Incidental Mutation 'R2111:Xrn1'
ID 232564
Institutional Source Beutler Lab
Gene Symbol Xrn1
Ensembl Gene ENSMUSG00000032410
Gene Name 5'-3' exoribonuclease 1
Synonyms mXrn1, Dhm2
MMRRC Submission 040115-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.917) question?
Stock # R2111 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 95836813-95939856 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 95921885 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Asparagine at position 1433 (H1433N)
Ref Sequence ENSEMBL: ENSMUSP00000140278 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034981] [ENSMUST00000185633]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000034981
AA Change: H1433N

PolyPhen 2 Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: H1433N

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: H1433N

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: H1433N

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 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.6%
Validation Efficiency 100% (86/86)
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: 89 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9330161L09Rik T C 12: 103,373,848 (GRCm39) probably benign Het
Abca2 A T 2: 25,327,517 (GRCm39) I669F possibly damaging Het
Adam9 C T 8: 25,472,142 (GRCm39) probably benign Het
Adprhl1 A G 8: 13,298,694 (GRCm39) Y79H probably damaging Het
Akp3 A T 1: 87,054,607 (GRCm39) probably null Het
Alpk2 T C 18: 65,482,845 (GRCm39) S388G probably benign Het
Amph G A 13: 19,300,436 (GRCm39) probably benign Het
Arr3 T A X: 99,658,247 (GRCm39) F269L possibly damaging Het
Atp2a2 A G 5: 122,597,609 (GRCm39) F808S probably damaging Het
Baz1a T A 12: 54,958,170 (GRCm39) N1027I probably damaging Het
C2cd4c G T 10: 79,448,255 (GRCm39) H297Q probably damaging Het
Calr3 T A 8: 73,181,112 (GRCm39) D160V probably damaging Het
Cdc42ep1 C T 15: 78,731,692 (GRCm39) R46C probably damaging Het
Cdh23 G T 10: 60,141,362 (GRCm39) F3127L probably damaging Het
Cfhr4 T A 1: 139,702,417 (GRCm39) probably benign Het
Cps1 T A 1: 67,216,139 (GRCm39) D821E probably benign Het
Cyp2e1 C A 7: 140,353,547 (GRCm39) T328K probably damaging Het
Dcp1a T C 14: 30,241,327 (GRCm39) V379A probably benign Het
Dst T C 1: 34,208,259 (GRCm39) S737P probably damaging Het
Dtx2 C T 5: 136,059,431 (GRCm39) S493F probably damaging Het
Eci2 A G 13: 35,174,699 (GRCm39) probably null Het
Ercc6l2 A G 13: 63,982,563 (GRCm39) T126A probably damaging Het
Fgf6 T C 6: 126,992,723 (GRCm39) S59P probably damaging Het
Fmnl2 A G 2: 52,995,549 (GRCm39) E424G probably damaging Het
Gapvd1 G T 2: 34,574,329 (GRCm39) A1256D probably benign Het
Gcfc2 C A 6: 81,900,759 (GRCm39) D24E probably benign Het
Gigyf2 A G 1: 87,368,452 (GRCm39) H1044R probably damaging Het
Gk2 T C 5: 97,604,164 (GRCm39) I225V probably benign Het
Gm3944 C A 12: 18,903,895 (GRCm39) S8* probably null Het
Gnl3l A G X: 149,780,290 (GRCm39) S217P probably damaging Het
Gpr156 A G 16: 37,799,113 (GRCm39) D109G probably benign Het
Hoxd1 A T 2: 74,593,710 (GRCm39) T89S probably benign Het
Ift172 G A 5: 31,443,423 (GRCm39) T112M probably benign Het
Igkv1-115 C A 6: 68,138,613 (GRCm39) S72* probably null Het
Ildr1 A G 16: 36,542,341 (GRCm39) E247G probably damaging Het
Insr A G 8: 3,219,748 (GRCm39) S925P probably benign Het
Itpr1 T G 6: 108,355,270 (GRCm39) probably benign Het
Khdrbs3 C T 15: 68,896,673 (GRCm39) T111I probably benign Het
Mageb3 A G 2: 121,785,306 (GRCm39) probably null Het
Mcf2l A T 8: 13,051,867 (GRCm39) K433N probably damaging Het
Mdn1 A G 4: 32,700,409 (GRCm39) E1456G probably damaging Het
Mta1 C T 12: 113,095,248 (GRCm39) T467I probably damaging Het
Mtr A T 13: 12,259,487 (GRCm39) I196N possibly damaging Het
Mtus1 G T 8: 41,475,608 (GRCm39) P819T probably damaging Het
Myh1 G A 11: 67,105,446 (GRCm39) D1079N possibly damaging Het
Nav1 C T 1: 135,376,742 (GRCm39) R1694Q probably damaging Het
Neb A G 2: 52,174,275 (GRCm39) I1528T probably benign Het
Nek1 T A 8: 61,577,360 (GRCm39) probably null Het
Nes A G 3: 87,884,618 (GRCm39) E915G probably benign Het
Nlrp4f T C 13: 65,347,167 (GRCm39) I30M probably benign Het
Nup153 A G 13: 46,837,404 (GRCm39) S1273P probably benign Het
Nup155 A G 15: 8,150,951 (GRCm39) I334V probably benign Het
Or10j2 A T 1: 173,097,879 (GRCm39) M46L probably benign Het
Or1e1f A G 11: 73,855,740 (GRCm39) Y102C probably damaging Het
Or5b3 G A 19: 13,388,307 (GRCm39) A125T probably damaging Het
Or5d41 A G 2: 88,054,818 (GRCm39) V186A possibly damaging Het
Or6d13 T C 6: 116,517,611 (GRCm39) Y66H possibly damaging Het
Or8b46 T A 9: 38,450,576 (GRCm39) N128K probably benign Het
Or8k38 G T 2: 86,488,781 (GRCm39) T7K probably damaging Het
Parn G A 16: 13,420,933 (GRCm39) S473L probably damaging Het
Pcnt T C 10: 76,256,360 (GRCm39) K627E probably damaging Het
Pja2 T A 17: 64,597,031 (GRCm39) D553V probably damaging Het
Prune2 T C 19: 17,185,602 (GRCm39) F3004L probably damaging Het
Rasgrp3 T C 17: 75,807,753 (GRCm39) probably null Het
Rdh13 A G 7: 4,448,482 (GRCm39) V10A probably benign Het
Rimbp2 T C 5: 128,850,565 (GRCm39) Y906C probably damaging Het
Ripor1 T C 8: 106,341,344 (GRCm39) F59S probably damaging Het
Rnf185 T C 11: 3,382,393 (GRCm39) probably benign Het
Runx3 T C 4: 134,882,627 (GRCm39) V107A probably damaging Het
Scn3b T C 9: 40,193,741 (GRCm39) V156A probably benign Het
Serpina3a G A 12: 104,082,481 (GRCm39) A85T probably damaging Het
Slc12a7 C T 13: 73,933,274 (GRCm39) R111* probably null Het
Slc5a5 A T 8: 71,342,395 (GRCm39) probably null Het
Snx13 A T 12: 35,188,084 (GRCm39) L787F probably damaging Het
Spef2 A T 15: 9,589,659 (GRCm39) M1535K probably damaging Het
Sphkap T G 1: 83,253,602 (GRCm39) K1382N probably benign Het
Tagap1 A G 17: 7,224,259 (GRCm39) S146P probably benign Het
Tagln3 A G 16: 45,531,957 (GRCm39) Y192H probably damaging Het
Tbc1d15 A C 10: 115,076,819 (GRCm39) S22A possibly damaging Het
Tbc1d31 A G 15: 57,796,040 (GRCm39) E211G probably benign Het
Tmod3 A G 9: 75,416,645 (GRCm39) V229A probably damaging Het
Ubr2 A G 17: 47,274,071 (GRCm39) probably null Het
Ugt2b36 T C 5: 87,240,100 (GRCm39) E95G probably benign Het
Unc45b G A 11: 82,802,515 (GRCm39) A4T probably benign Het
Usp40 A G 1: 87,877,936 (GRCm39) I1117T probably benign Het
Vcan T A 13: 89,841,422 (GRCm39) D414V probably damaging Het
Zfp353-ps T A 8: 42,536,005 (GRCm39) noncoding transcript Het
Zfp74 G A 7: 29,634,443 (GRCm39) Q422* probably null Het
Zmym3 A T X: 100,450,993 (GRCm39) V1208D 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
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'- GCCACCTAAGTCTAACGTTTGTTC -3'
(R):5'- AGAACTGACTCCTCCAAGTTATCC -3'

Sequencing Primer
(F):5'- ACCTAAGTCTAACGTTTGTTCTCCTC -3'
(R):5'- GGTCATCACCACATGTGTGC -3'
Posted On 2014-09-18