Incidental Mutation 'R1921:Xrn1'
ID 213072
Institutional Source Beutler Lab
Gene Symbol Xrn1
Ensembl Gene ENSMUSG00000032410
Gene Name 5'-3' exoribonuclease 1
Synonyms mXrn1, Dhm2
MMRRC Submission 039939-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.917) question?
Stock # R1921 (G1)
Quality Score 225
Status Not validated
Chromosome 9
Chromosomal Location 95836813-95939856 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 95881550 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 700 (I700T)
Ref Sequence ENSEMBL: ENSMUSP00000139510 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034981] [ENSMUST00000185633] [ENSMUST00000190665]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000034981
AA Change: I808T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: I808T

DomainStartEndE-ValueType
Pfam:XRN_N 1 227 8.4e-99 PFAM
low complexity region 372 389 N/A INTRINSIC
low complexity region 414 430 N/A INTRINSIC
low complexity region 662 673 N/A INTRINSIC
low complexity region 1054 1066 N/A INTRINSIC
low complexity region 1555 1566 N/A INTRINSIC
low complexity region 1665 1684 N/A INTRINSIC
low complexity region 1696 1711 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000185633
AA Change: I808T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: I808T

DomainStartEndE-ValueType
Pfam:XRN_N 1 228 1.2e-103 PFAM
low complexity region 372 389 N/A INTRINSIC
low complexity region 414 430 N/A INTRINSIC
low complexity region 662 673 N/A INTRINSIC
low complexity region 1054 1066 N/A INTRINSIC
low complexity region 1551 1562 N/A INTRINSIC
low complexity region 1661 1680 N/A INTRINSIC
low complexity region 1692 1707 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000187175
Predicted Effect noncoding transcript
Transcript: ENSMUST00000189612
Predicted Effect probably benign
Transcript: ENSMUST00000190665
AA Change: I700T

PolyPhen 2 Score 0.044 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000139510
Gene: ENSMUSG00000032410
AA Change: I700T

DomainStartEndE-ValueType
Pfam:XRN_N 1 228 4.9e-104 PFAM
low complexity region 372 389 N/A INTRINSIC
low complexity region 414 430 N/A INTRINSIC
PDB:2Y35|A 654 939 2e-36 PDB
low complexity region 946 958 N/A INTRINSIC
Coding Region Coverage
  • 1x: 97.3%
  • 3x: 96.7%
  • 10x: 94.9%
  • 20x: 91.3%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the 5'-3' exonuclease family. The encoded protein may be involved in replication-dependent histone mRNA degradation, and interacts directly with the enhancer of mRNA-decapping protein 4. In addition to mRNA metabolism, a similar protein in yeast has been implicated in a variety of nuclear and cytoplasmic functions, including homologous recombination, meiosis, telomere maintenance, and microtubule assembly. Mutations in this gene are associated with osteosarcoma, suggesting that the encoded protein may also play a role in bone formation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
Allele List at MGI
Other mutations in this stock
Total: 86 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A2m C A 6: 121,631,571 (GRCm39) L623M probably benign Het
Abhd2 T C 7: 78,998,104 (GRCm39) I212T possibly damaging Het
Adam7 A C 14: 68,750,074 (GRCm39) S449A possibly damaging Het
Alkbh2 C T 5: 114,262,287 (GRCm39) E148K probably damaging Het
Aox3 T C 1: 58,219,810 (GRCm39) Y1137H probably damaging Het
Atp11b T C 3: 35,888,474 (GRCm39) Y715H probably damaging Het
Atrn A G 2: 130,836,971 (GRCm39) Y1145C probably damaging Het
Btbd7 A G 12: 102,760,055 (GRCm39) I631T probably benign Het
Cadps T C 14: 12,465,859 (GRCm38) K1017R possibly damaging Het
Cfap45 A G 1: 172,372,679 (GRCm39) E458G probably damaging Het
Cptp C T 4: 155,950,995 (GRCm39) R157H probably damaging Het
Dcbld1 A C 10: 52,195,747 (GRCm39) E318D possibly damaging Het
Ddr2 G T 1: 169,831,814 (GRCm39) P197Q probably damaging Het
Dlg5 T C 14: 24,226,639 (GRCm39) Y421C probably damaging Het
Dlgap2 A G 8: 14,893,624 (GRCm39) K980E probably benign Het
Drc7 T C 8: 95,782,644 (GRCm39) V3A unknown Het
Dst T C 1: 34,200,110 (GRCm39) V96A probably damaging Het
Ect2l T C 10: 18,018,752 (GRCm39) D548G possibly damaging Het
Efcab10 A T 12: 33,448,434 (GRCm39) Y89F probably benign Het
Eif1ad CGAGGAGGAGGAGGAGGAGG CGAGGAGGAGGAGGAGG 19: 5,420,086 (GRCm39) probably benign Het
Entpd6 A G 2: 150,600,732 (GRCm39) T147A probably damaging Het
Fbxl5 T A 5: 43,922,832 (GRCm39) E189D probably benign Het
Fer1l6 T A 15: 58,497,080 (GRCm39) S1217T probably damaging Het
Frem2 A T 3: 53,560,916 (GRCm39) V1197D possibly damaging Het
Fsip2 T A 2: 82,811,127 (GRCm39) L2482* probably null Het
Fsip2 A T 2: 82,817,164 (GRCm39) D4299V probably benign Het
Gipc3 T A 10: 81,174,049 (GRCm39) I242F probably damaging Het
Hoxb1 T A 11: 96,256,938 (GRCm39) Y96N probably damaging Het
Ibsp A G 5: 104,458,078 (GRCm39) E205G probably damaging Het
Ibtk A G 9: 85,585,135 (GRCm39) S1170P probably benign Het
Igfn1 A G 1: 135,893,801 (GRCm39) probably null Het
Iqsec1 A G 6: 90,639,877 (GRCm39) S954P probably benign Het
Kalrn A T 16: 34,212,463 (GRCm39) D28E probably benign Het
Lrmda T C 14: 22,627,938 (GRCm39) F52L probably damaging Het
Lrp2 T C 2: 69,353,631 (GRCm39) D543G probably damaging Het
Lrrtm3 T C 10: 63,924,157 (GRCm39) T337A probably benign Het
Marf1 C T 16: 13,946,465 (GRCm39) D1219N possibly damaging Het
Mkln1 A G 6: 31,405,113 (GRCm39) K118R probably benign Het
Nedd4l T C 18: 65,300,646 (GRCm39) probably null Het
Neu2 A G 1: 87,525,023 (GRCm39) E336G probably benign Het
Nfasc A G 1: 132,538,543 (GRCm39) F448S probably damaging Het
Nlrx1 C A 9: 44,165,431 (GRCm39) E822* probably null Het
Nr5a1 T C 2: 38,584,108 (GRCm39) Y437C probably damaging Het
Or4c119 A G 2: 88,986,925 (GRCm39) V198A probably benign Het
Or7a37 T A 10: 78,805,975 (GRCm39) L164* probably null Het
Or8b38 T C 9: 37,972,981 (GRCm39) Y122H probably damaging Het
Phtf1 C T 3: 103,876,438 (GRCm39) Q13* probably null Het
Pnldc1 A G 17: 13,107,815 (GRCm39) L525P possibly damaging Het
Ppl T A 16: 4,923,988 (GRCm39) D162V possibly damaging Het
Prkdc T A 16: 15,532,079 (GRCm39) S1448T possibly damaging Het
Ptgdr A G 14: 45,090,738 (GRCm39) I340T probably benign Het
Recql T C 6: 142,311,315 (GRCm39) I458M probably benign Het
Rrbp1 A T 2: 143,830,211 (GRCm39) V652E probably benign Het
Rtp1 T A 16: 23,250,160 (GRCm39) I175N probably damaging Het
Ryr1 A G 7: 28,754,369 (GRCm39) M3523T probably damaging Het
S100a16 T C 3: 90,449,703 (GRCm39) L62P probably damaging Het
Samd11 T C 4: 156,333,166 (GRCm39) E364G probably damaging Het
Satb1 C A 17: 52,049,143 (GRCm39) G603* probably null Het
Shroom3 T A 5: 93,110,224 (GRCm39) probably null Het
Slc25a15 A G 8: 22,885,777 (GRCm39) S3P probably benign Het
Socs2 A T 10: 95,248,900 (GRCm39) L71* probably null Het
Sptbn1 T C 11: 30,054,469 (GRCm39) E2208G probably damaging Het
St14 A G 9: 31,001,166 (GRCm39) V855A possibly damaging Het
Susd1 T A 4: 59,412,191 (GRCm39) T121S probably benign Het
Svs3b A T 2: 164,097,848 (GRCm39) S158T probably benign Het
Synpo C T 18: 60,736,661 (GRCm39) M428I probably benign Het
Syt10 C T 15: 89,674,979 (GRCm39) D456N probably damaging Het
Taar4 A G 10: 23,837,239 (GRCm39) D283G probably damaging Het
Tango6 T A 8: 107,415,426 (GRCm39) D82E probably benign Het
Tcof1 T C 18: 60,971,927 (GRCm39) T127A possibly damaging Het
Tle3 G A 9: 61,318,622 (GRCm39) probably null Het
Tmem45a A G 16: 56,642,665 (GRCm39) F169L probably benign Het
Trp53rkb T A 2: 166,637,743 (GRCm39) V233E probably damaging Het
Ttc7b C T 12: 100,381,389 (GRCm39) probably null Het
Tubgcp3 A T 8: 12,671,932 (GRCm39) L770* probably null Het
Tut1 G A 19: 8,943,466 (GRCm39) G851D probably benign Het
Ubr1 G A 2: 120,761,449 (GRCm39) T576I probably benign Het
Vmn1r125 T A 7: 21,006,530 (GRCm39) Y143N probably damaging Het
Vmn2r120 T A 17: 57,831,839 (GRCm39) I317F probably benign Het
Vmn2r95 T A 17: 18,644,575 (GRCm39) N70K probably benign Het
Vps35l A G 7: 118,432,971 (GRCm39) N568S probably damaging Het
Wdr59 A T 8: 112,213,582 (GRCm39) L311* probably null Het
Wnt2 A G 6: 18,030,252 (GRCm39) L12P unknown Het
Ypel1 A G 16: 16,900,443 (GRCm39) H98R probably benign Het
Zfp219 T C 14: 52,245,691 (GRCm39) T434A probably benign Het
Zik1 A C 7: 10,223,943 (GRCm39) C385G probably damaging Het
Other mutations in Xrn1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00487:Xrn1 APN 9 95,921,002 (GRCm39) missense probably benign 0.05
IGL00778:Xrn1 APN 9 95,855,500 (GRCm39) splice site probably benign
IGL01936:Xrn1 APN 9 95,930,397 (GRCm39) missense probably damaging 0.98
IGL01983:Xrn1 APN 9 95,855,421 (GRCm39) critical splice donor site probably null
IGL02106:Xrn1 APN 9 95,859,858 (GRCm39) missense probably benign 0.28
IGL02330:Xrn1 APN 9 95,855,401 (GRCm39) nonsense probably null
IGL02338:Xrn1 APN 9 95,859,880 (GRCm39) missense probably benign 0.42
IGL02830:Xrn1 APN 9 95,900,234 (GRCm39) critical splice donor site probably null
R0063:Xrn1 UTSW 9 95,851,588 (GRCm39) missense probably damaging 1.00
R0063:Xrn1 UTSW 9 95,851,588 (GRCm39) missense probably damaging 1.00
R0467:Xrn1 UTSW 9 95,906,244 (GRCm39) missense probably damaging 1.00
R0508:Xrn1 UTSW 9 95,933,789 (GRCm39) missense probably benign 0.00
R0605:Xrn1 UTSW 9 95,908,930 (GRCm39) nonsense probably null
R0670:Xrn1 UTSW 9 95,873,109 (GRCm39) missense probably damaging 1.00
R0691:Xrn1 UTSW 9 95,855,592 (GRCm39) missense probably damaging 0.96
R0781:Xrn1 UTSW 9 95,873,322 (GRCm39) missense probably benign 0.00
R0947:Xrn1 UTSW 9 95,880,316 (GRCm39) missense possibly damaging 0.60
R1034:Xrn1 UTSW 9 95,921,790 (GRCm39) missense probably damaging 1.00
R1124:Xrn1 UTSW 9 95,885,918 (GRCm39) missense probably benign 0.02
R1171:Xrn1 UTSW 9 95,873,064 (GRCm39) missense possibly damaging 0.47
R1199:Xrn1 UTSW 9 95,863,814 (GRCm39) splice site probably benign
R1609:Xrn1 UTSW 9 95,856,946 (GRCm39) missense probably benign 0.03
R1953:Xrn1 UTSW 9 95,906,274 (GRCm39) critical splice donor site probably null
R2000:Xrn1 UTSW 9 95,927,616 (GRCm39) nonsense probably null
R2109:Xrn1 UTSW 9 95,861,273 (GRCm39) missense probably benign 0.13
R2111:Xrn1 UTSW 9 95,921,885 (GRCm39) missense probably benign 0.03
R2164:Xrn1 UTSW 9 95,888,873 (GRCm39) missense possibly damaging 0.95
R2266:Xrn1 UTSW 9 95,888,765 (GRCm39) missense possibly damaging 0.64
R3754:Xrn1 UTSW 9 95,849,841 (GRCm39) missense probably damaging 1.00
R3783:Xrn1 UTSW 9 95,851,338 (GRCm39) missense probably benign 0.10
R3921:Xrn1 UTSW 9 95,851,337 (GRCm39) missense probably benign 0.01
R3929:Xrn1 UTSW 9 95,870,926 (GRCm39) missense possibly damaging 0.89
R4011:Xrn1 UTSW 9 95,867,278 (GRCm39) nonsense probably null
R4082:Xrn1 UTSW 9 95,863,973 (GRCm39) missense probably benign 0.02
R4455:Xrn1 UTSW 9 95,855,698 (GRCm39) intron probably benign
R4736:Xrn1 UTSW 9 95,915,689 (GRCm39) missense probably damaging 1.00
R4756:Xrn1 UTSW 9 95,921,862 (GRCm39) missense probably benign 0.00
R4780:Xrn1 UTSW 9 95,856,797 (GRCm39) intron probably benign
R5152:Xrn1 UTSW 9 95,846,118 (GRCm39) missense probably benign 0.40
R5261:Xrn1 UTSW 9 95,927,596 (GRCm39) missense probably benign 0.00
R5741:Xrn1 UTSW 9 95,927,604 (GRCm39) missense probably benign 0.24
R6108:Xrn1 UTSW 9 95,856,480 (GRCm39) missense possibly damaging 0.91
R6127:Xrn1 UTSW 9 95,851,542 (GRCm39) missense probably damaging 0.99
R6268:Xrn1 UTSW 9 95,846,067 (GRCm39) missense probably damaging 1.00
R6418:Xrn1 UTSW 9 95,915,763 (GRCm39) splice site probably null
R7002:Xrn1 UTSW 9 95,929,843 (GRCm39) missense probably benign 0.00
R7067:Xrn1 UTSW 9 95,851,565 (GRCm39) missense probably damaging 0.98
R7155:Xrn1 UTSW 9 95,861,198 (GRCm39) missense possibly damaging 0.92
R7439:Xrn1 UTSW 9 95,933,682 (GRCm39) missense probably benign
R7447:Xrn1 UTSW 9 95,927,547 (GRCm39) missense probably benign
R7454:Xrn1 UTSW 9 95,930,411 (GRCm39) missense probably benign 0.03
R7473:Xrn1 UTSW 9 95,861,194 (GRCm39) missense probably benign 0.07
R7561:Xrn1 UTSW 9 95,881,511 (GRCm39) missense probably benign 0.18
R7580:Xrn1 UTSW 9 95,893,732 (GRCm39) missense not run
R7642:Xrn1 UTSW 9 95,903,906 (GRCm39) missense possibly damaging 0.95
R7763:Xrn1 UTSW 9 95,880,401 (GRCm39) critical splice donor site probably null
R8225:Xrn1 UTSW 9 95,917,720 (GRCm39) missense probably benign
R8372:Xrn1 UTSW 9 95,906,166 (GRCm39) missense probably benign 0.42
R8516:Xrn1 UTSW 9 95,930,444 (GRCm39) nonsense probably null
R8710:Xrn1 UTSW 9 95,884,285 (GRCm39) missense
R8850:Xrn1 UTSW 9 95,920,732 (GRCm39) missense probably benign
R8865:Xrn1 UTSW 9 95,873,246 (GRCm39) missense probably benign 0.00
R8951:Xrn1 UTSW 9 95,870,999 (GRCm39) missense probably benign 0.00
R9013:Xrn1 UTSW 9 95,920,981 (GRCm39) missense probably benign 0.00
R9162:Xrn1 UTSW 9 95,915,660 (GRCm39) missense probably benign 0.01
R9163:Xrn1 UTSW 9 95,880,274 (GRCm39) missense probably benign 0.00
R9415:Xrn1 UTSW 9 95,851,527 (GRCm39) missense probably damaging 1.00
R9438:Xrn1 UTSW 9 95,893,287 (GRCm39) missense probably benign 0.30
R9544:Xrn1 UTSW 9 95,920,756 (GRCm39) missense probably benign
R9588:Xrn1 UTSW 9 95,920,756 (GRCm39) missense probably benign
R9674:Xrn1 UTSW 9 95,855,647 (GRCm39) missense possibly damaging 0.65
R9674:Xrn1 UTSW 9 95,855,645 (GRCm39) missense probably damaging 0.99
R9716:Xrn1 UTSW 9 95,927,632 (GRCm39) missense possibly damaging 0.71
Z1176:Xrn1 UTSW 9 95,846,243 (GRCm39) missense probably damaging 1.00
Z1177:Xrn1 UTSW 9 95,873,058 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- GCGCATTTGTTTGCAGTGATAC -3'
(R):5'- GCAAGTAGTCTGTTTCTAAGCTG -3'

Sequencing Primer
(F):5'- CATTTGTTTGCAGTGATACAGGGG -3'
(R):5'- CTGGCTTAGATAGACCTTGAACCTG -3'
Posted On 2014-07-14