Mutagenetix > Incidental Mutations

Incidental Mutation 'R8516:Xrn1'

656159

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: 0.906) question?

Stock #

R8516 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

95954760-96057803 bp(+) (GRCm38)

Type of Mutation

nonsense

DNA Base Change (assembly)

T to A at 96048391 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Stop codon at position 1554 (Y1554*)

Ref Sequence

ENSEMBL: ENSMUSP00000034981 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably null
Transcript: ENSMUST00000034981
AA Change: Y1554*

SMART Domains

Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: Y1554*

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 null
Transcript: ENSMUST00000185633
AA Change: Y1550*

SMART Domains

Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: Y1550*

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.6%

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: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aasdhppt	A	T	9: 4,309,373	S22T	probably benign	Het
Actr8	G	T	14: 29,990,899	A500S	probably benign	Het
Adamtsl1	A	G	4: 86,342,543	Y1005C	probably damaging	Het
Ank3	T	A	10: 69,927,729	Y884*	probably null	Het
Arhgap28	T	C	17: 67,873,073	R306G	probably benign	Het
Atp8a2	A	C	14: 59,691,472	I1044M	probably benign	Het
Bahd1	A	G	2: 118,916,971	Y357C	probably benign	Het
Btd	A	T	14: 31,666,867	T182S	probably damaging	Het
Casc3	C	T	11: 98,822,781	R280C	probably damaging	Het
Cisd2	T	C	3: 135,411,013	T106A	probably damaging	Het
Cldn15	G	T	5: 136,974,696	C184F	probably damaging	Het
Clk4	G	A	11: 51,275,261	R198Q	probably damaging	Het
Coprs	G	T	8: 13,885,065	F163L	probably damaging	Het
Csmd3	G	A	15: 47,629,365	R2216*	probably null	Het
Defb7	A	T	8: 19,497,607	I43F	possibly damaging	Het
Dpp8	C	A	9: 65,078,009	T783K	probably damaging	Het
Eif2s1	G	A	12: 78,881,162	G204D	probably damaging	Het
Elavl4	T	C	4: 110,251,379	N56S	probably damaging	Het
Emilin1	G	A	5: 30,917,171	R252H	probably damaging	Het
Exd1	A	T	2: 119,520,073	L569Q	probably damaging	Het
Gm498	T	A	7: 143,897,274	I342N	probably damaging	Het
Gpn2	C	T	4: 133,584,831	R125C	probably damaging	Het
Gria2	T	C	3: 80,706,987	E582G	probably benign	Het
Hadha	A	T	5: 30,126,584	V458E	probably damaging	Het
Hap1	T	C	11: 100,356,067	K4R	possibly damaging	Het
Hectd4	A	T	5: 121,349,010	H3356L	possibly damaging	Het
Herc2	G	A	7: 56,206,570	V3919I	probably benign	Het
Lgr6	G	T	1: 135,075,283	N76K	probably damaging	Het
Olfr692	A	G	7: 105,368,769	I148V	probably benign	Het
P4ha3	A	G	7: 100,314,662	M462V	probably damaging	Het
Pde3b	A	T	7: 114,526,849	M773L	probably benign	Het
Peak1	T	C	9: 56,260,000	S215G	probably damaging	Het
Pgm5	T	A	19: 24,815,710	M331L	probably benign	Het
Piwil2	A	G	14: 70,420,739	V213A	probably benign	Het
Plch2	T	C	4: 154,986,307	H1205R	probably benign	Het
Pop4	A	T	7: 38,267,402	M85K	probably benign	Het
Ppp3ca	T	A	3: 136,877,768	I212N	probably damaging	Het
Prom1	T	C	5: 44,007,099	K714R	probably benign	Het
Psip1	C	T	4: 83,466,715	G207S	probably benign	Het
Rgs22	A	G	15: 36,010,335	*1259Q	probably null	Het
Scn1a	C	T	2: 66,326,134	G477D	possibly damaging	Het
Sf3b1	T	C	1: 55,012,103	E222G	probably null	Het
Snrpa1	G	A	7: 66,070,633	G195R	probably benign	Het
Spem2	T	C	11: 69,816,895	R415G	possibly damaging	Het
Tmem167	T	A	13: 90,098,396	V13E	probably damaging	Het
Trim2	C	T	3: 84,208,320	A102T	probably damaging	Het
Trim30b	A	G	7: 104,357,404	S82P	probably benign	Het
Uba6	A	C	5: 86,127,748	S760R	possibly damaging	Het
Upf2	T	C	2: 6,018,971	F711L	unknown	Het
Utrn	T	A	10: 12,486,510	D2693V	probably damaging	Het
Vmn1r30	T	G	6: 58,435,124	Y241S	probably damaging	Het
Vmn2r110	A	G	17: 20,574,613	L598P	probably damaging	Het
Wfdc18	T	A	11: 83,709,158	F14Y	probably benign	Het
Wnt10b	A	T	15: 98,772,880	C256S	probably damaging	Het
Zc3h12a	T	A	4: 125,119,839	S411C	probably damaging	Het
Zfp112	G	A	7: 24,123,964	G63E	probably benign	Het
Zfp786	A	T	6: 47,820,543	L487Q	probably damaging	Het
Zfp953	T	A	13: 67,345,355	Y75F	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
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
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'- TTACTGGTACATGGGCCACAG -3'
(R):5'- TGATGTACGCTTGTGCACAC -3'

Sequencing Primer
(F):5'- AGATGTTGTGAGCTGCCCTACAC -3'
(R):5'- ACCTTACCAGTAGGTTGG -3'

Posted On

2020-10-20