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

Dhm2, mXrn1

MMRRC Submission

041993-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.932) question?

Stock #

R4780 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

95954760-96057803 bp(+) (GRCm38)

Type of Mutation

intron

DNA Base Change (assembly)

A to T at 95974744 bp (GRCm38)

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: 138,065,370	N107D	probably benign	Het
4833413E03Rik	A	C	17: 31,558,764		noncoding transcript	Het
4931429L15Rik	G	T	9: 46,308,846	H129Q	possibly damaging	Het
A730018C14Rik	A	G	12: 112,415,635		noncoding transcript	Het
Abcc6	T	A	7: 45,996,691	K791N	probably benign	Het
Adcy4	T	G	14: 55,775,036	Q550P	probably benign	Het
Add3	C	A	19: 53,234,792	A325E	possibly damaging	Het
Agbl4	T	A	4: 111,657,331	I513N	possibly damaging	Het
Agfg1	C	A	1: 82,886,387	T392K	probably damaging	Het
Akna	C	A	4: 63,379,254	M854I	probably benign	Het
Ankrd44	T	C	1: 54,763,757	N194S	probably benign	Het
Anks1b	A	G	10: 89,873,732	K21E	probably damaging	Het
Ap1s3	A	G	1: 79,609,172	F154L	probably benign	Het
Apbb2	T	A	5: 66,362,817	N477I	probably damaging	Het
Apobec3	T	C	15: 79,899,024	C101R	possibly damaging	Het
Arnt	G	T	3: 95,488,385	V410F	probably damaging	Het
Arsg	G	A	11: 109,534,013	R270H	possibly damaging	Het
B3gnt7	T	A	1: 86,305,270	D79E	probably damaging	Het
BC067074	A	G	13: 113,317,858	Y146C	probably damaging	Het
Cd44	G	T	2: 102,861,565	A126D	probably damaging	Het
Cd69	A	G	6: 129,271,355	I56T	probably damaging	Het
Cep120	G	A	18: 53,724,536	P286S	probably benign	Het
Ces2a	T	C	8: 104,737,208	F184S	probably damaging	Het
Chrng	A	G	1: 87,207,524	N185S	probably damaging	Het
Cldn6	A	T	17: 23,681,247	M62L	probably benign	Het
Cntn6	T	A	6: 104,845,784	N765K	probably damaging	Het
Ctnnal1	T	C	4: 56,847,857	D94G	probably damaging	Het
Cyp2c69	T	C	19: 39,877,594	N185S	probably benign	Het
Depdc1a	A	G	3: 159,526,706	N698S	probably benign	Het
Dnah2	A	T	11: 69,473,871	I1986N	probably damaging	Het
Dnah7b	A	G	1: 46,353,014	E3845G	probably benign	Het
Dpysl3	C	T	18: 43,354,802	V159I	probably benign	Het
Dync1h1	T	C	12: 110,661,196	Y4047H	probably damaging	Het
E130308A19Rik	C	T	4: 59,691,057	P297L	probably benign	Het
E2f5	A	G	3: 14,587,319	T72A	probably benign	Het
Ephb6	G	T	6: 41,616,139	R437L	probably damaging	Het
Erbb4	T	C	1: 68,298,314	H615R	probably damaging	Het
Erbin	T	C	13: 103,884,206	T82A	probably damaging	Het
Eri2	T	C	7: 119,785,680	N533D	probably benign	Het
Fkbp9	A	G	6: 56,850,716	N174S	probably damaging	Het
Fsbp	C	T	4: 11,583,709	T136I	possibly damaging	Het
Fubp3	C	A	2: 31,583,211	D47E	probably damaging	Het
Gm21850	G	A	2: 154,056,499		noncoding transcript	Het
Gm5141	T	A	13: 62,774,950	Y135F	unknown	Het
Gm7353	T	A	7: 3,110,725		noncoding transcript	Het
Gm8765	C	A	13: 50,701,080	S251R	probably damaging	Het
Gm9925	T	C	18: 74,065,273		probably benign	Het
Greb1l	T	C	18: 10,541,792	S1180P	probably benign	Het
Hist1h2ag	G	A	13: 22,042,909	Q7*	probably null	Het
Kiz	A	G	2: 146,889,246	T192A	possibly damaging	Het
Klhl24	T	A	16: 20,106,958	C79S	probably damaging	Het
Map3k11	A	G	19: 5,690,938	H231R	probably damaging	Het
Mbd4	C	A	6: 115,849,384	R194S	probably benign	Het
Mettl21e	A	C	1: 44,211,143	S34R	probably benign	Het
Mrps5	T	C	2: 127,598,241	V245A	probably benign	Het
Mtrf1	T	C	14: 79,401,688	Y87H	probably benign	Het
Myh15	T	C	16: 49,120,057	I790T	probably benign	Het
Necab1	T	G	4: 14,989,248	I176L	probably benign	Het
Nfkb2	T	A	19: 46,309,922	L555Q	probably damaging	Het
Nhlrc3	T	A	3: 53,458,567	E168D	probably benign	Het
Nlrp5	T	A	7: 23,435,778	C949S	probably damaging	Het
Nup155	C	A	15: 8,157,703	A1372E	probably benign	Het
Nynrin	G	T	14: 55,863,263	R170L	probably damaging	Het
Ogfrl1	T	A	1: 23,370,321	N275Y	probably damaging	Het
Olfr1110	C	T	2: 87,135,877	S148N	probably damaging	Het
Olfr1302	A	G	2: 111,780,845	D175G	probably damaging	Het
Olfr1480	A	G	19: 13,529,955	N138S	probably benign	Het
Olfr912	A	G	9: 38,581,969	T231A	possibly damaging	Het
Olr1	A	T	6: 129,488,876	S56T	probably damaging	Het
Ovol2	A	T	2: 144,331,283		probably benign	Het
Pcdha6	A	T	18: 36,969,853	I700F	probably damaging	Het
Prkcz	C	T	4: 155,289,702	V86M	probably damaging	Het
Ptpn13	A	G	5: 103,586,773	T2124A	probably benign	Het
Ranbp3	G	T	17: 56,673,346		probably benign	Het
Rapgef2	A	G	3: 79,169,769		probably benign	Het
Rbl1	A	G	2: 157,174,804	V625A	probably benign	Het
Rbm38	G	T	2: 173,022,151	G38C	probably damaging	Het
Reg1	T	G	6: 78,426,350	F7C	possibly damaging	Het
Retnlg	A	T	16: 48,874,334	Q115L	possibly damaging	Het
Rhobtb1	G	A	10: 69,270,153	V183I	probably benign	Het
Rims1	T	C	1: 22,291,105	Q1186R	probably damaging	Het
Ryr1	A	G	7: 29,095,097	F1246L	possibly damaging	Het
Samm50	A	G	15: 84,210,610	N401S	possibly damaging	Het
Scn3a	T	A	2: 65,506,193	I690F	probably damaging	Het
Sdk1	A	G	5: 141,959,238	D304G	probably damaging	Het
Skint6	T	C	4: 113,236,397	Y183C	probably damaging	Het
Slamf1	A	T	1: 171,777,261	T200S	probably benign	Het
Slc34a2	C	T	5: 53,069,451	R639C	probably damaging	Het
Smap1	A	T	1: 23,853,436	M149K	probably benign	Het
Sorcs1	T	C	19: 50,143,981		probably benign	Het
Sp140	T	A	1: 85,610,828	D95E	possibly damaging	Het
Spata13	G	A	14: 60,753,907	W366*	probably null	Het
Strip1	G	A	3: 107,626,998	T136I	probably benign	Het
Tacr1	A	T	6: 82,557,072	T360S	probably benign	Het
Tbc1d14	T	A	5: 36,571,256		probably benign	Het
Tcaf2	T	C	6: 42,628,062	Y596C	probably damaging	Het
Tspoap1	C	T	11: 87,778,443	T1454I	possibly damaging	Het
Ttc30a2	A	C	2: 75,977,576	C197W	probably benign	Het
Ttn	A	T	2: 76,914,583	M5374K	probably benign	Het
Uts2r	G	A	11: 121,160,879	V190I	possibly damaging	Het
Vmn1r181	A	G	7: 23,984,583	T158A	possibly damaging	Het
Wdr35	A	T	12: 9,018,150	T778S	probably benign	Het
Zfp35	A	T	18: 24,003,269	K223N	probably damaging	Het
Zfp764	T	C	7: 127,404,771	Q396R	probably benign	Het
Zfyve1	T	C	12: 83,558,647	Y11C	probably damaging	Het

Other mutations in Xrn1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00487:Xrn1	APN	9	96038949	missense	probably benign	0.05
IGL00778:Xrn1	APN	9	95973447	splice site	probably benign
IGL01936:Xrn1	APN	9	96048344	missense	probably damaging	0.98
IGL01983:Xrn1	APN	9	95973368	critical splice donor site	probably null
IGL02106:Xrn1	APN	9	95977805	missense	probably benign	0.28
IGL02330:Xrn1	APN	9	95973348	nonsense	probably null
IGL02338:Xrn1	APN	9	95977827	missense	probably benign	0.42
IGL02830:Xrn1	APN	9	96018181	critical splice donor site	probably null
R0063:Xrn1	UTSW	9	95969535	missense	probably damaging	1.00
R0063:Xrn1	UTSW	9	95969535	missense	probably damaging	1.00
R0467:Xrn1	UTSW	9	96024191	missense	probably damaging	1.00
R0508:Xrn1	UTSW	9	96051736	missense	probably benign	0.00
R0605:Xrn1	UTSW	9	96026877	nonsense	probably null
R0670:Xrn1	UTSW	9	95991056	missense	probably damaging	1.00
R0691:Xrn1	UTSW	9	95973539	missense	probably damaging	0.96
R0781:Xrn1	UTSW	9	95991269	missense	probably benign	0.00
R0947:Xrn1	UTSW	9	95998263	missense	possibly damaging	0.60
R1034:Xrn1	UTSW	9	96039737	missense	probably damaging	1.00
R1124:Xrn1	UTSW	9	96003865	missense	probably benign	0.02
R1171:Xrn1	UTSW	9	95991011	missense	possibly damaging	0.47
R1199:Xrn1	UTSW	9	95981761	splice site	probably benign
R1609:Xrn1	UTSW	9	95974893	missense	probably benign	0.03
R1921:Xrn1	UTSW	9	95999497	missense	probably benign	0.04
R1953:Xrn1	UTSW	9	96024221	critical splice donor site	probably null
R2000:Xrn1	UTSW	9	96045563	nonsense	probably null
R2109:Xrn1	UTSW	9	95979220	missense	probably benign	0.13
R2111:Xrn1	UTSW	9	96039832	missense	probably benign	0.03
R2164:Xrn1	UTSW	9	96006820	missense	possibly damaging	0.95
R2266:Xrn1	UTSW	9	96006712	missense	possibly damaging	0.64
R3754:Xrn1	UTSW	9	95967788	missense	probably damaging	1.00
R3783:Xrn1	UTSW	9	95969285	missense	probably benign	0.10
R3921:Xrn1	UTSW	9	95969284	missense	probably benign	0.01
R3929:Xrn1	UTSW	9	95988873	missense	possibly damaging	0.89
R4011:Xrn1	UTSW	9	95985225	nonsense	probably null
R4082:Xrn1	UTSW	9	95981920	missense	probably benign	0.02
R4455:Xrn1	UTSW	9	95973645	intron	probably benign
R4736:Xrn1	UTSW	9	96033636	missense	probably damaging	1.00
R4756:Xrn1	UTSW	9	96039809	missense	probably benign	0.00
R5152:Xrn1	UTSW	9	95964065	missense	probably benign	0.40
R5261:Xrn1	UTSW	9	96045543	missense	probably benign	0.00
R5741:Xrn1	UTSW	9	96045551	missense	probably benign	0.24
R6108:Xrn1	UTSW	9	95974427	missense	possibly damaging	0.91
R6127:Xrn1	UTSW	9	95969489	missense	probably damaging	0.99
R6268:Xrn1	UTSW	9	95964014	missense	probably damaging	1.00
R6418:Xrn1	UTSW	9	96033710	splice site	probably null
R7002:Xrn1	UTSW	9	96047790	missense	probably benign	0.00
R7067:Xrn1	UTSW	9	95969512	missense	probably damaging	0.98
R7155:Xrn1	UTSW	9	95979145	missense	possibly damaging	0.92
R7439:Xrn1	UTSW	9	96051629	missense	probably benign
R7447:Xrn1	UTSW	9	96045494	missense	probably benign
R7454:Xrn1	UTSW	9	96048358	missense	probably benign	0.03
R7473:Xrn1	UTSW	9	95979141	missense	probably benign	0.07
R7561:Xrn1	UTSW	9	95999458	missense	probably benign	0.18
R7580:Xrn1	UTSW	9	96011679	missense	not run
R7642:Xrn1	UTSW	9	96021853	missense	possibly damaging	0.95
R7763:Xrn1	UTSW	9	95998348	critical splice donor site	probably null
R8225:Xrn1	UTSW	9	96035667	missense	probably benign
R8372:Xrn1	UTSW	9	96024113	missense	probably benign	0.42
R8516:Xrn1	UTSW	9	96048391	nonsense	probably null
R8710:Xrn1	UTSW	9	96002232	missense
R8850:Xrn1	UTSW	9	96038679	missense	probably benign
R8865:Xrn1	UTSW	9	95991193	missense	probably benign	0.00
R8951:Xrn1	UTSW	9	95988946	missense	probably benign	0.00
R9013:Xrn1	UTSW	9	96038928	missense	probably benign	0.00
R9162:Xrn1	UTSW	9	96033607	missense	probably benign	0.01
R9163:Xrn1	UTSW	9	95998221	missense	probably benign	0.00
R9415:Xrn1	UTSW	9	95969474	missense	probably damaging	1.00
R9438:Xrn1	UTSW	9	96011234	missense	probably benign	0.30
R9544:Xrn1	UTSW	9	96038703	missense	probably benign
R9588:Xrn1	UTSW	9	96038703	missense	probably benign
R9674:Xrn1	UTSW	9	95973592	missense	probably damaging	0.99
R9674:Xrn1	UTSW	9	95973594	missense	possibly damaging	0.65
R9716:Xrn1	UTSW	9	96045579	missense	possibly damaging	0.71
Z1176:Xrn1	UTSW	9	95964190	missense	probably damaging	1.00
Z1177:Xrn1	UTSW	9	95991005	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