Incidental Mutation 'R2000:Xrn1'
ID 225844
Institutional Source Beutler Lab
Gene Symbol Xrn1
Ensembl Gene ENSMUSG00000032410
Gene Name 5'-3' exoribonuclease 1
Synonyms mXrn1, Dhm2
MMRRC Submission 040010-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.917) question?
Stock # R2000 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 95836813-95939856 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) C to T at 95927616 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Stop codon at position 1463 (Q1463*)
Ref Sequence ENSEMBL: ENSMUSP00000140278 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034981] [ENSMUST00000185633]
AlphaFold no structure available at present
Predicted Effect probably null
Transcript: ENSMUST00000034981
AA Change: Q1467*
SMART Domains Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: Q1467*

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 null
Transcript: ENSMUST00000185633
AA Change: Q1463*
SMART Domains Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: Q1463*

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: ENSMUST00000189281
Meta Mutation Damage Score 0.9712 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.0%
Validation Efficiency 98% (62/63)
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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Atf2 T C 2: 73,693,584 (GRCm39) probably null Het
Atrn T C 2: 130,777,508 (GRCm39) Y186H probably damaging Het
Birc6 T C 17: 74,911,614 (GRCm39) V1528A possibly damaging Het
Brpf3 A C 17: 29,040,531 (GRCm39) E984A probably benign Het
Btnl9 T C 11: 49,059,948 (GRCm39) N600S probably benign Het
Camk1d A T 2: 5,366,836 (GRCm39) Y126* probably null Het
Casp8ap2 T A 4: 32,634,874 (GRCm39) L136H probably damaging Het
Cd46 A G 1: 194,760,012 (GRCm39) I280T probably benign Het
Cip2a A T 16: 48,835,332 (GRCm39) Q699L probably damaging Het
Crebbp A T 16: 3,902,116 (GRCm39) H2374Q probably damaging Het
Dock3 A G 9: 106,870,160 (GRCm39) probably benign Het
Dph7 T A 2: 24,861,653 (GRCm39) D355E probably benign Het
Dync1li1 C A 9: 114,542,631 (GRCm39) F264L probably benign Het
Fer1l6 G A 15: 58,474,160 (GRCm39) probably benign Het
Flt3 T C 5: 147,278,048 (GRCm39) D842G probably damaging Het
Fosl1 A G 19: 5,500,383 (GRCm39) probably benign Het
Gabrr2 T A 4: 33,084,400 (GRCm39) I162N probably damaging Het
Gata6 T C 18: 11,054,113 (GRCm39) F14S probably benign Het
Gm15446 T C 5: 110,090,677 (GRCm39) S310P possibly damaging Het
Gmppa A C 1: 75,418,172 (GRCm39) D190A probably damaging Het
Gpr108 C T 17: 57,543,712 (GRCm39) G455S probably benign Het
Gstm1 A G 3: 107,922,127 (GRCm39) F170S probably damaging Het
Gvin-ps6 G A 7: 106,022,438 (GRCm39) S188L probably benign Het
Gzf1 T C 2: 148,526,531 (GRCm39) I334T probably benign Het
Hadh A T 3: 131,038,888 (GRCm39) I156K probably benign Het
Htr5a G A 5: 28,055,887 (GRCm39) V293M possibly damaging Het
Ice1 C T 13: 70,750,546 (GRCm39) V47M possibly damaging Het
Ifnl3 G T 7: 28,222,354 (GRCm39) A32S possibly damaging Het
Itsn2 T A 12: 4,716,176 (GRCm39) Y978* probably null Het
Kif1a G T 1: 92,982,051 (GRCm39) T792N probably damaging Het
Lgals9 T C 11: 78,863,996 (GRCm39) N50D probably benign Het
Lrp2 A G 2: 69,297,434 (GRCm39) Y3176H probably damaging Het
Lvrn A T 18: 47,038,374 (GRCm39) N976I probably benign Het
Magea10 A T X: 71,426,379 (GRCm39) I205K probably benign Het
Myo1c A T 11: 75,561,405 (GRCm39) M820L probably damaging Het
Neb A T 2: 52,102,982 (GRCm39) C4222* probably null Het
Nkain2 T A 10: 32,766,281 (GRCm39) probably benign Het
Or10g6 A G 9: 39,933,985 (GRCm39) I99V probably benign Het
Or3a1b A G 11: 74,012,406 (GRCm39) Y97C probably benign Het
Or5d16 G A 2: 87,773,490 (GRCm39) L161F probably benign Het
Parp4 C T 14: 56,851,181 (GRCm39) T728M probably damaging Het
Pnma8a T A 7: 16,694,964 (GRCm39) V273D probably benign Het
Ppp1r9b A G 11: 94,887,446 (GRCm39) E486G probably damaging Het
Pth2 C A 7: 44,831,146 (GRCm39) R98S possibly damaging Het
Ramacl A T 13: 67,056,214 (GRCm39) N69I possibly damaging Het
Rif1 T A 2: 51,971,310 (GRCm39) F263I probably damaging Het
Rnf213 A T 11: 119,326,848 (GRCm39) I1613F probably damaging Het
Rsbn1l G A 5: 21,107,368 (GRCm39) H549Y probably damaging Het
Rtl1 C A 12: 109,560,321 (GRCm39) W506L probably damaging Het
Slc4a4 C T 5: 89,176,206 (GRCm39) P59L probably damaging Het
Smarcad1 A G 6: 65,050,200 (GRCm39) E273G probably damaging Het
Tectb C G 19: 55,169,431 (GRCm39) probably benign Het
Ttf1 T A 2: 28,955,197 (GRCm39) L187Q possibly damaging Het
Ttn A T 2: 76,800,047 (GRCm39) I387N probably damaging Het
Ufsp1 T C 5: 137,293,166 (GRCm39) probably null Het
Uox A C 3: 146,316,154 (GRCm39) K30Q possibly damaging Het
Ush1c A G 7: 45,870,857 (GRCm39) S327P probably damaging Het
Wwc1 A T 11: 35,767,374 (GRCm39) L419Q probably damaging Het
Yeats2 G A 16: 20,005,141 (GRCm39) A393T probably benign Het
Zfp101 C T 17: 33,600,491 (GRCm39) A422T possibly 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
R1921:Xrn1 UTSW 9 95,881,550 (GRCm39) missense probably benign 0.04
R1953:Xrn1 UTSW 9 95,906,274 (GRCm39) critical splice donor site 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'- AACCCAGCCTGTTGTTGTTAAC -3'
(R):5'- AGTTCAAATCCTAGTGCTGCTG -3'

Sequencing Primer
(F):5'- TGCTGTGAAGAGATCTCCATGACC -3'
(R):5'- GGCATTCCAACAAGGGAA -3'
Posted On 2014-08-25