Mutagenetix > Incidental Mutation

Incidental Mutation 'R1171:Xrn1'

99425

Institutional Source

Beutler Lab

Gene Symbol

Xrn1

Ensembl Gene

ENSMUSG00000032410

Gene Name

5'-3' exoribonuclease 1

Synonyms

Dhm2, mXrn1

MMRRC Submission

039244-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.932) question?

Stock #

R1171 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

95954760-96057803 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 95991011 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 640 (D640G)

Ref Sequence

ENSEMBL: ENSMUSP00000034981 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000034981
AA Change: D640G

PolyPhen 2 Score 0.468 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: D640G

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
AA Change: D640G

PolyPhen 2 Score 0.176 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: D640G

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: ENSMUST00000187175

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189612

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: 99.6%
3x: 98.6%
10x: 96.2%
20x: 91.6%

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017D01Rik	T	C	19: 11,112,377	Y48C	probably damaging	Het
Acsm5	A	T	7: 119,540,852	E492V	probably damaging	Het
Arid4a	G	A	12: 71,075,338	S509N	probably benign	Het
Atr	T	C	9: 95,907,323	F1511L	probably damaging	Het
BC005561	T	C	5: 104,520,903	V1097A	possibly damaging	Het
Bdkrb2	G	T	12: 105,592,157	R219L	probably benign	Het
Bhmt2	A	T	13: 93,662,329	M328K	probably benign	Het
Btbd3	A	G	2: 138,283,961	D286G	probably benign	Het
Bub1b	T	G	2: 118,606,686	L122V	probably benign	Het
Caml	T	C	13: 55,625,007	S155P	probably damaging	Het
Cfap43	T	C	19: 47,835,711	K74E	probably benign	Het
Chst4	A	G	8: 110,030,623	S120P	probably damaging	Het
Col11a1	A	G	3: 114,066,564	D213G	unknown	Het
Cxcl10	TACTCAC	TACTCACTCAC	5: 92,348,082		probably null	Het
Cxcl10	CAC	CACTAAC	5: 92,348,086		probably null	Het
Cyp26b1	A	T	6: 84,576,671	I167N	possibly damaging	Het
Dchs1	A	G	7: 105,757,714	S2195P	probably benign	Het
Ddx25	T	A	9: 35,546,846	K326*	probably null	Het
Dip2c	A	T	13: 9,493,126	Y36F	possibly damaging	Het
Dock2	T	C	11: 34,695,241	D538G	probably damaging	Het
E4f1	C	T	17: 24,451,549	D55N	probably damaging	Het
Emp1	G	T	6: 135,381,079	W141L	probably damaging	Het
Faim2	T	A	15: 99,500,254	H271L	probably benign	Het
Fbxw9	T	C	8: 85,066,078	M352T	possibly damaging	Het
Fcrls	A	T	3: 87,256,860	F321I	probably benign	Het
Frzb	C	T	2: 80,438,490		probably null	Het
Gal3st1	G	T	11: 3,998,931	K379N	probably damaging	Het
Gm5519	G	A	19: 33,822,972	C22Y	possibly damaging	Het
Gpn3	T	C	5: 122,378,520	F71L	probably benign	Het
H2-M9	A	G	17: 36,641,653	V167A	probably benign	Het
Hars	A	G	18: 36,771,414	F182L	possibly damaging	Het
Hid1	T	C	11: 115,352,717	T502A	probably benign	Het
Hipk3	G	T	2: 104,471,676	T57K	probably benign	Het
Iqsec2	A	G	X: 152,144,731	S87G	probably benign	Het
Itpk1	G	A	12: 102,606,119	L112F	probably damaging	Het
Klk9	T	A	7: 43,794,393	D110E	possibly damaging	Het
Lemd3	A	T	10: 120,949,341	M535K	possibly damaging	Het
Lipg	A	T	18: 74,945,823	S453T	possibly damaging	Het
Lrrc75a	A	T	11: 62,609,243	W150R	probably damaging	Het
Lyg1	T	C	1: 37,947,224	E143G	probably damaging	Het
Map3k1	A	G	13: 111,755,643	V1026A	probably benign	Het
Mgat3	T	A	15: 80,211,637	F222I	probably benign	Het
Mindy4	A	T	6: 55,255,616	N348I	possibly damaging	Het
Myo1b	A	C	1: 51,778,525	F532C	probably damaging	Het
Naif1	T	A	2: 32,452,546	N36K	probably damaging	Het
Nkpd1	C	A	7: 19,524,087	A597E	possibly damaging	Het
Npr2	A	G	4: 43,647,260	D772G	possibly damaging	Het
Olfr2	T	C	7: 107,001,584	N92S	probably benign	Het
Olfr658	T	G	7: 104,644,997	D123A	probably damaging	Het
Pcolce2	A	T	9: 95,694,740	M355L	probably benign	Het
Pdgfra	A	T	5: 75,173,447	I394F	probably damaging	Het
Pdzrn3	G	A	6: 101,150,877	R943C	probably damaging	Het
Pml	A	G	9: 58,234,538	V337A	probably damaging	Het
Pnpla2	T	A	7: 141,458,881	M321K	probably benign	Het
Poln	A	T	5: 34,103,940	N546K	probably damaging	Het
Ppp1r16a	C	T	15: 76,693,669	Q328*	probably null	Het
Prss28	T	A	17: 25,310,055	F123L	possibly damaging	Het
Psg18	A	G	7: 18,346,079	V399A	probably benign	Het
Rab5a	T	C	17: 53,506,415	C212R	probably damaging	Het
Ranbp6	A	T	19: 29,812,279	D224E	probably benign	Het
Recql4	T	C	15: 76,704,039	I1104M	possibly damaging	Het
Rev1	A	T	1: 38,088,500	N226K	possibly damaging	Het
Rhbdl3	T	A	11: 80,353,592	V375E	possibly damaging	Het
Senp6	T	A	9: 80,116,725	N423K	possibly damaging	Het
Sertad2	C	G	11: 20,648,091	L96V	probably benign	Het
Slc33a1	T	A	3: 63,953,894	T296S	probably benign	Het
Smurf2	G	A	11: 106,852,618	P188S	possibly damaging	Het
Spta1	T	A	1: 174,211,614	Y1174*	probably null	Het
Stra6l	A	T	4: 45,864,982	T103S	probably benign	Het
Swt1	C	T	1: 151,405,521	A352T	probably damaging	Het
Tdgf1	C	A	9: 110,943,167	V54L	probably benign	Het
Tigd2	T	A	6: 59,211,376	N409K	possibly damaging	Het
Tlr6	G	T	5: 64,955,250	H105N	probably benign	Het
Tmprss9	A	C	10: 80,879,858	T15P	possibly damaging	Het
Tnik	C	T	3: 28,532,940	T120M	probably damaging	Het
Tnr	T	A	1: 159,858,210	I337N	probably damaging	Het
Top3a	A	G	11: 60,750,593	Y422H	probably benign	Het
Trim67	A	G	8: 124,829,081	N768S	probably damaging	Het
Ttn	A	G	2: 76,705,966	V35016A	probably benign	Het
Utrn	A	C	10: 12,481,308	S312R	probably damaging	Het
Vdac2	A	G	14: 21,837,811	Y62C	probably damaging	Het
Vwa5b2	A	G	16: 20,604,984	T1216A	probably benign	Het
Wfdc16	T	C	2: 164,638,483	K31E	possibly damaging	Het
Wtip	C	T	7: 34,125,496	C221Y	probably damaging	Het
Zdhhc5	T	C	2: 84,692,341	R293G	probably benign	Het
Zfp536	T	C	7: 37,569,634	D119G	probably damaging	Het
Zfp81	T	C	17: 33,335,280	T187A	probably benign	Het
Zfp810	C	T	9: 22,278,826	G262D	possibly damaging	Het
Zfp963	A	C	8: 69,743,019	I203M	possibly damaging	Het
Zfpm2	T	C	15: 41,101,679	M520T	probably damaging	Het
Zswim8	G	A	14: 20,713,113	R360Q	possibly damaging	Het
Zwilch	T	A	9: 64,158,717	H254L	possibly 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
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
R4780:Xrn1	UTSW	9	95974744	intron	probably benign
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

Posted On

2014-01-15