Incidental Mutation 'R4645:Ly96'
ID 350149
Institutional Source Beutler Lab
Gene Symbol Ly96
Ensembl Gene ENSMUSG00000025779
Gene Name lymphocyte antigen 96
Synonyms myeloid differentiation factor-2, ESOP-1, MD2, MD-2
MMRRC Submission 041906-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.136) question?
Stock # R4645 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 16758680-16779829 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) G to T at 16761940 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Stop codon at position 49 (E49*)
Ref Sequence ENSEMBL: ENSMUSP00000140411 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026881] [ENSMUST00000190366]
AlphaFold Q9JHF9
Predicted Effect probably null
Transcript: ENSMUST00000026881
AA Change: E49*
SMART Domains Protein: ENSMUSP00000026881
Gene: ENSMUSG00000025779
AA Change: E49*

DomainStartEndE-ValueType
signal peptide 1 16 N/A INTRINSIC
ML 34 153 7.82e-29 SMART
Predicted Effect probably null
Transcript: ENSMUST00000190366
AA Change: E49*
SMART Domains Protein: ENSMUSP00000140411
Gene: ENSMUSG00000025779
AA Change: E49*

DomainStartEndE-ValueType
signal peptide 1 16 N/A INTRINSIC
Pfam:E1_DerP2_DerF2 66 137 1.8e-11 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000191260
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.7%
Validation Efficiency 98% (53/54)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein which associates with toll-like receptor 4 on the cell surface and confers responsiveness to lipopolysaccyaride (LPS), thus providing a link between the receptor and LPS signaling. Studies of the mouse ortholog suggest that this gene may be involved in endotoxin neutralization. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2010]
PHENOTYPE: Mice homozygous for a knock-out allele display impaired responsiveness to LPS, are resistant to LPS-induced lethal toxicity but show increased susceptibility to Salmonella typhimurium infection. [provided by MGI curators]
Allele List at MGI

All alleles(2) : Targeted(2)
Other mutations in this stock
Total: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc10 T C 17: 46,635,700 (GRCm39) E101G probably damaging Het
Adgrf5 A G 17: 43,748,416 (GRCm39) E29G probably damaging Het
Agfg2 T A 5: 137,682,854 (GRCm39) probably benign Het
Ap4b1 A G 3: 103,728,765 (GRCm39) S468G probably benign Het
AY702103 G T 17: 50,546,941 (GRCm39) noncoding transcript Het
Ccdc14 T C 16: 34,542,110 (GRCm39) L536S probably damaging Het
Ccr9 G T 9: 123,608,658 (GRCm39) M101I probably benign Het
Celsr1 A T 15: 85,800,957 (GRCm39) V2496E probably benign Het
Celsr2 C A 3: 108,303,285 (GRCm39) G2486V probably damaging Het
Cntnap3 A G 13: 64,926,602 (GRCm39) probably null Het
Erlin1 T C 19: 44,057,759 (GRCm39) Y22C probably damaging Het
Fam135b T C 15: 71,334,189 (GRCm39) T1002A probably benign Het
Gas2l3 CACTCGTCATACT CACT 10: 89,266,820 (GRCm39) probably benign Het
Glud1 T C 14: 34,033,063 (GRCm39) V70A probably damaging Het
Hdlbp A G 1: 93,349,842 (GRCm39) probably benign Het
Immt T C 6: 71,833,923 (GRCm39) L184P probably damaging Het
Iqsec1 T G 6: 90,644,995 (GRCm39) K983T probably damaging Het
Klhl6 A T 16: 19,765,897 (GRCm39) N568K probably damaging Het
Lbhd1 T G 19: 8,861,452 (GRCm39) probably benign Het
Lrit2 C T 14: 36,794,432 (GRCm39) R499C probably benign Het
Lrp6 T C 6: 134,461,213 (GRCm39) D748G probably damaging Het
Lrriq4 A G 3: 30,704,892 (GRCm39) K292E probably benign Het
Lztr1 C T 16: 17,341,955 (GRCm39) probably benign Het
Mmp12 A G 9: 7,347,515 (GRCm39) M31V probably benign Het
Mok A T 12: 110,774,873 (GRCm39) probably benign Het
Mpi T C 9: 57,458,040 (GRCm39) H54R probably damaging Het
Naip5 T A 13: 100,356,338 (GRCm39) E1092D probably benign Het
Or4c101 T C 2: 88,390,722 (GRCm39) I292T probably damaging Het
Pomt1 G T 2: 32,132,888 (GRCm39) probably benign Het
Ptpn20 G A 14: 33,353,169 (GRCm39) V303I probably benign Het
Pyroxd1 C G 6: 142,300,467 (GRCm39) S199* probably null Het
Shank2 A G 7: 143,964,159 (GRCm39) K799R possibly damaging Het
Sim1 A T 10: 50,860,093 (GRCm39) T652S probably benign Het
Slc8a2 C T 7: 15,868,164 (GRCm39) T132I probably damaging Het
Spaca6 A T 17: 18,056,307 (GRCm39) probably benign Het
Sympk G T 7: 18,777,385 (GRCm39) R545L possibly damaging Het
Tenm4 G T 7: 96,544,949 (GRCm39) G2322W probably damaging Het
Thap1 A G 8: 26,652,597 (GRCm39) T135A probably damaging Het
Traf3 T C 12: 111,228,400 (GRCm39) V537A probably damaging Het
Ttn T C 2: 76,578,680 (GRCm39) D24071G probably damaging Het
Tysnd1 G T 10: 61,531,962 (GRCm39) V205L probably benign Het
Unc79 T C 12: 103,079,081 (GRCm39) S1749P probably benign Het
Vmn2r50 T A 7: 9,771,162 (GRCm39) *846C probably null Het
Vmn2r74 C T 7: 85,606,317 (GRCm39) S343N probably benign Het
Zfyve28 T G 5: 34,379,787 (GRCm39) probably benign Het
Zmym2 T C 14: 57,165,764 (GRCm39) S696P probably damaging Het
Zscan4e T C 7: 11,041,002 (GRCm39) Y290C possibly damaging Het
Zswim2 G T 2: 83,745,891 (GRCm39) H516N probably benign Het
Other mutations in Ly96
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00588:Ly96 APN 1 16,776,452 (GRCm39) splice site probably null
IGL01588:Ly96 APN 1 16,779,678 (GRCm39) missense probably benign 0.11
pique UTSW 1 16,761,940 (GRCm39) nonsense probably null
H8562:Ly96 UTSW 1 16,761,918 (GRCm39) missense probably damaging 1.00
R1186:Ly96 UTSW 1 16,771,118 (GRCm39) missense possibly damaging 0.90
R1751:Ly96 UTSW 1 16,776,399 (GRCm39) missense probably benign 0.00
R1767:Ly96 UTSW 1 16,776,399 (GRCm39) missense probably benign 0.00
R5189:Ly96 UTSW 1 16,771,091 (GRCm39) missense probably damaging 1.00
R5470:Ly96 UTSW 1 16,779,710 (GRCm39) missense probably benign 0.16
R7031:Ly96 UTSW 1 16,758,787 (GRCm39) missense possibly damaging 0.58
Predicted Primers PCR Primer
(F):5'- TCCTGCATGTGACCATAACAG -3'
(R):5'- AAGGCCCATGTATCCAACAG -3'

Sequencing Primer
(F):5'- CATGTGACCATAACAGAGTGGACC -3'
(R):5'- CTTTATAAGGGGCCCTGAATGAC -3'
Posted On 2015-10-08