Phenotypic Mutation 'Plain_sight' (pdf version)
Allele | Plain_sight |
Mutation Type |
missense
|
Chromosome | 17 |
Coordinate | 57,604,122 bp (GRCm39) |
Base Change | G ⇒ A (forward strand) |
Gene |
Vav1
|
Gene Name | vav 1 oncogene |
Chromosomal Location |
57,586,100-57,635,031 bp (+) (GRCm39)
|
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the VAV gene family. The VAV proteins are guanine nucleotide exchange factors (GEFs) for Rho family GTPases that activate pathways leading to actin cytoskeletal rearrangements and transcriptional alterations. The encoded protein is important in hematopoiesis, playing a role in T-cell and B-cell development and activation. The encoded protein has been identified as the specific binding partner of Nef proteins from HIV-1. Coexpression and binding of these partners initiates profound morphological changes, cytoskeletal rearrangements and the JNK/SAPK signaling cascade, leading to increased levels of viral transcription and replication. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Apr 2012] PHENOTYPE: Homozygous null mutants exhibit defective T cell maturation, interleukin-2 production, and cell cycle progression. Immunoglobulin class switching is also impaired and attributed to defective T cell help. [provided by MGI curators]
|
Accession Number | NCBI RefSeq: NM_011691, NM_001163815, NM_001163816; MGI:98923
|
Mapped | Yes |
Amino Acid Change |
Glutamic Acid changed to Lysine
|
Institutional Source | Beutler Lab |
Gene Model |
predicted gene model for protein(s):
[ENSMUSP00000005889]
[ENSMUSP00000108491]
[ENSMUSP00000126694]
|
AlphaFold |
P27870 |
PDB Structure |
NMR STRUCTURE OF THE Y174 AUTOINHIBITED DBL HOMOLOGY DOMAIN [SOLUTION NMR]
CRYSTAL STRUCTURE OF VAV SH3 DOMAIN [X-RAY DIFFRACTION]
CRYSTAL STRUCTURE OF VAV AND GRB2 SH3 DOMAINS [X-RAY DIFFRACTION]
Solution structure of N-terminal SH3 domain mutant(P33G) of murine Vav [SOLUTION NMR]
Attachment of an NMR-invisible solubility enhancement tag (INSET) using a sortase-mediated protein ligation method [SOLUTION NMR]
CRITICAL STRUCTURAL ROLE FOR THE PH AND C1 DOMAINS OF THE VAV1 EXCHANGE FACTOR [X-RAY DIFFRACTION]
|
SMART Domains |
Protein: ENSMUSP00000005889 Gene: ENSMUSG00000034116 AA Change: E175K
Domain | Start | End | E-Value | Type |
CH
|
3 |
115 |
5.69e-15 |
SMART |
RhoGEF
|
198 |
372 |
7.89e-62 |
SMART |
PH
|
403 |
506 |
8.45e-12 |
SMART |
C1
|
516 |
564 |
3.67e-9 |
SMART |
SH3
|
595 |
659 |
1.65e-8 |
SMART |
SH2
|
669 |
751 |
8.88e-25 |
SMART |
SH3
|
785 |
841 |
1.44e-22 |
SMART |
|
Predicted Effect |
probably damaging
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000005889)
|
SMART Domains |
Protein: ENSMUSP00000108491 Gene: ENSMUSG00000034116 AA Change: E175K
Domain | Start | End | E-Value | Type |
CH
|
3 |
115 |
5.69e-15 |
SMART |
RhoGEF
|
198 |
372 |
7.89e-62 |
SMART |
PH
|
403 |
506 |
8.45e-12 |
SMART |
C1
|
516 |
564 |
3.67e-9 |
SMART |
SH3
|
595 |
659 |
1.65e-8 |
SMART |
SH2
|
633 |
712 |
3.93e-2 |
SMART |
SH3
|
746 |
802 |
1.44e-22 |
SMART |
|
Predicted Effect |
probably damaging
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
(Using ENSMUST00000112870)
|
SMART Domains |
Protein: ENSMUSP00000126694 Gene: ENSMUSG00000034116 AA Change: E151K
Domain | Start | End | E-Value | Type |
Pfam:CAMSAP_CH
|
27 |
79 |
6.2e-11 |
PFAM |
RhoGEF
|
174 |
348 |
7.89e-62 |
SMART |
PH
|
379 |
482 |
8.45e-12 |
SMART |
C1
|
492 |
540 |
3.67e-9 |
SMART |
SH3
|
571 |
635 |
1.65e-8 |
SMART |
SH2
|
645 |
727 |
8.88e-25 |
SMART |
SH3
|
761 |
817 |
1.44e-22 |
SMART |
|
Predicted Effect |
probably damaging
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000169220)
|
Meta Mutation Damage Score |
0.3360 |
Is this an essential gene? |
Possibly nonessential (E-score: 0.257) |
Phenotypic Category |
Autosomal Semidominant |
Candidate Explorer Status |
loading ... |
Single pedigree Linkage Analysis Data
|
|
Penetrance | |
Alleles Listed at MGI | All Mutations and Alleles(10) : Chemically induced (ENU)(1) Targeted(9)
|
Lab Alleles |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL01071:Vav1
|
APN |
17 |
57606176 |
missense |
probably benign |
0.21 |
IGL01613:Vav1
|
APN |
17 |
57614067 |
missense |
possibly damaging |
0.93 |
IGL02032:Vav1
|
APN |
17 |
57604090 |
missense |
possibly damaging |
0.91 |
IGL02213:Vav1
|
APN |
17 |
57612351 |
missense |
possibly damaging |
0.84 |
IGL03009:Vav1
|
APN |
17 |
57603582 |
missense |
probably benign |
0.38 |
Belated
|
UTSW |
17 |
57608214 |
missense |
probably benign |
0.06 |
Delayed
|
UTSW |
17 |
57603552 |
missense |
probably damaging |
1.00 |
Endlich
|
UTSW |
17 |
57604086 |
missense |
probably damaging |
1.00 |
finally
|
UTSW |
17 |
57618860 |
nonsense |
probably null |
|
Last
|
UTSW |
17 |
57603039 |
missense |
probably damaging |
0.99 |
Late
|
UTSW |
17 |
57608870 |
missense |
possibly damaging |
0.91 |
tardive
|
UTSW |
17 |
57610079 |
nonsense |
probably null |
|
R0116:Vav1
|
UTSW |
17 |
57603039 |
missense |
probably damaging |
0.99 |
R0125:Vav1
|
UTSW |
17 |
57606847 |
missense |
probably damaging |
1.00 |
R0268:Vav1
|
UTSW |
17 |
57603090 |
missense |
probably damaging |
1.00 |
R0344:Vav1
|
UTSW |
17 |
57603090 |
missense |
probably damaging |
1.00 |
R0579:Vav1
|
UTSW |
17 |
57586271 |
missense |
probably benign |
0.01 |
R0634:Vav1
|
UTSW |
17 |
57610862 |
missense |
probably benign |
0.00 |
R1313:Vav1
|
UTSW |
17 |
57616498 |
splice site |
probably benign |
|
R1345:Vav1
|
UTSW |
17 |
57608214 |
missense |
probably benign |
0.06 |
R1402:Vav1
|
UTSW |
17 |
57610849 |
missense |
probably benign |
0.18 |
R1402:Vav1
|
UTSW |
17 |
57610849 |
missense |
probably benign |
0.18 |
R1579:Vav1
|
UTSW |
17 |
57604252 |
missense |
probably benign |
0.05 |
R1872:Vav1
|
UTSW |
17 |
57631750 |
missense |
probably damaging |
1.00 |
R1971:Vav1
|
UTSW |
17 |
57634697 |
missense |
probably damaging |
1.00 |
R2197:Vav1
|
UTSW |
17 |
57610140 |
missense |
probably benign |
0.37 |
R2903:Vav1
|
UTSW |
17 |
57613187 |
missense |
probably benign |
0.05 |
R4623:Vav1
|
UTSW |
17 |
57606839 |
splice site |
probably null |
|
R4753:Vav1
|
UTSW |
17 |
57613140 |
missense |
probably damaging |
0.98 |
R4779:Vav1
|
UTSW |
17 |
57603552 |
missense |
probably damaging |
1.00 |
R5232:Vav1
|
UTSW |
17 |
57610846 |
missense |
possibly damaging |
0.81 |
R5240:Vav1
|
UTSW |
17 |
57604122 |
missense |
probably damaging |
1.00 |
R5503:Vav1
|
UTSW |
17 |
57610079 |
nonsense |
probably null |
|
R5592:Vav1
|
UTSW |
17 |
57611835 |
missense |
probably benign |
0.00 |
R5782:Vav1
|
UTSW |
17 |
57603001 |
missense |
probably damaging |
1.00 |
R5945:Vav1
|
UTSW |
17 |
57608870 |
missense |
possibly damaging |
0.91 |
R6113:Vav1
|
UTSW |
17 |
57608884 |
missense |
probably benign |
0.00 |
R6514:Vav1
|
UTSW |
17 |
57634660 |
missense |
probably damaging |
1.00 |
R6575:Vav1
|
UTSW |
17 |
57612280 |
missense |
probably damaging |
0.97 |
R6932:Vav1
|
UTSW |
17 |
57609330 |
missense |
possibly damaging |
0.92 |
R7024:Vav1
|
UTSW |
17 |
57586268 |
missense |
probably damaging |
1.00 |
R7063:Vav1
|
UTSW |
17 |
57618860 |
nonsense |
probably null |
|
R7322:Vav1
|
UTSW |
17 |
57609266 |
missense |
probably benign |
|
R7335:Vav1
|
UTSW |
17 |
57603720 |
missense |
probably benign |
|
R7474:Vav1
|
UTSW |
17 |
57606102 |
missense |
probably benign |
0.07 |
R7665:Vav1
|
UTSW |
17 |
57604086 |
missense |
probably damaging |
1.00 |
R8964:Vav1
|
UTSW |
17 |
57606122 |
missense |
probably benign |
|
R8978:Vav1
|
UTSW |
17 |
57631650 |
missense |
probably benign |
|
R8978:Vav1
|
UTSW |
17 |
57603710 |
missense |
probably benign |
0.04 |
R9165:Vav1
|
UTSW |
17 |
57618895 |
missense |
probably damaging |
1.00 |
R9453:Vav1
|
UTSW |
17 |
57613191 |
missense |
probably benign |
|
R9728:Vav1
|
UTSW |
17 |
57612459 |
missense |
probably benign |
0.00 |
Z1176:Vav1
|
UTSW |
17 |
57610853 |
missense |
probably damaging |
1.00 |
Z1177:Vav1
|
UTSW |
17 |
57610040 |
missense |
probably benign |
0.18 |
|
Mode of Inheritance |
Autosomal Semidominant |
Local Stock | |
Repository | |
Last Updated |
2019-09-04 9:39 PM
by Diantha La Vine
|
Record Created |
2017-08-21 8:21 AM
by Bruce Beutler
|
Record Posted |
2018-06-13 |
Phenotypic Description |
The Plain_sight phenotype was identified among N-ethyl-N-nitrosourea (ENU)-mutagenized G3 mice of the pedigree R5240, some of which showed reduced frequencies of B1 cells in the peripheral blood (Figure 1).
|
Nature of Mutation |
Whole exome HiSeq sequencing of the G1 grandsire identified 67 mutations. The B1 cell phenotype was linked by continuous variable mapping to a mutation in Vav1: a G to A transition at base pair 57,297,122 (v38) on chromosome 17, or base pair 18,044 in the GenBank genomic region NC_000083. Linkage was found with an additive model of inheritance, wherein nine variant homozygotes and 35 heterozygous mice departed phenotypically from 16 homozygous reference mice with a P value of 1.71 x 10-5 (Figure 2). The mutation corresponds to residue 621 in the mRNA sequence NM_011691 within exon 5 of 27 total exons.
606 GGGGACGAGATCTACGAGGACCTAATGCGCTTG
170 -G--D--E--I--Y--E--D--L--M--R--L-
|
The mutated nucleotide is indicated in red. The mutation results in a glutamic acid to lysine substitution at amino acid 175 (E175K) in the VAV1 protein, and is strongly predicted by PolyPhen-2 to be damaging (score = 1.000).
|
Illustration of Mutations in
Gene & Protein |
|
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Protein Prediction |
Vav1 has several domains, including a calponin-homology (CH) domain, an acidic (Ac) motif, a DBL homology (DH) domain, a pleckstrin homology (PH) domain, a phorbol-ester/DAG-type zinc finger (alternatively, C1 domain), a proline-rich region, a Src homology 2 (SH2) domain, and two Src homology 3 (SH3) domains [PDB: 3KY9; (1;2); reviewed in (3)]. Vav1 also has two nuclear localization sequences. The Plain_sight mutation results in a glutamic acid to lysine substitution at amino acid 175 (E175K). Amino acid 175 is within the Ac motif. The Ac motif contains three regulatory tyrosines: Tyr142, Tyr160, and Tyr174 (in mouse). Tyr174 binds the GTPase interaction pocket of the DH domain to control the guanine exchange factor (GEF) activity of Vav1 towards the Rho family GTPases Rac1, Rac2 (see the record for bingo), Cdc42, and RhoA . Phosphorylation of Tyr174 after receptor stimulation releases it from the binding pocket and alleviates the autoinhibition (2;4). Please see the record tardive for more information about Vav1.
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Putative Mechanism | Vav1 is a guanine nucleotide exchange factor (GEF) for Rho family GTPases. Vav1 is essential for hematopoiesis, including T- and B-cell development and activation (5-7). Vav1 also functions in the adhesion, migration, and phagocytosis of mature hematopoietic cells by regulating cytoskeletal rearrangement [reviewed in (8)]. In NK cells, the Vav1 GEF activity is required for activation of NK-associated killing (9). Vav1 has several functions in macrophages, including Rac-dependent complement-mediated phagocytosis (10), cell migration (11), and chemotaxis to CSF-1 (12). Vav1 functions downstream of several immune receptors, including the T-cell receptor (TCR) (13), B-cell receptor (BCR) (14), natural killer (NK) receptors (15), FcRI (16), cytokine receptors (17), chemokine receptors (18), and integrins (19).
Vav1 is a binding partner of Nef proteins from HIV-1 (20). Binding of VAV1 and Nef results in morphological changes, cytoskeletal rearrangements, and activation of the JNK/SAPK signaling cascade, subsequently leading to increased viral transcription and replication. Vav1-deficient (Vav1-/-) mice exhibited embryonic lethality between embryonic day (E) 3.5 and E7.5 (21). A second Vav1-/- mouse model was viable, and exhibited impaired negative T cell selection (22). Single-positive (namely CD4+ T cells), double-positive, and double-negative T cell numbers as well as the number of mature B cells and B1 cells were reduced in the Vav1-/- mice (23-28). T cells from the Vav1-/- mice showed reduced proliferative responses to anti-CD3 stimulation as well as reduced T cell receptor-induced calcium fluxes (22;24;25). The T-dependent IgG response to VSV infection and to NIP-OVA was reduced (28). Homozygous mice expressing an ENU-induced Vav1 allele (F203S) exhibited increased numbers of T cells after immunization (MGI; accessed September 14, 2017).
|
Primers |
PCR Primer
Plain_sight_pcr_F: GTTTAAGGTGACACATTGCAAGAC
Plain_sight_pcr_R: GGAGCCCAGTGTGTCTGTATAC
Sequencing Primer
Plain_sight_seq_F: TGACACATTGCAAGACGTGGG
Plain_sight_seq_R: GAGCCCAGTGTGTCTGTATACTTCTC
|
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 401 nucleotides is amplified (chromosome 17, + strand):
1 gtttaaggtg acacattgca agacgtgggg ggaggggtgg cattgtgcat ttattcttca 61 ttctgaaagt ttctgatggg tccctggctt gggacatggc ctgaatctgt cccctagtga 121 caccgcagag gaagacgagg acctttatga ctgcgtggaa aatgaggagg cagaggggga 181 cgagatctac gaggacctaa tgcgcttgga gtcggtgcct acgccagtga gtgggcctgg 241 gaagggcggg gcaggtggga agggtagaga tggctgcagg gagcttcacc agcctctatg 301 gtctctgctc acagcccaag atgacagagt atgataagcg ctgctgctgc ctgcgggaga 361 tccagcagac ggaggagaag tatacagaca cactgggctc c
Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red. |
References |
2. Yu, B., Martins, I. R., Li, P., Amarasinghe, G. K., Umetani, J., Fernandez-Zapico, M. E., Billadeau, D. D., Machius, M., Tomchick, D. R., and Rosen, M. K. (2010) Structural and Energetic Mechanisms of Cooperative Autoinhibition and Activation of Vav1. Cell. 140, 246-256.
5. Turner, M., Mee, P. J., Walters, A. E., Quinn, M. E., Mellor, A. L., Zamoyska, R., and Tybulewicz, V. L. (1997) A Requirement for the Rho-Family GTP Exchange Factor Vav in Positive and Negative Selection of Thymocytes. Immunity. 7, 451-460.
6. Arana, E., Vehlow, A., Harwood, N. E., Vigorito, E., Henderson, R., Turner, M., Tybulewicz, V. L., and Batista, F. D. (2008) Activation of the Small GTPase Rac2 Via the B Cell Receptor Regulates B Cell Adhesion and Immunological-Synapse Formation. Immunity. 28, 88-99.
7. Krawczyk, C., Oliveira-dos-Santos, A., Sasaki, T., Griffiths, E., Ohashi, P. S., Snapper, S., Alt, F., and Penninger, J. M. (2002) Vav1 Controls Integrin Clustering and MHC/peptide-Specific Cell Adhesion to Antigen-Presenting Cells. Immunity. 16, 331-343.
8. Bertagnolo, V., Brugnoli, F., Grassilli, S., Nika, E., and Capitani, S. (2012) Vav1 in Differentiation of Tumoral Promyelocytes. Cell Signal. 24, 612-620.
9. Billadeau, D. D., Brumbaugh, K. M., Dick, C. J., Schoon, R. A., Bustelo, X. R., and Leibson, P. J. (1998) The Vav-Rac1 Pathway in Cytotoxic Lymphocytes Regulates the Generation of Cell-Mediated Killing. J Exp Med. 188, 549-559.
10. Hall, A. B., Gakidis, M. A., Glogauer, M., Wilsbacher, J. L., Gao, S., Swat, W., and Brugge, J. S. (2006) Requirements for Vav Guanine Nucleotide Exchange Factors and Rho GTPases in FcgammaR- and Complement-Mediated Phagocytosis. Immunity. 24, 305-316.
11. Wells, C. M., Bhavsar, P. J., Evans, I. R., Vigorito, E., Turner, M., Tybulewicz, V., and Ridley, A. J. (2005) Vav1 and Vav2 Play Different Roles in Macrophage Migration and Cytoskeletal Organization. Exp Cell Res. 310, 303-310.
15. Galandrini, R., Palmieri, G., Piccoli, M., Frati, L., and Santoni, A. (1999) Role for the Rac1 Exchange Factor Vav in the Signaling Pathways Leading to NK Cell Cytotoxicity. J Immunol. 162, 3148-3152.
16. Manetz, T. S., Gonzalez-Espinosa, C., Arudchandran, R., Xirasagar, S., Tybulewicz, V., and Rivera, J. (2001) Vav1 Regulates Phospholipase Cgamma Activation and Calcium Responses in Mast Cells. Mol Cell Biol. 21, 3763-3774.
18. Garcia-Bernal, D., Wright, N., Sotillo-Mallo, E., Nombela-Arrieta, C., Stein, J. V., Bustelo, X. R., and Teixido, J. (2005) Vav1 and Rac Control Chemokine-Promoted T Lymphocyte Adhesion Mediated by the Integrin alpha4beta1. Mol Biol Cell. 16, 3223-3235.
20. Fackler, O. T., Luo, W., Geyer, M., Alberts, A. S., and Peterlin, B. M. (1999) Activation of Vav by Nef Induces Cytoskeletal Rearrangements and Downstream Effector Functions. Mol Cell. 3, 729-739.
21. Zmuidzinas, A., Fischer, K. D., Lira, S. A., Forrester, L., Bryant, S., Bernstein, A., and Barbacid, M. (1995) The Vav Proto-Oncogene is Required Early in Embryogenesis but Not for Hematopoietic Development in Vitro. EMBO J. 14, 1-11.
22. Turner, M., Mee, P. J., Walters, A. E., Quinn, M. E., Mellor, A. L., Zamoyska, R., and Tybulewicz, V. L. (1997) A Requirement for the Rho-Family GTP Exchange Factor Vav in Positive and Negative Selection of Thymocytes. Immunity. 7, 451-460.
23. Saveliev, A., Vanes, L., Ksionda, O., Rapley, J., Smerdon, S. J., Rittinger, K., and Tybulewicz, V. L. (2009) Function of the Nucleotide Exchange Activity of vav1 in T Cell Development and Activation. Sci Signal. 2, ra83.
24. Fujikawa, K., Miletic, A. V., Alt, F. W., Faccio, R., Brown, T., Hoog, J., Fredericks, J., Nishi, S., Mildiner, S., Moores, S. L., Brugge, J., Rosen, F. S., and Swat, W. (2003) Vav1/2/3-Null Mice Define an Essential Role for Vav Family Proteins in Lymphocyte Development and Activation but a Differential Requirement in MAPK Signaling in T and B Cells. J Exp Med. 198, 1595-1608.
25. Prisco, A., Vanes, L., Ruf, S., Trigueros, C., and Tybulewicz, V. L. (2005) Lineage-Specific Requirement for the PH Domain of Vav1 in the Activation of CD4+ but Not CD8+ T Cells. Immunity. 23, 263-274.
26. Raberger, J., Boucheron, N., Sakaguchi, S., Penninger, J. M., and Ellmeier, W. (2008) Impaired T-Cell Development in the Absence of Vav1 and Itk. Eur J Immunol. 38, 3530-3542.
27. Fischer, K. D., Kong, Y. Y., Nishina, H., Tedford, K., Marengere, L. E., Kozieradzki, I., Sasaki, T., Starr, M., Chan, G., Gardener, S., Nghiem, M. P., Bouchard, D., Barbacid, M., Bernstein, A., and Penninger, J. M. (1998) Vav is a Regulator of Cytoskeletal Reorganization Mediated by the T-Cell Receptor. Curr Biol. 8, 554-562.
28. Bachmann, M. F., Nitschke, L., Krawczyk, C., Tedford, K., Ohashi, P. S., Fischer, K. D., and Penninger, J. M. (1999) The Guanine-Nucleotide Exchange Factor Vav is a Crucial Regulator of B Cell Receptor Activation and B Cell Responses to Nonrepetitive Antigens. J Immunol. 163, 137-142.
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Science Writers | Anne Murray |
Authors | Xue Zhong, Jin Huk Choi, and Bruce Beutler |