Mutagenetix > Incidental Mutation

Incidental Mutation 'R4780:Xrn1'

366429

Institutional Source

Beutler Lab

Gene Symbol

Xrn1

Ensembl Gene

ENSMUSG00000032410

Gene Name

5'-3' exoribonuclease 1

Synonyms

mXrn1, Dhm2

MMRRC Submission

041993-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.917) question?

Stock #

R4780 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

95836813-95939856 bp(+) (GRCm39)

Type of Mutation

intron

DNA Base Change (assembly)

A to T at 95856797 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000139510 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000034981] [ENSMUST00000185633] [ENSMUST00000190665]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000034981

SMART Domains

Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410

Domain	Start	End	E-Value	Type
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

SMART Domains

Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410

Domain	Start	End	E-Value	Type
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: ENSMUST00000185759

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000187175

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189612

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189806

Predicted Effect

probably benign
Transcript: ENSMUST00000190665

SMART Domains

Protein: ENSMUSP00000139510
Gene: ENSMUSG00000032410

Domain	Start	End	E-Value	Type
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: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.6%

Validation Efficiency

98% (107/109)

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: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	A	G	3: 137,771,131 (GRCm39)	N107D	probably benign	Het
4833413E03Rik	A	C	17: 31,777,738 (GRCm39)		noncoding transcript	Het
4931429L15Rik	G	T	9: 46,220,144 (GRCm39)	H129Q	possibly damaging	Het
A730018C14Rik	A	G	12: 112,382,069 (GRCm39)		noncoding transcript	Het
Abcc6	T	A	7: 45,646,115 (GRCm39)	K791N	probably benign	Het
Adcy4	T	G	14: 56,012,493 (GRCm39)	Q550P	probably benign	Het
Add3	C	A	19: 53,223,223 (GRCm39)	A325E	possibly damaging	Het
Agbl4	T	A	4: 111,514,528 (GRCm39)	I513N	possibly damaging	Het
Agfg1	C	A	1: 82,864,108 (GRCm39)	T392K	probably damaging	Het
Akna	C	A	4: 63,297,491 (GRCm39)	M854I	probably benign	Het
Ankrd44	T	C	1: 54,802,916 (GRCm39)	N194S	probably benign	Het
Anks1b	A	G	10: 89,709,594 (GRCm39)	K21E	probably damaging	Het
Ap1s3	A	G	1: 79,586,889 (GRCm39)	F154L	probably benign	Het
Apbb2	T	A	5: 66,520,160 (GRCm39)	N477I	probably damaging	Het
Apobec3	T	C	15: 79,783,225 (GRCm39)	C101R	possibly damaging	Het
Arnt	G	T	3: 95,395,696 (GRCm39)	V410F	probably damaging	Het
Arsg	G	A	11: 109,424,839 (GRCm39)	R270H	possibly damaging	Het
B3gnt7	T	A	1: 86,232,992 (GRCm39)	D79E	probably damaging	Het
Cd44	G	T	2: 102,691,910 (GRCm39)	A126D	probably damaging	Het
Cd69	A	G	6: 129,248,318 (GRCm39)	I56T	probably damaging	Het
Cep120	G	A	18: 53,857,608 (GRCm39)	P286S	probably benign	Het
Ces2a	T	C	8: 105,463,840 (GRCm39)	F184S	probably damaging	Het
Chrng	A	G	1: 87,135,246 (GRCm39)	N185S	probably damaging	Het
Cldn6	A	T	17: 23,900,221 (GRCm39)	M62L	probably benign	Het
Cntn6	T	A	6: 104,822,745 (GRCm39)	N765K	probably damaging	Het
Cspg4b	A	G	13: 113,454,392 (GRCm39)	Y146C	probably damaging	Het
Ctnnal1	T	C	4: 56,847,857 (GRCm39)	D94G	probably damaging	Het
Cyp2c69	T	C	19: 39,866,038 (GRCm39)	N185S	probably benign	Het
Depdc1a	A	G	3: 159,232,343 (GRCm39)	N698S	probably benign	Het
Dnah2	A	T	11: 69,364,697 (GRCm39)	I1986N	probably damaging	Het
Dnah7b	A	G	1: 46,392,174 (GRCm39)	E3845G	probably benign	Het
Dpysl3	C	T	18: 43,487,867 (GRCm39)	V159I	probably benign	Het
Dync1h1	T	C	12: 110,627,630 (GRCm39)	Y4047H	probably damaging	Het
E130308A19Rik	C	T	4: 59,691,057 (GRCm39)	P297L	probably benign	Het
E2f5	A	G	3: 14,652,379 (GRCm39)	T72A	probably benign	Het
Ephb6	G	T	6: 41,593,073 (GRCm39)	R437L	probably damaging	Het
Erbb4	T	C	1: 68,337,473 (GRCm39)	H615R	probably damaging	Het
Erbin	T	C	13: 104,020,714 (GRCm39)	T82A	probably damaging	Het
Eri2	T	C	7: 119,384,903 (GRCm39)	N533D	probably benign	Het
Fkbp9	A	G	6: 56,827,701 (GRCm39)	N174S	probably damaging	Het
Fsbp	C	T	4: 11,583,709 (GRCm39)	T136I	possibly damaging	Het
Fubp3	C	A	2: 31,473,223 (GRCm39)	D47E	probably damaging	Het
Gm21850	G	A	2: 153,898,419 (GRCm39)		noncoding transcript	Het
Gm5141	T	A	13: 62,922,764 (GRCm39)	Y135F	unknown	Het
Gm7353	T	A	7: 3,160,725 (GRCm39)		noncoding transcript	Het
Gm9925	T	C	18: 74,198,344 (GRCm39)		probably benign	Het
Greb1l	T	C	18: 10,541,792 (GRCm39)	S1180P	probably benign	Het
H2ac11	G	A	13: 22,227,079 (GRCm39)	Q7*	probably null	Het
Ift70a2	A	C	2: 75,807,920 (GRCm39)	C197W	probably benign	Het
Kiz	A	G	2: 146,731,166 (GRCm39)	T192A	possibly damaging	Het
Klhl24	T	A	16: 19,925,708 (GRCm39)	C79S	probably damaging	Het
Map3k11	A	G	19: 5,740,966 (GRCm39)	H231R	probably damaging	Het
Mbd4	C	A	6: 115,826,345 (GRCm39)	R194S	probably benign	Het
Mettl21e	A	C	1: 44,250,303 (GRCm39)	S34R	probably benign	Het
Mrps5	T	C	2: 127,440,161 (GRCm39)	V245A	probably benign	Het
Mtrf1	T	C	14: 79,639,128 (GRCm39)	Y87H	probably benign	Het
Myh15	T	C	16: 48,940,420 (GRCm39)	I790T	probably benign	Het
Necab1	T	G	4: 14,989,248 (GRCm39)	I176L	probably benign	Het
Nfkb2	T	A	19: 46,298,361 (GRCm39)	L555Q	probably damaging	Het
Nhlrc3	T	A	3: 53,365,988 (GRCm39)	E168D	probably benign	Het
Nlrp5	T	A	7: 23,135,203 (GRCm39)	C949S	probably damaging	Het
Nup155	C	A	15: 8,187,187 (GRCm39)	A1372E	probably benign	Het
Nynrin	G	T	14: 56,100,720 (GRCm39)	R170L	probably damaging	Het
Ogfrl1	T	A	1: 23,409,402 (GRCm39)	N275Y	probably damaging	Het
Olr1	A	T	6: 129,465,839 (GRCm39)	S56T	probably damaging	Het
Or4k52	A	G	2: 111,611,190 (GRCm39)	D175G	probably damaging	Het
Or5aq1	C	T	2: 86,966,221 (GRCm39)	S148N	probably damaging	Het
Or5b121	A	G	19: 13,507,319 (GRCm39)	N138S	probably benign	Het
Or8b48	A	G	9: 38,493,265 (GRCm39)	T231A	possibly damaging	Het
Ovol2	A	T	2: 144,173,203 (GRCm39)		probably benign	Het
Pcdha6	A	T	18: 37,102,906 (GRCm39)	I700F	probably damaging	Het
Prkcz	C	T	4: 155,374,159 (GRCm39)	V86M	probably damaging	Het
Ptpn13	A	G	5: 103,734,639 (GRCm39)	T2124A	probably benign	Het
Ranbp3	G	T	17: 56,980,346 (GRCm39)		probably benign	Het
Rapgef2	A	G	3: 79,077,076 (GRCm39)		probably benign	Het
Rbl1	A	G	2: 157,016,724 (GRCm39)	V625A	probably benign	Het
Rbm38	G	T	2: 172,863,944 (GRCm39)	G38C	probably damaging	Het
Reg1	T	G	6: 78,403,333 (GRCm39)	F7C	possibly damaging	Het
Retnlg	A	T	16: 48,694,697 (GRCm39)	Q115L	possibly damaging	Het
Rhobtb1	G	A	10: 69,105,983 (GRCm39)	V183I	probably benign	Het
Rims1	T	C	1: 22,361,329 (GRCm39)	Q1186R	probably damaging	Het
Ryr1	A	G	7: 28,794,522 (GRCm39)	F1246L	possibly damaging	Het
Samm50	A	G	15: 84,094,811 (GRCm39)	N401S	possibly damaging	Het
Scn3a	T	A	2: 65,336,537 (GRCm39)	I690F	probably damaging	Het
Sdk1	A	G	5: 141,944,993 (GRCm39)	D304G	probably damaging	Het
Skint6	T	C	4: 113,093,594 (GRCm39)	Y183C	probably damaging	Het
Slamf1	A	T	1: 171,604,829 (GRCm39)	T200S	probably benign	Het
Slc34a2	C	T	5: 53,226,793 (GRCm39)	R639C	probably damaging	Het
Smap1	A	T	1: 23,892,517 (GRCm39)	M149K	probably benign	Het
Sorcs1	T	C	19: 50,132,419 (GRCm39)		probably benign	Het
Sp140	T	A	1: 85,538,549 (GRCm39)	D95E	possibly damaging	Het
Spata13	G	A	14: 60,991,356 (GRCm39)	W366*	probably null	Het
Spata31e4	C	A	13: 50,855,116 (GRCm39)	S251R	probably damaging	Het
Strip1	G	A	3: 107,534,314 (GRCm39)	T136I	probably benign	Het
Tacr1	A	T	6: 82,534,053 (GRCm39)	T360S	probably benign	Het
Tbc1d14	T	A	5: 36,728,600 (GRCm39)		probably benign	Het
Tcaf2	T	C	6: 42,604,996 (GRCm39)	Y596C	probably damaging	Het
Tspoap1	C	T	11: 87,669,269 (GRCm39)	T1454I	possibly damaging	Het
Ttn	A	T	2: 76,744,927 (GRCm39)	M5374K	probably benign	Het
Uts2r	G	A	11: 121,051,705 (GRCm39)	V190I	possibly damaging	Het
Vmn1r181	A	G	7: 23,684,008 (GRCm39)	T158A	possibly damaging	Het
Wdr35	A	T	12: 9,068,150 (GRCm39)	T778S	probably benign	Het
Zfp35	A	T	18: 24,136,326 (GRCm39)	K223N	probably damaging	Het
Zfp764	T	C	7: 127,003,943 (GRCm39)	Q396R	probably benign	Het
Zfyve1	T	C	12: 83,605,421 (GRCm39)	Y11C	probably damaging	Het

Other mutations in Xrn1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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'- GGTCGCTGTAAATGGTCATTAAC -3'
(R):5'- AAGAGCCCTGAAGCTGATGG -3'

Sequencing Primer
(F):5'- ACCAGAAAAGACAGTTTTGTAGC -3'
(R):5'- GCTGATGGCTCACCTTCG -3'

Posted On

2015-12-21