Incidental Mutation 'R7473:Xrn1'
ID 579277
Institutional Source Beutler Lab
Gene Symbol Xrn1
Ensembl Gene ENSMUSG00000032410
Gene Name 5'-3' exoribonuclease 1
Synonyms mXrn1, Dhm2
MMRRC Submission 045547-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.917) question?
Stock # R7473 (G1)
Quality Score 225.009
Status Validated
Chromosome 9
Chromosomal Location 95836813-95939856 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 95861194 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 451 (F451L)
Ref Sequence ENSEMBL: ENSMUSP00000034981 (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: F451L

PolyPhen 2 Score 0.074 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: F451L

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: F451L

PolyPhen 2 Score 0.074 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: F451L

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 probably benign
Transcript: ENSMUST00000190665
AA Change: F451L

PolyPhen 2 Score 0.143 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000139510
Gene: ENSMUSG00000032410
AA Change: F451L

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: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 96% (80/83)
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: 82 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933434E20Rik T C 3: 89,965,960 (GRCm39) probably null Het
A630095N17Rik G A 1: 75,208,675 (GRCm39) T15I unknown Het
Actr1b A G 1: 36,748,900 (GRCm39) V12A probably benign Het
Add1 A G 5: 34,776,697 (GRCm39) T473A possibly damaging Het
Akap11 A T 14: 78,751,328 (GRCm39) V353E Het
Alcam G A 16: 52,272,882 (GRCm39) probably benign Het
Alpi A G 1: 87,027,369 (GRCm39) probably null Het
Ap3s2 A G 7: 79,565,779 (GRCm39) F49S probably damaging Het
Arpc1a A G 5: 145,037,886 (GRCm39) K174E probably benign Het
Bbox1 A T 2: 110,095,843 (GRCm39) S374T probably damaging Het
Bean1 CT C 8: 104,908,664 (GRCm39) probably null Het
Bltp2 T C 11: 78,157,941 (GRCm39) S368P possibly damaging Het
Bmp2k A G 5: 97,204,871 (GRCm39) N402S probably benign Het
Bmper C A 9: 23,286,926 (GRCm39) A284D probably benign Het
Bnip5 G A 17: 29,124,298 (GRCm39) R335W probably damaging Het
Bpifb2 A T 2: 153,723,116 (GRCm39) H124L possibly damaging Het
Bsn C T 9: 107,989,449 (GRCm39) R2101Q probably damaging Het
Cacng1 T A 11: 107,607,018 (GRCm39) D67V probably damaging Het
Catsperg1 A G 7: 28,894,903 (GRCm39) S565P probably damaging Het
Cep126 C T 9: 8,101,779 (GRCm39) E252K probably damaging Het
Cep55 G A 19: 38,058,384 (GRCm39) E326K probably damaging Het
Cfap58 T A 19: 47,963,064 (GRCm39) Y491* probably null Het
Cpeb2 T C 5: 43,434,848 (GRCm39) S747P Het
Cryz T A 3: 154,312,157 (GRCm39) S85T probably benign Het
D2hgdh T C 1: 93,765,800 (GRCm39) V367A probably damaging Het
Dgkh T C 14: 78,836,483 (GRCm39) N703S probably benign Het
Dnah11 T C 12: 117,866,911 (GRCm39) S4077G probably benign Het
Dnah14 A G 1: 181,579,704 (GRCm39) H3079R probably damaging Het
Dnah2 T A 11: 69,382,484 (GRCm39) T1209S probably damaging Het
Dnmt3b A G 2: 153,526,370 (GRCm39) D804G probably damaging Het
Ell2 A G 13: 75,898,154 (GRCm39) E143G probably damaging Het
Exoc2 A G 13: 31,006,613 (GRCm39) probably null Het
Fahd2a A T 2: 127,282,376 (GRCm39) I131N probably damaging Het
Fer1l5 A G 1: 36,460,689 (GRCm39) N1976D possibly damaging Het
Flt1 A G 5: 147,531,405 (GRCm39) S853P probably damaging Het
Frg2f1 C T 4: 119,387,990 (GRCm39) V170I probably benign Het
Gcn1 G A 5: 115,719,863 (GRCm39) V373M probably benign Het
Gm19965 A G 1: 116,749,602 (GRCm39) T428A unknown Het
Gm4792 A G 10: 94,129,730 (GRCm39) I124T unknown Het
Grik2 A T 10: 48,989,618 (GRCm39) C804S probably benign Het
Heatr6 T A 11: 83,672,217 (GRCm39) I1075N probably damaging Het
Hunk G A 16: 90,250,588 (GRCm39) A211T probably damaging Het
Ighe T C 12: 113,234,976 (GRCm39) I395V probably damaging Het
Ino80e A T 7: 126,456,484 (GRCm39) S104T probably damaging Het
Inpp4a A G 1: 37,408,534 (GRCm39) Y305C probably benign Het
Insrr T A 3: 87,711,838 (GRCm39) probably null Het
Itgae T G 11: 73,031,504 (GRCm39) D1073E possibly damaging Het
Klf11 G T 12: 24,705,141 (GRCm39) probably null Het
Lrguk A T 6: 34,006,630 (GRCm39) K80M probably benign Het
Map2 A T 1: 66,454,617 (GRCm39) D1169V probably damaging Het
Mpst G T 15: 78,297,726 (GRCm39) C248F probably damaging Het
Myo9a C A 9: 59,802,527 (GRCm39) Q2005K probably benign Het
Nfatc4 C T 14: 56,069,421 (GRCm39) T649I probably benign Het
Nmt1 A G 11: 102,937,226 (GRCm39) R88G probably benign Het
Nqo1 G A 8: 108,129,729 (GRCm39) probably benign Het
Nudt2 T G 4: 41,477,576 (GRCm39) M19R probably benign Het
Or10a49 T A 7: 108,467,476 (GRCm39) K295M probably damaging Het
Or12d2 T A 17: 37,624,522 (GRCm39) Y251F probably benign Het
Or9q2 C T 19: 13,772,526 (GRCm39) V150M probably benign Het
P2ry1 T A 3: 60,911,509 (GRCm39) I216N probably damaging Het
Pcx T A 19: 4,669,589 (GRCm39) L823* probably null Het
Pkhd1 A G 1: 20,619,980 (GRCm39) V880A probably damaging Het
Plcb1 A T 2: 135,186,196 (GRCm39) N721I probably damaging Het
Prdm15 T C 16: 97,623,046 (GRCm39) K269E possibly damaging Het
Prl7b1 A G 13: 27,785,996 (GRCm39) V224A possibly damaging Het
Reln A G 5: 22,134,125 (GRCm39) V2601A probably benign Het
Rspo4 G A 2: 151,714,993 (GRCm39) R210Q unknown Het
Slc7a5 A T 8: 122,615,162 (GRCm39) D228E probably benign Het
Spopfm2 T A 3: 94,083,509 (GRCm39) K101* probably null Het
Tas2r115 A G 6: 132,714,214 (GRCm39) S246P probably damaging Het
Tenm4 A G 7: 96,423,353 (GRCm39) Y716C probably damaging Het
Tgfb3 T C 12: 86,108,923 (GRCm39) K269E possibly damaging Het
Thoc6 A G 17: 23,889,841 (GRCm39) I27T probably benign Het
Tigd5 G A 15: 75,781,748 (GRCm39) G37S probably benign Het
Tmem259 C T 10: 79,815,506 (GRCm39) D102N possibly damaging Het
Tpo T G 12: 30,142,589 (GRCm39) I712L probably benign Het
Ttn G A 2: 76,700,892 (GRCm39) T21M possibly damaging Het
Utp20 A T 10: 88,656,572 (GRCm39) probably null Het
Xrcc5 A G 1: 72,351,748 (GRCm39) D106G probably damaging Het
Zar1l T A 5: 150,441,203 (GRCm39) D141V probably damaging Het
Zfp27 A T 7: 29,595,324 (GRCm39) C214S possibly damaging Het
Znfx1 A T 2: 166,880,744 (GRCm39) C1211S 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
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
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
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'- CTTAAGTACACACAGCAGGATTAAC -3'
(R):5'- CCCAGCCCATTTTGATACAGATTG -3'

Sequencing Primer
(F):5'- CACACAGCAGGATTAACTATGTTG -3'
(R):5'- GCCCATTTTGATACAGATTGATACAG -3'
Posted On 2019-10-07