Incidental Mutation 'R5893:Havcr2'
ID457314
Institutional Source Beutler Lab
Gene Symbol Havcr2
Ensembl Gene ENSMUSG00000020399
Gene Namehepatitis A virus cellular receptor 2
SynonymsTim3, Timd3, TIM-3
MMRRC Submission 044094-MU
Accession Numbers
Is this an essential gene? Non essential (E-score: 0.000) question?
Stock #R5893 (G1)
Quality Score225
Status Validated
Chromosome11
Chromosomal Location46454935-46481255 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to G at 46456316 bp
ZygosityHeterozygous
Amino Acid Change Tyrosine to Cysteine at position 40 (Y40C)
Ref Sequence ENSEMBL: ENSMUSP00000020668 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020668] [ENSMUST00000109229]
PDB Structure
Structure of Tim-3 in complex with phosphatidylserine [X-RAY DIFFRACTION]
Predicted Effect probably damaging
Transcript: ENSMUST00000020668
AA Change: Y40C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000020668
Gene: ENSMUSG00000020399
AA Change: Y40C

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
SMART Domains Protein: ENSMUSP00000104852
Gene: ENSMUSG00000020399

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000119051
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.1%
  • 20x: 94.4%
Validation Efficiency 95% (73/77)
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: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ablim1 T A 19: 57,215,853 R35S probably benign Het
Acacb A T 5: 114,229,851 I1637F probably benign Het
Adamts18 A T 8: 113,773,077 C402S probably damaging Het
Adra2b T A 2: 127,364,482 D306E probably benign Het
Ammecr1l C T 18: 31,778,920 T263I probably damaging Het
Antxr1 T C 6: 87,137,259 I509V probably benign Het
Bahcc1 A G 11: 120,285,430 E1967G probably damaging Het
Brap T A 5: 121,679,342 Y337* probably null Het
Brca2 T C 5: 150,569,138 V3206A probably benign Het
C330027C09Rik A G 16: 48,997,500 S78G probably benign Het
Cacna1e A T 1: 154,437,323 F1486I probably damaging Het
Cbx4 A G 11: 119,082,190 Y120H probably damaging Het
Ccar2 T A 14: 70,151,351 Q137L probably benign Het
Ceacam12 A G 7: 18,069,374 D235G probably damaging Het
Celsr1 A G 15: 85,904,014 V2679A probably benign Het
Champ1 C T 8: 13,878,777 P312S probably benign Het
Chst5 A G 8: 111,890,196 L264S probably damaging Het
Colec10 T A 15: 54,410,789 F4L probably benign Het
Cyp2a4 G A 7: 26,308,928 G165D probably damaging Het
Cyp2c29 G C 19: 39,330,389 A438P possibly damaging Het
Dlat A G 9: 50,644,139 probably benign Het
Dmxl2 A G 9: 54,387,420 V2457A possibly damaging Het
Dnah7a A G 1: 53,457,785 M3104T possibly damaging Het
Dock8 C T 19: 25,122,447 H645Y probably damaging Het
Ehbp1l1 T C 19: 5,718,431 E948G probably benign Het
Eps8l2 C T 7: 141,357,624 R384C probably damaging Het
Fam174a A T 1: 95,325,159 N162I probably damaging Het
Fbp2 T A 13: 62,837,102 N335I probably benign Het
Foxred2 C A 15: 77,947,144 G490C probably damaging Het
Fyttd1 T G 16: 32,898,913 D200E probably damaging Het
Gdf15 A T 8: 70,629,823 V211E possibly damaging Het
Gm13084 T A 4: 143,810,468 Y431F probably damaging Het
Gm13178 C T 4: 144,703,196 V408I probably benign Het
Gm5065 A T 7: 5,359,624 T85S probably benign Het
Gm6214 A G 3: 140,839,346 noncoding transcript Het
Htra1 T G 7: 130,961,591 V184G probably damaging Het
Hydin A T 8: 110,490,676 I1399F probably benign Het
Igtp T C 11: 58,206,648 L215P probably damaging Het
Kctd1 T C 18: 14,969,688 E812G possibly damaging Het
Lap3 T C 5: 45,511,279 probably benign Het
Lrp1b C A 2: 40,601,587 A223S probably damaging Het
Mtnr1b A T 9: 15,863,244 V173E probably damaging Het
Nat10 A C 2: 103,721,839 probably benign Het
Ndfip2 T A 14: 105,294,857 V229E probably damaging Het
Nefh G A 11: 4,941,323 T432M probably damaging Het
Nfe2l3 A G 6: 51,457,852 Y464C probably damaging Het
Nrip1 C A 16: 76,293,953 A239S probably damaging Het
Olfml2b A G 1: 170,662,473 S221G probably benign Het
Orc4 G T 2: 48,905,547 S389* probably null Het
P4hb A G 11: 120,571,650 S77P probably damaging Het
Pcyt2 T C 11: 120,617,797 probably null Het
Plagl1 T C 10: 13,128,194 probably benign Het
Poglut1 C T 16: 38,529,595 R272Q probably damaging Het
Rdh5 T C 10: 128,914,221 probably null Het
Rogdi A T 16: 5,013,394 L3* probably null Het
Skap1 T C 11: 96,581,398 *166Q probably null Het
Slc38a4 A G 15: 96,999,551 I461T probably benign Het
Snx31 A C 15: 36,523,455 I360M probably damaging Het
Spata22 A T 11: 73,336,247 K96* probably null Het
Strn3 A T 12: 51,643,223 probably null Het
Trip12 A C 1: 84,759,163 probably benign Het
Uggt1 A T 1: 36,227,628 probably null Het
Upk3a A C 15: 85,019,337 D79A probably damaging Het
Uts2r A T 11: 121,161,279 Y323F probably benign Het
Vmn2r1 A T 3: 64,086,553 N107Y probably damaging Het
Vps13c A T 9: 67,902,839 probably null Het
Wnt7b A G 15: 85,581,374 probably benign Het
Zfp410 T A 12: 84,337,611 probably null Het
Other mutations in Havcr2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00766:Havcr2 APN 11 46469546 missense probably damaging 0.99
IGL01122:Havcr2 APN 11 46456427 missense probably damaging 1.00
IGL01383:Havcr2 APN 11 46469548 missense probably damaging 1.00
IGL02303:Havcr2 APN 11 46479281 splice site probably benign
IGL02665:Havcr2 APN 11 46479394 missense probably benign 0.03
R1688:Havcr2 UTSW 11 46479364 missense probably damaging 1.00
R1782:Havcr2 UTSW 11 46455017 missense unknown
R1945:Havcr2 UTSW 11 46455050 missense unknown
R4429:Havcr2 UTSW 11 46456560 missense probably damaging 1.00
R5846:Havcr2 UTSW 11 46469516 missense probably benign 0.09
R6744:Havcr2 UTSW 11 46455060 critical splice donor site probably null
R6915:Havcr2 UTSW 11 46475911 missense probably benign 0.01
R7262:Havcr2 UTSW 11 46469561 missense probably benign 0.14
Predicted Primers PCR Primer
(F):5'- CTCTCAAATCAGAGAATCATTGGCAC -3'
(R):5'- CAGTAGGTCCCATGGTCATC -3'

Sequencing Primer
(F):5'- GCACAGCCAATCCTCCTC -3'
(R):5'- TGGTCATCCAGAGTCACATTC -3'
Posted On2017-02-15