Incidental Mutation 'R9674:Xrn1'
ID 728240
Institutional Source Beutler Lab
Gene Symbol Xrn1
Ensembl Gene ENSMUSG00000032410
Gene Name 5'-3' exoribonuclease 1
Synonyms mXrn1, Dhm2
MMRRC Submission
Accession Numbers
Essential gene? Probably essential (E-score: 0.917) question?
Stock # R9674 (G1)
Quality Score 225.009
Status Not validated
Chromosome 9
Chromosomal Location 95836813-95939856 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 95855645 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Phenylalanine at position 314 (Y314F)
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 damaging
Transcript: ENSMUST00000034981
AA Change: Y314F

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: Y314F

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 damaging
Transcript: ENSMUST00000185633
AA Change: Y314F

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: Y314F

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 damaging
Transcript: ENSMUST00000190665
AA Change: Y314F

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000139510
Gene: ENSMUSG00000032410
AA Change: Y314F

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: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
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: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aadacl2 A T 3: 59,914,472 (GRCm39) D25V possibly damaging Het
Abca16 A G 7: 120,074,668 (GRCm39) probably null Het
Adam9 T A 8: 25,441,014 (GRCm39) T820S possibly damaging Het
Adamts6 G A 13: 104,563,448 (GRCm39) V647I probably benign Het
Afap1l2 T A 19: 56,922,195 (GRCm39) R14S probably damaging Het
Aff3 C T 1: 38,248,864 (GRCm39) V748I probably damaging Het
Aldh5a1 T C 13: 25,110,038 (GRCm39) I166V probably benign Het
Alx4 G T 2: 93,507,858 (GRCm39) L384F probably damaging Het
Ank3 T A 10: 69,824,549 (GRCm39) S1073T Het
Ankrd50 A G 3: 38,506,574 (GRCm39) C275R unknown Het
Apol11a G A 15: 77,401,347 (GRCm39) S278N possibly damaging Het
Astn2 T A 4: 65,460,963 (GRCm39) D1057V probably damaging Het
Atp11a T C 8: 12,877,525 (GRCm39) V317A probably benign Het
Cacna1i A G 15: 80,264,629 (GRCm39) T1486A probably damaging Het
Cadps A G 14: 12,454,291 (GRCm38) F1076L probably damaging Het
Cct6b T C 11: 82,645,838 (GRCm39) T154A probably damaging Het
Cfap69 A G 5: 5,697,021 (GRCm39) F92L possibly damaging Het
Cyp19a1 A T 9: 54,074,141 (GRCm39) I471K possibly damaging Het
Cyp26a1 T A 19: 37,689,726 (GRCm39) M474K probably damaging Het
Cyp4a12a T C 4: 115,186,156 (GRCm39) S439P probably benign Het
Cyp4f37 T A 17: 32,846,841 (GRCm39) probably null Het
Dgki A G 6: 37,027,157 (GRCm39) Y395H probably damaging Het
Dlg1 T C 16: 31,610,580 (GRCm39) V287A probably damaging Het
Dlx2 C T 2: 71,376,496 (GRCm39) G81S possibly damaging Het
Dnah8 G T 17: 30,998,112 (GRCm39) K3448N possibly damaging Het
Dnhd1 C T 7: 105,363,429 (GRCm39) P3997L probably damaging Het
Drosha C G 15: 12,890,170 (GRCm39) D910E probably damaging Het
Dscam A G 16: 96,442,036 (GRCm39) V1597A probably benign Het
Eif1b A G 9: 120,323,265 (GRCm39) K42E possibly damaging Het
Enpp2 C A 15: 54,816,135 (GRCm39) G10W unknown Het
Exd2 A G 12: 80,536,372 (GRCm39) N334S probably benign Het
Glt6d1 T A 2: 25,684,382 (GRCm39) N208I probably benign Het
Grin2a T A 16: 9,471,265 (GRCm39) K668* probably null Het
Grm1 A G 10: 10,609,028 (GRCm39) V535A possibly damaging Het
H2ac7 A G 13: 23,758,862 (GRCm39) D73G possibly damaging Het
Hey2 A T 10: 30,710,413 (GRCm39) D113E probably benign Het
Ighm T A 12: 113,385,139 (GRCm39) I274F Het
Ighv1-58 G T 12: 115,275,847 (GRCm39) T97K probably damaging Het
Igkv6-20 T C 6: 70,312,852 (GRCm39) H107R possibly damaging Het
Il15 C T 8: 83,069,938 (GRCm39) G42D probably damaging Het
Jakmip2 T A 18: 43,704,961 (GRCm39) M347L probably benign Het
Kcnh7 T C 2: 62,595,060 (GRCm39) Y670C probably damaging Het
Ktn1 G C 14: 47,922,213 (GRCm39) C458S possibly damaging Het
Lama5 C T 2: 179,840,267 (GRCm39) probably null Het
Lce1i T C 3: 92,685,113 (GRCm39) Q21R unknown Het
Lmo7 A T 14: 102,078,340 (GRCm39) E81D probably damaging Het
Lrrc4b A T 7: 44,111,852 (GRCm39) I575F probably damaging Het
Mmrn1 C T 6: 60,948,072 (GRCm39) Q272* probably null Het
Nbea A T 3: 55,966,183 (GRCm39) D426E probably damaging Het
Neto1 G A 18: 86,491,827 (GRCm39) V243M probably damaging Het
Notch1 G A 2: 26,361,308 (GRCm39) R1061C probably damaging Het
Or5g25 T G 2: 85,478,593 (GRCm39) Q24P possibly damaging Het
Or5p67 A T 7: 107,922,271 (GRCm39) I204N probably benign Het
Osgin1 A G 8: 120,172,499 (GRCm39) D431G possibly damaging Het
Ppp4r1 A G 17: 66,140,127 (GRCm39) D675G probably damaging Het
Pramel25 T A 4: 143,520,162 (GRCm39) H135Q probably benign Het
Prkdc T A 16: 15,533,819 (GRCm39) H1552Q probably damaging Het
Rbfox1 T C 16: 7,170,885 (GRCm39) F282L probably benign Het
Ret T C 6: 118,130,830 (GRCm39) D1111G probably damaging Het
Rnf224 A T 2: 25,126,330 (GRCm39) Y8N probably benign Het
Rtl1 G T 12: 109,559,024 (GRCm39) H938Q possibly damaging Het
Sec23ip T G 7: 128,380,187 (GRCm39) D867E probably damaging Het
Sema3f A T 9: 107,566,947 (GRCm39) L194Q possibly damaging Het
Sfmbt1 C T 14: 30,495,851 (GRCm39) R45C probably damaging Het
Slc7a4 T C 16: 17,392,208 (GRCm39) I409V probably benign Het
Slco6c1 T A 1: 97,047,565 (GRCm39) D246V probably damaging Het
Smap2 C T 4: 120,826,745 (GRCm39) M426I probably benign Het
Spata31h1 C T 10: 82,120,030 (GRCm39) V4327I possibly damaging Het
Tmem184b T A 15: 79,249,524 (GRCm39) T315S probably benign Het
Trpm4 A T 7: 44,982,811 (GRCm39) D30E possibly damaging Het
Ttc7b T A 12: 100,432,553 (GRCm39) K154N probably benign Het
Vps13b T A 15: 35,607,380 (GRCm39) H1104Q probably damaging Het
Wnk4 T A 11: 101,166,874 (GRCm39) L1010Q unknown Het
Xpo6 T A 7: 125,723,700 (GRCm39) H537L probably benign Het
Zap70 T C 1: 36,810,150 (GRCm39) Y87H probably benign Het
Zbtb4 T C 11: 69,669,973 (GRCm39) Y899H probably damaging Het
Zcchc7 T A 4: 44,931,418 (GRCm39) H202Q possibly damaging Het
Zeb2 A G 2: 44,891,725 (GRCm39) Y276H probably damaging Het
Zfp867 T G 11: 59,355,850 (GRCm39) Q68P probably benign 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
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
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'- CAGGGTATGTGCACCAGAAG -3'
(R):5'- TCACCTGGAGTCAGCTTCTTTAG -3'

Sequencing Primer
(F):5'- TGTGCACCAGAAGAAACGACATTTC -3'
(R):5'- CTTCTTTAGCATCCACTGAAAATGAC -3'
Posted On 2022-10-06