Incidental Mutation 'R5440:Havcr1'
ID 428595
Institutional Source Beutler Lab
Gene Symbol Havcr1
Ensembl Gene ENSMUSG00000040405
Gene Name hepatitis A virus cellular receptor 1
Synonyms Timd1, Tim1, TIM-1, KIM-1
MMRRC Submission 043005-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5440 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 46630644-46670405 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 46643197 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Phenylalanine at position 39 (Y39F)
Ref Sequence ENSEMBL: ENSMUSP00000104846 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047568] [ENSMUST00000081819] [ENSMUST00000109223] [ENSMUST00000109224]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000047568
AA Change: Y39F

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000043827
Gene: ENSMUSG00000040405
AA Change: Y39F

DomainStartEndE-ValueType
IG 22 128 4.82e-6 SMART
low complexity region 132 152 N/A INTRINSIC
low complexity region 154 177 N/A INTRINSIC
transmembrane domain 237 259 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000081819
AA Change: Y39F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000080503
Gene: ENSMUSG00000040405
AA Change: Y39F

DomainStartEndE-ValueType
IG 22 128 4.82e-6 SMART
low complexity region 132 152 N/A INTRINSIC
low complexity region 154 177 N/A INTRINSIC
transmembrane domain 214 236 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000109223
AA Change: Y39F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000104846
Gene: ENSMUSG00000040405
AA Change: Y39F

DomainStartEndE-ValueType
IG 22 128 4.82e-6 SMART
low complexity region 132 152 N/A INTRINSIC
low complexity region 154 177 N/A INTRINSIC
transmembrane domain 214 236 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000109224
AA Change: Y39F

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000104847
Gene: ENSMUSG00000040405
AA Change: Y39F

DomainStartEndE-ValueType
IG 22 128 4.82e-6 SMART
low complexity region 132 152 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.3%
Validation Efficiency
MGI Phenotype PHENOTYPE: Mice homozygous for a knock-out allele exhibit normal response to S. mansoni egg challenge. Mice homozygous for an allele lacking the mucin domain display impaired regulatory B cell function and systemic autoimmunity. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Apc G T 18: 34,354,213 (GRCm39) probably benign Het
Apol11b T A 15: 77,519,793 (GRCm39) K96* probably null Het
Arhgap35 C T 7: 16,296,849 (GRCm39) G739S probably damaging Het
Atp6v0a4 A C 6: 38,069,752 (GRCm39) F47V probably damaging Het
Bcl9 G A 3: 97,117,881 (GRCm39) P271L probably benign Het
Cd109 T C 9: 78,587,446 (GRCm39) probably null Het
Col12a1 T A 9: 79,521,645 (GRCm39) I2771F probably benign Het
Col6a1 A G 10: 76,559,288 (GRCm39) V116A probably damaging Het
Cpsf2 C G 12: 101,963,138 (GRCm39) L401V probably benign Het
Cwf19l2 G A 9: 3,475,549 (GRCm39) E829K probably damaging Het
D7Ertd443e G A 7: 133,951,004 (GRCm39) T223I probably damaging Het
Dtx4 G A 19: 12,469,681 (GRCm39) R149C probably damaging Het
Fam186b C T 15: 99,171,734 (GRCm39) A838T possibly damaging Het
Fzd4 G T 7: 89,057,326 (GRCm39) E458* probably null Het
Gm17669 C T 18: 67,695,526 (GRCm39) P24S possibly damaging Het
Grin2b C T 6: 135,713,304 (GRCm39) G859D probably damaging Het
Gucy2e T C 11: 69,114,472 (GRCm39) Y1019C probably damaging Het
Gzme T A 14: 56,355,910 (GRCm39) N134I possibly damaging Het
Hint3 A T 10: 30,494,347 (GRCm39) M1K probably null Het
Hspa4l A G 3: 40,736,008 (GRCm39) K543R probably damaging Het
Ifna9 A G 4: 88,510,048 (GRCm39) probably null Het
Itgb4 C T 11: 115,874,983 (GRCm39) R447W probably benign Het
Lipo2 A G 19: 33,698,258 (GRCm39) I373T probably benign Het
Myo5c T A 9: 75,165,407 (GRCm39) I405N possibly damaging Het
Or10a49 T C 7: 108,467,833 (GRCm39) H176R probably damaging Het
P2rx1 A G 11: 72,899,329 (GRCm39) M108V probably benign Het
Pcsk2 T A 2: 143,388,463 (GRCm39) V18E probably benign Het
Pigr A T 1: 130,777,359 (GRCm39) probably null Het
Pkp1 A T 1: 135,810,230 (GRCm39) C447S probably benign Het
Prom1 T A 5: 44,215,988 (GRCm39) I96F probably benign Het
Prpf4b T C 13: 35,068,076 (GRCm39) probably benign Het
Ropn1 C A 16: 34,491,542 (GRCm39) D102E probably benign Het
Slc35e2 C T 4: 155,694,483 (GRCm39) P10L probably benign Het
Sphk1 T G 11: 116,425,714 (GRCm39) V17G possibly damaging Het
Syngr1 A G 15: 79,982,219 (GRCm39) N2S probably benign Het
Syt9 T G 7: 107,101,330 (GRCm39) S359A possibly damaging Het
Terb1 T C 8: 105,215,131 (GRCm39) I282V probably damaging Het
Ttn T A 2: 76,585,168 (GRCm39) I22042F probably damaging Het
Ttn A T 2: 76,739,600 (GRCm39) D3646E probably benign Het
Ube2d1 A G 10: 71,091,682 (GRCm39) W141R probably damaging Het
Vmn2r41 T A 7: 8,141,362 (GRCm39) I701F probably damaging Het
Zfp770 T C 2: 114,026,596 (GRCm39) D491G probably benign Het
Other mutations in Havcr1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02119:Havcr1 APN 11 46,666,320 (GRCm39) missense probably damaging 1.00
IGL02207:Havcr1 APN 11 46,669,403 (GRCm39) missense probably benign 0.28
R0355:Havcr1 UTSW 11 46,647,051 (GRCm39) missense possibly damaging 0.91
R0371:Havcr1 UTSW 11 46,643,416 (GRCm39) missense possibly damaging 0.95
R0488:Havcr1 UTSW 11 46,643,398 (GRCm39) missense probably damaging 1.00
R0883:Havcr1 UTSW 11 46,643,259 (GRCm39) missense probably damaging 1.00
R1307:Havcr1 UTSW 11 46,647,097 (GRCm39) missense probably damaging 0.99
R1308:Havcr1 UTSW 11 46,647,097 (GRCm39) missense probably damaging 0.99
R1554:Havcr1 UTSW 11 46,643,334 (GRCm39) missense probably benign
R1908:Havcr1 UTSW 11 46,664,511 (GRCm39) nonsense probably null
R2165:Havcr1 UTSW 11 46,669,379 (GRCm39) missense probably benign 0.14
R3085:Havcr1 UTSW 11 46,647,052 (GRCm39) missense probably damaging 0.99
R3757:Havcr1 UTSW 11 46,643,407 (GRCm39) missense probably damaging 1.00
R4719:Havcr1 UTSW 11 46,643,268 (GRCm39) missense probably benign 0.02
R5191:Havcr1 UTSW 11 46,647,024 (GRCm39) missense probably benign 0.40
R5710:Havcr1 UTSW 11 46,643,353 (GRCm39) missense probably damaging 1.00
R5988:Havcr1 UTSW 11 46,646,964 (GRCm39) missense probably damaging 1.00
R7570:Havcr1 UTSW 11 46,661,369 (GRCm39) critical splice donor site probably null
R7962:Havcr1 UTSW 11 46,643,402 (GRCm39) nonsense probably null
R8953:Havcr1 UTSW 11 46,647,006 (GRCm39) missense possibly damaging 0.91
R9259:Havcr1 UTSW 11 46,661,318 (GRCm39) missense probably damaging 1.00
R9424:Havcr1 UTSW 11 46,669,391 (GRCm39) missense probably benign
R9576:Havcr1 UTSW 11 46,669,391 (GRCm39) missense probably benign
Z1177:Havcr1 UTSW 11 46,666,325 (GRCm39) missense probably benign 0.25
Predicted Primers PCR Primer
(F):5'- AAAGGCCAGAACTGTTCAGC -3'
(R):5'- ATCGTCAAGGACACATCTCC -3'

Sequencing Primer
(F):5'- GCCAGAACTGTTCAGCACTCG -3'
(R):5'- GGACACATCTCCTTCTGAAATATGC -3'
Posted On 2016-09-01