and Suzuki, H. (2009) Gasp, a Grb2-Associating Protein, is Critical for Positive Selection of Thymocytes. Proc Natl Acad Sci U S A. 106, 16345-16350.
3. Johnson, A. L., Aravind, L., Shulzhenko, N., Morgun, A., Choi, S. Y., Crockford, T. L., Lambe, T., Domaschenz, H., Kucharska, E. M., Zheng, L., Vinuesa, C. G., Lenardo, M. J., Goodnow, C. C., Cornall, R. J., and Schwartz, R. H. (2009) Themis is a Member of a New Metazoan Gene Family and is Required for the Completion of Thymocyte Positive Selection. Nat Immunol. 10, 831-839.
4. Fu, G., Vallee, S., Rybakin, V., McGuire, M. V., Ampudia, J., Brockmeyer, C., Salek, M., Fallen, P. R., Hoerter, J. A., Munshi, A., Huang, Y. H., Hu, J., Fox, H. S., Sauer, K., Acuto, O., and Gascoigne, N. R. (2009) Themis Controls Thymocyte Selection through Regulation of T Cell Antigen Receptor-Mediated Signaling. Nat Immunol. 10, 848-856.
5. Kakugawa, K., Yasuda, T., Miura, I., Kobayashi, A., Fukiage, H., Satoh, R., Matsuda, M., Koseki, H., Wakana, S., Kawamoto, H., and Yoshida, H. (2009) A Novel Gene Essential for the Development of Single Positive Thymocytes. Mol Cell Biol. 29, 5128-5135.
6. Paster, W., Brockmeyer, C., Fu, G., Simister, P. C., de Wet, B., Martinez-Riano, A., Hoerter, J. A., Feller, S. M., Wulfing, C., Gascoigne, N. R., and Acuto, O. (2013) GRB2-Mediated Recruitment of THEMIS to LAT is Essential for Thymocyte Development. J Immunol. 190, 3749-3756.
7. Brockmeyer, C., Paster, W., Pepper, D., Tan, C. P., Trudgian, D. C., McGowan, S., Fu, G., Gascoigne, N. R., Acuto, O., and Salek, M. (2011) T Cell Receptor (TCR)-Induced Tyrosine Phosphorylation Dynamics Identifies THEMIS as a New TCR Signalosome Component. J Biol Chem. 286, 7535-7547.
8. Okada, T., Nitta, T., Kaji, K., Takashima, A., Oda, H., Tamehiro, N., Goto, M., Okamura, T., Patrick, M. S., and Suzuki, H. (2014) Differential Function of Themis CABIT Domains during T Cell Development. PLoS One. 9, e89115.
9. Dubois, P. C., Trynka, G., Franke, L., Hunt, K. A., Romanos, J., Curtotti, A., Zhernakova, A., Heap, G. A., Adany, R., Aromaa, A., Bardella, M. T., van den Berg, L. H., Bockett, N. A., de la Concha, E. G., Dema, B., Fehrmann, R. S., Fernandez-Arquero, M., Fiatal, S., Grandone, E., Green, P. M., Groen, H. J., Gwilliam, R., Houwen, R. H., Hunt, S. E., Kaukinen, K., Kelleher, D., Korponay-Szabo, I., Kurppa, K., MacMathuna, P., Maki, M., Mazzilli, M. C., McCann, O. T., Mearin, M. L., Mein, C. A., Mirza, M. M., Mistry, V., Mora, B., Morley, K. I., Mulder, C. J., Murray, J. A., Nunez, C., Oosterom, E., Ophoff, R. A., Polanco, I., Peltonen, L., Platteel, M., Rybak, A., Salomaa, V., Schweizer, J. J., Sperandeo, M. P., Tack, G. J., Turner, G., Veldink, J. H., Verbeek, W. H., Weersma, R. K., Wolters, V. M., Urcelay, E., Cukrowska, B., Greco, L., Neuhausen, S. L., McManus, R., Barisani, D., Deloukas, P., Barrett, J. C., Saavalainen, P., Wijmenga, C., and van Heel, D. A. (2010) Multiple Common Variants for Celiac Disease Influencing Immune Gene Expression. Nat Genet. 42, 295-302.
10. Bondar, C., Plaza-Izurieta, L., Fernandez-Jimenez, N., Irastorza, I., Withoff, S., Wijmenga, C., Chirdo, F., Bilbao, J. R., and CEGEC. (2014) THEMIS and PTPRK in Celiac Intestinal Mucosa: Coexpression in Disease and After in Vitro Gliadin Challenge. Eur J Hum Genet. 22, 358-362.
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Science Writers | Anne Murray |
Illustrators | Diantha La Vine |
Authors | Jin Huk Choi, Xue Zhong, and Bruce Beutler |