Incidental Mutation 'R1688:Havcr2'
ID 189507
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 039721-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1688 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 46345762-46372082 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 46370191 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 206 (I206T)
Ref Sequence ENSEMBL: ENSMUSP00000104852 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020668] [ENSMUST00000109229]
AlphaFold Q8VIM0
Predicted Effect probably damaging
Transcript: ENSMUST00000020668
AA Change: I255T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000020668
Gene: ENSMUSG00000020399
AA Change: I255T

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 damaging
Transcript: ENSMUST00000109229
AA Change: I206T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000104852
Gene: ENSMUSG00000020399
AA Change: I206T

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 0.7422 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.7%
  • 20x: 93.7%
Validation Efficiency 100% (71/71)
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: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930486L24Rik T C 13: 61,002,695 (GRCm39) T20A probably benign Het
Acaca T G 11: 84,129,722 (GRCm39) V359G probably damaging Het
Adgb G A 10: 10,226,061 (GRCm39) R1359* probably null Het
Aggf1 T C 13: 95,501,275 (GRCm39) E369G probably damaging Het
Alkbh8 T A 9: 3,382,765 (GRCm39) D418E probably damaging Het
Alox8 T C 11: 69,080,732 (GRCm39) D203G probably benign Het
Ank A G 15: 27,557,320 (GRCm39) D168G probably damaging Het
Ap5m1 A G 14: 49,318,291 (GRCm39) probably null Het
Arhgap45 A G 10: 79,864,929 (GRCm39) Y964C probably damaging Het
Arhgef2 A G 3: 88,547,607 (GRCm39) D571G probably benign Het
Bdh2 A T 3: 135,007,399 (GRCm39) Y223F possibly damaging Het
Bin1 T C 18: 32,552,988 (GRCm39) probably benign Het
Bin1 G A 18: 32,558,025 (GRCm39) probably benign Het
Cacna1g T A 11: 94,316,779 (GRCm39) M1514L possibly damaging Het
Cd109 T A 9: 78,612,373 (GRCm39) F1253L probably benign Het
Cfap57 T A 4: 118,426,843 (GRCm39) E1065V probably null Het
Chmp2b T C 16: 65,347,922 (GRCm39) N14S probably benign Het
Cplane1 T C 15: 8,258,093 (GRCm39) V2113A probably benign Het
Crybg1 A T 10: 43,849,794 (GRCm39) F1660L probably damaging Het
Cyp2c37 T G 19: 39,982,887 (GRCm39) probably null Het
Daam1 A T 12: 71,993,820 (GRCm39) I408F unknown Het
Dsc3 T A 18: 20,099,284 (GRCm39) D744V probably damaging Het
Eprs1 T C 1: 185,117,093 (GRCm39) F379L probably damaging Het
Ewsr1 G T 11: 5,022,870 (GRCm39) D417E unknown Het
Eya4 A T 10: 22,999,759 (GRCm39) N424K probably damaging Het
Gm9312 A C 12: 24,301,920 (GRCm39) noncoding transcript Het
Igfbp2 T C 1: 72,864,125 (GRCm39) probably null Het
Ikzf2 T C 1: 69,581,439 (GRCm39) K196R possibly damaging Het
Il12rb1 G A 8: 71,272,046 (GRCm39) G587R probably damaging Het
Immt A T 6: 71,833,995 (GRCm39) H208L probably damaging Het
Kcnq2 C T 2: 180,728,826 (GRCm39) V540I probably damaging Het
Klk1b8 T A 7: 43,595,229 (GRCm39) probably benign Het
Mc2r T A 18: 68,541,090 (GRCm39) I68F possibly damaging Het
Neil3 T C 8: 54,054,069 (GRCm39) E320G probably damaging Het
Nell2 T C 15: 95,329,494 (GRCm39) T276A probably damaging Het
Nphp3 T C 9: 103,880,323 (GRCm39) L115P probably damaging Het
Nras T C 3: 102,967,689 (GRCm39) L95P probably benign Het
Ogt G A X: 100,699,296 (GRCm39) V190I probably damaging Het
Or11h6 A T 14: 50,880,705 (GRCm39) K322N probably benign Het
Or5t17 A G 2: 86,832,730 (GRCm39) Y139C probably benign Het
P2ry6 T A 7: 100,587,591 (GRCm39) H256L probably damaging Het
Pcbp4 T C 9: 106,338,533 (GRCm39) S153P probably damaging Het
Pclo T C 5: 14,838,507 (GRCm39) probably null Het
Per2 A G 1: 91,351,551 (GRCm39) L985P probably damaging Het
Pgap6 C T 17: 26,337,882 (GRCm39) A422V possibly damaging Het
Phip T C 9: 82,753,710 (GRCm39) N1678S probably benign Het
Pkd1l3 A G 8: 110,350,450 (GRCm39) S432G probably benign Het
Plin4 T A 17: 56,416,363 (GRCm39) D47V possibly damaging Het
Ppp2cb A G 8: 34,105,480 (GRCm39) I163M probably benign Het
Ptpdc1 T C 13: 48,739,700 (GRCm39) E577G probably benign Het
Ptprd G T 4: 75,900,921 (GRCm39) P1063T probably damaging Het
Ptpru T C 4: 131,514,656 (GRCm39) D866G probably benign Het
Rdx T C 9: 51,972,211 (GRCm39) probably benign Het
Rgsl1 C T 1: 153,680,422 (GRCm39) R760H probably damaging Het
Rhno1 A G 6: 128,334,897 (GRCm39) V142A probably benign Het
Sema5a C T 15: 32,669,570 (GRCm39) T698I probably benign Het
Serpina3a A T 12: 104,084,902 (GRCm39) D99V probably benign Het
Slc22a3 A T 17: 12,652,694 (GRCm39) M350K probably damaging Het
Spata31d1b T A 13: 59,863,274 (GRCm39) S141T possibly damaging Het
Tada2a T C 11: 83,975,585 (GRCm39) probably null Het
Tspan10 A G 11: 120,333,608 (GRCm39) M2V probably damaging Het
Ttll11 T C 2: 35,685,391 (GRCm39) T566A probably damaging Het
Vwa8 A G 14: 79,438,543 (GRCm39) Q1872R possibly damaging Het
Zfp605 T A 5: 110,276,907 (GRCm39) I675N possibly damaging Het
Zkscan8 A T 13: 21,704,324 (GRCm39) N538K possibly damaging 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
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
R7262:Havcr2 UTSW 11 46,360,388 (GRCm39) missense probably benign 0.14
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'- TGAAGGGCCATGAATGTCAACTAGC -3'
(R):5'- AGTGGGAGATCCGATCCCTGAAAC -3'

Sequencing Primer
(F):5'- GAATGTCAACTAGCTGCTGTC -3'
(R):5'- TGTGGTCAGAACCTCCAATG -3'
Posted On 2014-05-14