Incidental Mutation 'R7454:Xrn1'
ID 578009
Institutional Source Beutler Lab
Gene Symbol Xrn1
Ensembl Gene ENSMUSG00000032410
Gene Name 5'-3' exoribonuclease 1
Synonyms mXrn1, Dhm2
MMRRC Submission 045528-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.917) question?
Stock # R7454 (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 95930411 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 1543 (S1543R)
Ref Sequence ENSEMBL: ENSMUSP00000034981 (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: S1543R

PolyPhen 2 Score 0.030 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: S1543R

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: S1539R

PolyPhen 2 Score 0.030 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: S1539R

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (90/90)
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
2510002D24Rik A G 16: 18,655,601 (GRCm39) E57G possibly damaging Het
4932414N04Rik C A 2: 68,518,648 (GRCm39) T159K unknown Het
Adamts10 T A 17: 33,763,979 (GRCm39) F616L possibly damaging Het
Adtrp G A 13: 41,981,791 (GRCm39) S26L unknown Het
Alpk3 A C 7: 80,728,310 (GRCm39) E480A probably benign Het
Anks6 T C 4: 47,038,919 (GRCm39) T529A unknown Het
Arl4d A G 11: 101,557,486 (GRCm39) H4R probably benign Het
Ash1l A G 3: 88,891,172 (GRCm39) H1017R probably benign Het
Bbs12 T C 3: 37,375,102 (GRCm39) S517P possibly damaging Het
Bcl11b C A 12: 107,882,467 (GRCm39) R616L possibly damaging Het
Bean1 G A 8: 104,937,658 (GRCm39) G79D probably damaging Het
Bicra C G 7: 15,706,059 (GRCm39) G1461R probably benign Het
Bptf T C 11: 106,935,466 (GRCm39) T124A probably benign Het
Btnl4 A T 17: 34,691,348 (GRCm39) V312E probably benign Het
Ccdc7a A G 8: 129,670,997 (GRCm39) M503T unknown Het
Celf5 T C 10: 81,318,357 (GRCm39) E28G probably damaging Het
Cilp2 G A 8: 70,336,040 (GRCm39) L350F probably damaging Het
Clec4a2 T C 6: 123,119,411 (GRCm39) I245T probably damaging Het
Ctnnal1 A T 4: 56,844,544 (GRCm39) V140D probably damaging Het
Dennd4a A C 9: 64,759,852 (GRCm39) H319P probably damaging Het
Dlgap3 G T 4: 127,128,852 (GRCm39) L857F probably null Het
Dnah6 T A 6: 73,189,475 (GRCm39) T58S probably damaging Het
Dnah7a T A 1: 53,557,923 (GRCm39) M2164L probably benign Het
Dspp T A 5: 104,323,476 (GRCm39) H206Q probably benign Het
Dzip1l G A 9: 99,541,727 (GRCm39) V443M possibly damaging Het
Erc2 A G 14: 28,024,948 (GRCm39) H939R possibly damaging Het
Fam149a G T 8: 45,801,583 (GRCm39) H513N probably benign Het
Fam171a2 T C 11: 102,330,543 (GRCm39) T280A possibly damaging Het
Fkbp5 A C 17: 28,634,999 (GRCm39) V170G probably damaging Het
Fnbp4 ACCACCTCCACCTCCACCTCC ACCACCTCCACCTCCACCTCCACCTCC 2: 90,608,159 (GRCm39) probably benign Het
Fzd2 T C 11: 102,495,955 (GRCm39) F133S probably damaging Het
Galm A G 17: 80,445,550 (GRCm39) N100S possibly damaging Het
Gbp2b T A 3: 142,303,920 (GRCm39) I5N possibly damaging Het
Gga2 T C 7: 121,601,369 (GRCm39) R245G probably benign Het
Gm10053 A G 19: 24,853,264 (GRCm39) T50A probably benign Het
Gm1110 T C 9: 26,831,945 (GRCm39) T69A probably benign Het
Heatr5a T C 12: 52,008,326 (GRCm39) S6G probably benign Het
Hmcn1 A G 1: 150,439,355 (GRCm39) S5610P probably damaging Het
Hmgb4 A G 4: 128,154,199 (GRCm39) V123A probably damaging Het
Itgal C A 7: 126,926,936 (GRCm39) Q943K probably benign Het
Jakmip1 C A 5: 37,332,498 (GRCm39) D1059E probably damaging Het
Jazf1 T C 6: 52,870,929 (GRCm39) probably null Het
Kat6a A G 8: 23,425,788 (GRCm39) E1111G possibly damaging Het
Kdm4b C A 17: 56,696,639 (GRCm39) P452T probably benign Het
Krit1 T C 5: 3,862,474 (GRCm39) Y210H probably damaging Het
Krtap6-2 A T 16: 89,216,800 (GRCm39) Y56N unknown Het
Lig1 A T 7: 13,022,647 (GRCm39) D158V probably damaging Het
Lmo1 A T 7: 108,739,873 (GRCm39) L94Q probably benign Het
Lrrc30 A T 17: 67,939,238 (GRCm39) L114H probably damaging Het
Ltn1 T C 16: 87,194,700 (GRCm39) I1400V probably benign Het
Mark3 T C 12: 111,570,961 (GRCm39) I87T probably damaging Het
Mfrp G T 9: 44,016,480 (GRCm39) V392F possibly damaging Het
Mrgprg A G 7: 143,318,872 (GRCm39) L80P probably damaging Het
Ndufaf3 A T 9: 108,444,125 (GRCm39) M1K probably null Het
Nme7 T A 1: 164,208,217 (GRCm39) L295* probably null Het
Noct G T 3: 51,157,151 (GRCm39) C163F probably damaging Het
Or11h4b T A 14: 50,918,281 (GRCm39) Q270L possibly damaging Het
Or13a26 A T 7: 140,284,547 (GRCm39) I128F probably damaging Het
Or4b1 T A 2: 89,979,763 (GRCm39) I196F possibly damaging Het
Or5ak22 T A 2: 85,229,955 (GRCm39) K307N probably damaging Het
Or6c203 T A 10: 129,010,324 (GRCm39) T189S probably damaging Het
Or8g2 A G 9: 39,821,200 (GRCm39) I34V probably benign Het
Patz1 C T 11: 3,248,297 (GRCm39) probably benign Het
Per3 A G 4: 151,097,185 (GRCm39) L780P probably benign Het
Pira1 T G 7: 3,738,509 (GRCm39) E622D probably benign Het
Pla2g4a T C 1: 149,748,441 (GRCm39) M256V possibly damaging Het
Pnliprp1 A G 19: 58,729,532 (GRCm39) K395R probably benign Het
Poc5 G T 13: 96,537,340 (GRCm39) G242V possibly damaging Het
Ppfia4 A G 1: 134,251,873 (GRCm39) S434P possibly damaging Het
Prss42 A G 9: 110,627,897 (GRCm39) N110S probably benign Het
Ralgapb T A 2: 158,274,822 (GRCm39) I241N possibly damaging Het
Rbak A C 5: 143,159,528 (GRCm39) Y508* probably null Het
S1pr2 G T 9: 20,878,845 (GRCm39) R328S possibly damaging Het
Sap130 T C 18: 31,783,565 (GRCm39) M214T probably benign Het
Slc46a1 T A 11: 78,357,337 (GRCm39) V130E probably damaging Het
Smc4 A T 3: 68,925,457 (GRCm39) H343L probably benign Het
Tarbp1 C A 8: 127,184,416 (GRCm39) R500L probably benign Het
Tasor2 A G 13: 3,635,332 (GRCm39) S492P probably benign Het
Tgfbr3 A T 5: 107,362,894 (GRCm39) H39Q probably damaging Het
Tpp2 T C 1: 43,993,819 (GRCm39) S235P probably benign Het
Trbc2 G T 6: 41,523,763 (GRCm39) R33M Het
Trim3 C T 7: 105,268,765 (GRCm39) R63Q probably damaging Het
Ttc28 T C 5: 111,433,350 (GRCm39) V2128A probably benign Het
Ttn C T 2: 76,556,162 (GRCm39) R30281H probably damaging Het
Ttn T A 2: 76,774,483 (GRCm39) Q2187L unknown Het
Ttyh3 T C 5: 140,615,180 (GRCm39) S403G possibly damaging Het
Vmn2r112 A T 17: 22,822,288 (GRCm39) D322V probably benign Het
Wdr38 C T 2: 38,888,352 (GRCm39) probably benign Het
Zbtb8b G A 4: 129,326,562 (GRCm39) T201I 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
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
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'- CCACAGTGCCACTCTGAAAG -3'
(R):5'- TTGATGTACGCTTGTGCACAC -3'

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