Mutagenetix > Incidental Mutation

Incidental Mutation 'R8865:Xrn1'

675870

Institutional Source

Beutler Lab

Gene Symbol

Xrn1

Ensembl Gene

ENSMUSG00000032410

Gene Name

5'-3' exoribonuclease 1

Synonyms

Dhm2, mXrn1

MMRRC Submission

Accession Numbers

Essential gene?

Probably essential (E-score: 0.932) question?

Stock #

R8865 (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 95991193 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Tyrosine at position 670 (F670Y)

Ref Sequence

ENSEMBL: ENSMUSP00000034981 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000034981
AA Change: F670Y

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: F670Y

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: F670Y

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: F670Y

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

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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

Validation Efficiency

100% (72/72)

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: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts2	T	A	11: 50,781,744	Y606*	probably null	Het
Adgrb1	A	G	15: 74,543,658	I696V	possibly damaging	Het
Ass1	A	G	2: 31,520,395	Q406R	probably benign	Het
Calcoco2	GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC	GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC	11: 96,099,982		probably benign	Het
Ccdc148	T	C	2: 58,829,820	K409R	possibly damaging	Het
Ccnl1	A	T	3: 65,946,848	S451T	probably benign	Het
Cdc123	T	C	2: 5,795,424		probably benign	Het
Cep192	T	C	18: 67,834,632	V729A	probably benign	Het
Chd6	G	A	2: 161,021,069	A444V	probably benign	Het
Chl1	A	G	6: 103,708,861	K898E	probably damaging	Het
Chrng	T	C	1: 87,207,497	V154A	probably damaging	Het
Cog1	T	G	11: 113,658,498	M799R	probably benign	Het
Col4a3	G	A	1: 82,669,762		probably null	Het
Coro6	C	A	11: 77,469,091	T366K	probably damaging	Het
Cwh43	G	A	5: 73,441,359	M640I	probably benign	Het
Cyp2c55	A	G	19: 39,031,434	E272G	probably benign	Het
Cyp4f39	A	G	17: 32,483,297	Y256C	probably damaging	Het
Dbx2	G	A	15: 95,632,400	R229*	probably null	Het
Dcdc2a	C	T	13: 25,202,283	A380V	probably benign	Het
En1	G	T	1: 120,603,000		probably benign	Het
F3	T	A	3: 121,729,411	V90E	probably damaging	Het
Fam171a1	A	G	2: 3,225,903	K691R	probably damaging	Het
Foxp2	C	T	6: 15,415,094	A609V	unknown	Het
Hemgn	A	T	4: 46,396,682	S185T	possibly damaging	Het
Hk1	C	T	10: 62,315,515	D33N	probably benign	Het
Igfbp1	T	A	11: 7,201,929	V244D	probably damaging	Het
Insr	A	T	8: 3,161,358	D1160E	probably damaging	Het
Irs1	A	T	1: 82,288,109	Y795*	probably null	Het
Krtap28-10	T	C	1: 83,042,087	K111E	unknown	Het
Lbx1	T	G	19: 45,235,166	D21A	probably benign	Het
Map6	G	T	7: 99,268,985	A322S	probably benign	Het
Mat1a	T	C	14: 41,121,831	Y336H	probably damaging	Het
Mcf2l	A	G	8: 12,880,003	I8V	probably benign	Het
Med12l	T	C	3: 59,071,882	V276A	probably benign	Het
Mettl17	A	G	14: 51,884,851		probably benign	Het
Mllt1	T	C	17: 56,900,295	D183G	possibly damaging	Het
Msmb	T	A	14: 32,150,260	C69*	probably null	Het
Mterf1a	A	G	5: 3,891,425	S148P	probably damaging	Het
Mybl2	A	G	2: 163,080,733	I583V	probably benign	Het
Nbr1	T	A	11: 101,564,694	D91E	probably benign	Het
Notch3	A	G	17: 32,122,116	Y2221H	probably benign	Het
Npat	C	A	9: 53,570,640	T1216N	probably benign	Het
Olfr1082	C	A	2: 86,594,400	V143F	possibly damaging	Het
Olfr127	T	C	17: 37,904,224	L226P	probably damaging	Het
Olfr137	T	A	17: 38,304,981	H160L	probably damaging	Het
Pawr	T	A	10: 108,382,742	Y170N	probably damaging	Het
Pde12	T	C	14: 26,669,125	D143G	possibly damaging	Het
Phactr2	A	G	10: 13,253,732	I264T	probably benign	Het
Pip5k1b	A	G	19: 24,397,058	L53P	probably damaging	Het
Pknox1	T	C	17: 31,599,546	I251T	probably benign	Het
Plcxd1	A	T	5: 110,101,975		probably benign	Het
Polr3c	C	T	3: 96,715,201		probably benign	Het
Ppil2	T	C	16: 17,097,405	N113S	probably benign	Het
Pramel4	G	C	4: 144,068,482	G483R	probably damaging	Het
Prdm10	T	C	9: 31,327,397	L195P	probably damaging	Het
Prss16	A	T	13: 22,003,005	L465Q	possibly damaging	Het
Psg25	G	T	7: 18,529,594	H101Q	possibly damaging	Het
Pstpip2	A	G	18: 77,846,408	D55G	possibly damaging	Het
Rfc1	A	T	5: 65,278,792	D636E	possibly damaging	Het
Scarf2	G	T	16: 17,803,110	C214F	probably damaging	Het
Sirt4	T	C	5: 115,482,645	E156G	probably damaging	Het
Spag6	C	T	2: 18,734,117	S286L	probably benign	Het
Stx17	T	A	4: 48,183,444	H267Q	unknown	Het
Tekt3	T	C	11: 63,070,232	C76R	probably benign	Het
Tln1	A	T	4: 43,538,281	V1807E	possibly damaging	Het
Tnfrsf21	A	G	17: 43,085,481	D552G	probably damaging	Het
Ttn	C	A	2: 76,730,320	V29246L	possibly damaging	Het
Usp43	C	A	11: 67,898,962	C252F	probably damaging	Het
Vmn2r16	T	C	5: 109,340,044	I261T	probably benign	Het
Vwa5b1	T	C	4: 138,581,219	E769G	probably benign	Het
Zc3h7b	G	A	15: 81,772,480	R166Q	probably benign	Het
Zdhhc14	A	T	17: 5,725,295	Y274F	possibly damaging	Het
Zeb2	T	A	2: 44,996,127	M973L	probably benign	Het
Zfp638	T	C	6: 83,977,053	V1380A	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
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
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'- TTGGCGCGTAGACATAAACAAG -3'
(R):5'- GCTGAATCTGAGTTATGGCAC -3'

Sequencing Primer
(F):5'- GAACAAAATAACCAGGGTTGACC -3'
(R):5'- AACTTGGTAGAGATAAGCAG -3'

Posted On

2021-07-15