Incidental Mutation 'R7262:Havcr2'
ID 564695
Institutional Source Beutler Lab
Gene Symbol Havcr2
Ensembl Gene ENSMUSG00000020399
Gene Name hepatitis A virus cellular receptor 2
Synonyms TIM-3, Tim3, Timd3
MMRRC Submission 045353-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7262 (G1)
Quality Score 225.009
Status Validated
Chromosome 11
Chromosomal Location 46345762-46372082 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 46360388 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 205 (T205I)
Ref Sequence ENSEMBL: ENSMUSP00000020668 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020668] [ENSMUST00000109229]
AlphaFold Q8VIM0
PDB Structure Structure of Tim-3 in complex with phosphatidylserine [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000020668
AA Change: T205I

PolyPhen 2 Score 0.145 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000020668
Gene: ENSMUSG00000020399
AA Change: T205I

DomainStartEndE-ValueType
signal peptide 1 19 N/A INTRINSIC
IG 23 131 9.8e-6 SMART
transmembrane domain 193 215 N/A INTRINSIC
low complexity region 259 277 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000109229
AA Change: T156I

PolyPhen 2 Score 0.225 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000104852
Gene: ENSMUSG00000020399
AA Change: T156I

DomainStartEndE-ValueType
Pfam:V-set 12 80 8.6e-9 PFAM
transmembrane domain 144 166 N/A INTRINSIC
low complexity region 210 228 N/A INTRINSIC
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (53/53)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the immunoglobulin superfamily, and TIM family of proteins. CD4-positive T helper lymphocytes can be divided into types 1 (Th1) and 2 (Th2) on the basis of their cytokine secretion patterns. Th1 cells are involved in cell-mediated immunity to intracellular pathogens and delayed-type hypersensitivity reactions, whereas, Th2 cells are involved in the control of extracellular helminthic infections and the promotion of atopic and allergic diseases. This protein is a Th1-specific cell surface protein that regulates macrophage activation, and inhibits Th1-mediated auto- and alloimmune responses, and promotes immunological tolerance. [provided by RefSeq, Sep 2011]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit normal thymic development and show no evidence of autoimmunity or lymphoproliferation. Mice homozygous for a different targeted allele exhibit improved survival following influenza infection. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acap2 A G 16: 30,946,137 (GRCm39) probably null Het
Adh5 C A 3: 138,151,133 (GRCm39) A32D possibly damaging Het
Ap1m2 A G 9: 21,213,762 (GRCm39) I295T possibly damaging Het
B230104I21Rik T C 4: 154,434,091 (GRCm39) S92P unknown Het
Carnmt1 A T 19: 18,655,228 (GRCm39) N127I probably benign Het
Ccdc42 A G 11: 68,485,399 (GRCm39) T106A probably damaging Het
Cdcp1 T C 9: 123,002,680 (GRCm39) E797G probably damaging Het
Cep112 T A 11: 108,555,467 (GRCm39) V821D probably damaging Het
Cpvl A T 6: 53,909,500 (GRCm39) V212D probably damaging Het
Cttnbp2nl A T 3: 104,940,062 (GRCm39) N2K probably damaging Het
Cyp2c69 T C 19: 39,875,176 (GRCm39) probably benign Het
Cyp2u1 T C 3: 131,091,605 (GRCm39) D305G probably damaging Het
Dab2ip A G 2: 35,512,298 (GRCm39) probably null Het
Ddx55 T C 5: 124,704,919 (GRCm39) L396P probably benign Het
Dhx34 G A 7: 15,937,623 (GRCm39) A786V probably benign Het
Efcab3 G A 11: 104,745,432 (GRCm39) probably null Het
Ehbp1l1 A T 19: 5,768,474 (GRCm39) L943* probably null Het
Epm2aip1 A G 9: 111,101,728 (GRCm39) T234A probably benign Het
Flot2 T C 11: 77,948,175 (GRCm39) M145T probably damaging Het
Fn3k T C 11: 121,339,741 (GRCm39) F168L probably damaging Het
Gmfb A T 14: 47,052,386 (GRCm39) C87S probably damaging Het
H2-M3 T C 17: 37,582,084 (GRCm39) F180S probably damaging Het
Hdac3 C T 18: 38,078,616 (GRCm39) C123Y probably damaging Het
Itpk1 T C 12: 102,641,712 (GRCm39) E37G possibly damaging Het
Jmjd7 A G 2: 119,862,467 (GRCm39) H283R probably benign Het
Kif26b T C 1: 178,745,219 (GRCm39) S1772P possibly damaging Het
Klhl6 T C 16: 19,801,546 (GRCm39) T70A probably damaging Het
Kntc1 C A 5: 123,925,036 (GRCm39) D1116E probably benign Het
Lama4 T A 10: 38,970,930 (GRCm39) H1498Q probably damaging Het
Lamp1 A T 8: 13,217,296 (GRCm39) T102S probably benign Het
Lrp8 A G 4: 107,704,661 (GRCm39) N168D probably benign Het
Ltbp1 G T 17: 75,671,363 (GRCm39) D1515Y probably damaging Het
Obscn A G 11: 59,006,715 (GRCm39) V1149A probably damaging Het
Or10q1 A T 19: 13,726,535 (GRCm39) T22S probably benign Het
Or4f6 A G 2: 111,838,902 (GRCm39) S210P probably damaging Het
Or52ad1 T C 7: 102,995,764 (GRCm39) R124G probably damaging Het
Pak4 C A 7: 28,264,625 (GRCm39) M92I possibly damaging Het
Pam T C 1: 97,782,448 (GRCm39) K157R Het
Pcdh9 A T 14: 93,253,141 (GRCm39) V1174E probably benign Het
Phf8-ps G A 17: 33,285,971 (GRCm39) T277I probably damaging Het
Ppp1r3a T C 6: 14,719,069 (GRCm39) D615G probably benign Het
Senp1 A T 15: 97,964,379 (GRCm39) D278E probably benign Het
Serpinc1 A G 1: 160,817,229 (GRCm39) N108D probably damaging Het
Srl C A 16: 4,315,415 (GRCm39) A76S probably damaging Het
Tbc1d16 C A 11: 119,045,921 (GRCm39) V509L probably benign Het
Tbc1d24 A G 17: 24,426,820 (GRCm39) F357S probably damaging Het
Tcaf3 A G 6: 42,570,735 (GRCm39) L339P probably damaging Het
Tmem232 A T 17: 65,807,112 (GRCm39) I27N probably benign Het
Ubr2 T C 17: 47,311,665 (GRCm39) D62G probably damaging Het
Vcan T G 13: 89,853,280 (GRCm39) D560A possibly damaging Het
Vmn2r80 T A 10: 79,005,579 (GRCm39) N405K probably damaging Het
Wdhd1 A T 14: 47,489,430 (GRCm39) I701K probably benign Het
Other mutations in Havcr2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00766:Havcr2 APN 11 46,360,373 (GRCm39) missense probably damaging 0.99
IGL01122:Havcr2 APN 11 46,347,254 (GRCm39) missense probably damaging 1.00
IGL01383:Havcr2 APN 11 46,360,375 (GRCm39) missense probably damaging 1.00
IGL02303:Havcr2 APN 11 46,370,108 (GRCm39) splice site probably benign
IGL02665:Havcr2 APN 11 46,370,221 (GRCm39) missense probably benign 0.03
R1688:Havcr2 UTSW 11 46,370,191 (GRCm39) missense probably damaging 1.00
R1782:Havcr2 UTSW 11 46,345,844 (GRCm39) missense unknown
R1945:Havcr2 UTSW 11 46,345,877 (GRCm39) missense unknown
R4429:Havcr2 UTSW 11 46,347,387 (GRCm39) missense probably damaging 1.00
R5846:Havcr2 UTSW 11 46,360,343 (GRCm39) missense probably benign 0.09
R5893:Havcr2 UTSW 11 46,347,143 (GRCm39) missense probably damaging 1.00
R6744:Havcr2 UTSW 11 46,345,887 (GRCm39) critical splice donor site probably null
R6915:Havcr2 UTSW 11 46,366,738 (GRCm39) missense probably benign 0.01
R7560:Havcr2 UTSW 11 46,349,889 (GRCm39) missense probably damaging 0.99
R7739:Havcr2 UTSW 11 46,347,384 (GRCm39) missense probably damaging 1.00
R8032:Havcr2 UTSW 11 46,370,118 (GRCm39) missense probably damaging 1.00
R8151:Havcr2 UTSW 11 46,366,722 (GRCm39) missense possibly damaging 0.77
R9124:Havcr2 UTSW 11 46,360,388 (GRCm39) missense probably benign 0.14
R9420:Havcr2 UTSW 11 46,347,350 (GRCm39) missense probably damaging 1.00
R9560:Havcr2 UTSW 11 46,347,164 (GRCm39) missense probably benign 0.14
Predicted Primers PCR Primer
(F):5'- GACCCTTGAACTGTGAGAGTATTTG -3'
(R):5'- GGTTTGCACTGGTTCTTATACC -3'

Sequencing Primer
(F):5'- AGAGTATTTGCGCATATTGCC -3'
(R):5'- TACAGACAGTTGTGAGCTGCC -3'
Posted On 2019-06-26