Mutagenetix > Incidental Mutations

Incidental Mutation 'R6268:Xrn1'

507166

Institutional Source

Beutler Lab

Gene Symbol

Xrn1

Ensembl Gene

ENSMUSG00000032410

Gene Name

5'-3' exoribonuclease 1

Synonyms

Dhm2, mXrn1

MMRRC Submission

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.870) question?

Stock #

R6268 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

95954760-96057803 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 95964014 bp

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Lysine at position 40 (I40K)

Ref Sequence

ENSEMBL: ENSMUSP00000139510 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000034981] [ENSMUST00000185633] [ENSMUST00000189106] [ENSMUST00000190665]

Predicted Effect

probably damaging
Transcript: ENSMUST00000034981
AA Change: I40K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: I40K

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

noncoding transcript
Transcript: ENSMUST00000180727

Predicted Effect

probably damaging
Transcript: ENSMUST00000185633
AA Change: I40K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: I40K

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

probably benign
Transcript: ENSMUST00000189106

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189612

Predicted Effect

probably damaging
Transcript: ENSMUST00000190665
AA Change: I40K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000139510
Gene: ENSMUSG00000032410
AA Change: I40K

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: 99.9%
3x: 99.6%
10x: 98.3%
20x: 95.5%

Validation Efficiency

99% (68/69)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921504E06Rik	A	G	2: 19,540,408	I78T	probably benign	Het
Afg3l1	A	T	8: 123,492,926	I398F	probably damaging	Het
Ahctf1	T	C	1: 179,763,483	H1244R	probably benign	Het
Ank1	A	T	8: 23,109,671	K797N	probably damaging	Het
Anxa6	G	T	11: 54,987,077		probably null	Het
Ap1b1	T	A	11: 5,019,493	V310E	probably damaging	Het
C2cd2l	T	C	9: 44,317,666	I123V	probably damaging	Het
Cars2	TCCCC	TCCC	8: 11,529,599		probably null	Het
Cfap54	T	A	10: 93,038,909	I542F	probably damaging	Het
Cfap57	G	T	4: 118,569,451	Y1100*	probably null	Het
Coq9	A	G	8: 94,850,234	E158G	probably benign	Het
Cox15	A	T	19: 43,739,926	W303R	possibly damaging	Het
Cpa5	A	G	6: 30,615,173	Y103C	probably damaging	Het
Crygn	A	T	5: 24,756,191	V39E	probably damaging	Het
Csf1	G	T	3: 107,747,157	S132R	possibly damaging	Het
Dapk1	G	A	13: 60,761,766	V1398M	possibly damaging	Het
Degs2	C	A	12: 108,692,580	V47L	probably damaging	Het
Dock5	C	A	14: 67,790,275	E1057*	probably null	Het
Doxl2	T	A	6: 48,977,682	Y585N	probably benign	Het
Dsg1b	C	A	18: 20,388,163	Q26K	probably benign	Het
Fam181a	T	C	12: 103,316,544	V236A	possibly damaging	Het
Fam78b	C	A	1: 167,078,553	P94T	probably damaging	Het
Fbxw25	T	G	9: 109,654,650	T165P	probably damaging	Het
Flg	C	A	3: 93,288,175		probably benign	Het
Frrs1	G	T	3: 116,903,099	V573F	probably damaging	Het
Gm7298	A	G	6: 121,779,073	T964A	possibly damaging	Het
Hoxd9	G	T	2: 74,698,089	V12L	probably damaging	Het
Ikbkap	T	C	4: 56,762,305	Y1098C	probably damaging	Het
Kcnt1	A	G	2: 25,903,597		probably null	Het
Klhl3	G	T	13: 58,013,842	R480S	probably damaging	Het
Klhl36	A	G	8: 119,870,667	D369G	probably damaging	Het
Lama3	T	A	18: 12,524,737	N303K	probably damaging	Het
Lhcgr	T	C	17: 88,742,704	T465A	probably damaging	Het
Llgl1	T	C	11: 60,712,163	V888A	probably benign	Het
Lrp1b	T	A	2: 40,821,717	T3164S	probably benign	Het
Mmp3	T	G	9: 7,447,622	D202E	possibly damaging	Het
Mocs1	C	A	17: 49,435,155	T104K	probably damaging	Het
Mrpl42	A	T	10: 95,496,707		probably null	Het
Mtch2	T	C	2: 90,863,648	C279R	probably benign	Het
Muc4	A	T	16: 32,768,767	D2836V	probably damaging	Het
Myh7	T	C	14: 54,989,284	E370G	probably benign	Het
Naa11	A	G	5: 97,392,210	Y30H	probably damaging	Het
Ntng1	T	C	3: 109,935,035	T141A	probably damaging	Het
Olfr1499	A	T	19: 13,815,307	Y94*	probably null	Het
Olfr196	A	C	16: 59,167,293		probably null	Het
Olfr251	T	C	9: 38,378,088	I69T	probably benign	Het
Pcdha12	G	A	18: 37,022,424	C732Y	possibly damaging	Het
Plekhm2	G	A	4: 141,632,341	Q392*	probably null	Het
Prr22	G	A	17: 56,771,587	V247M	probably damaging	Het
Rapgef6	T	A	11: 54,649,247	L716Q	probably damaging	Het
Rasgrp4	G	A	7: 29,143,068	V246I	probably damaging	Het
Rhbdd2	C	T	5: 135,643,260	T323I	probably benign	Het
Rsf1	CG	CGACGGCGGTG	7: 97,579,908		probably benign	Homo
Scgb2b20	A	T	7: 33,364,548	I99K	possibly damaging	Het
Scyl3	C	T	1: 163,946,217	R324*	probably null	Het
Slc23a1	T	C	18: 35,619,571	Y551C	probably damaging	Het
Slc5a5	A	T	8: 70,888,620	S358R	probably damaging	Het
Sorcs3	T	A	19: 48,790,166	N1007K	probably damaging	Het
Stxbp4	T	A	11: 90,540,201	K428*	probably null	Het
Tmem63c	T	A	12: 87,081,953	I584N	probably damaging	Het
Traf3ip3	C	T	1: 193,198,036		probably benign	Het
Trgv2	G	A	13: 19,336,831	T31I	probably benign	Het
Ttll3	C	T	6: 113,392,563	R23C	probably benign	Het
Ugt2a3	A	C	5: 87,329,613	L309R	probably damaging	Het
Urb1	A	G	16: 90,753,919	M2015T	probably benign	Het
Vmn2r14	A	C	5: 109,221,417	S97A	possibly damaging	Het
Vps13c	C	A	9: 67,951,449	T2727K	probably benign	Het
Zc3h11a	A	G	1: 133,624,557	V604A	probably benign	Het
Zfp410	G	A	12: 84,331,838	R259H	probably benign	Het
Zfp748	A	G	13: 67,542,586	V185A	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
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
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
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
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'- ACCTCCTTTATTCGACGGTG -3'
(R):5'- GCATGAACGAAGATGCACTG -3'

Sequencing Primer
(F):5'- ATGCAGGTAGTTGTACACAGCCTC -3'
(R):5'- CGAAGATGCACTGTATTTTGTCGAC -3'

Posted On

2018-03-15