Mutagenetix > Incidental Mutation

Incidental Mutation 'R4011:Xrn1'

311700

Institutional Source

Beutler Lab

Gene Symbol

Xrn1

Ensembl Gene

ENSMUSG00000032410

Gene Name

5'-3' exoribonuclease 1

Synonyms

mXrn1, Dhm2

MMRRC Submission

040948-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.917) question?

Stock #

R4011 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

95836813-95939856 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

T to A at 95867278 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Stop codon at position 545 (Y545*)

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 null
Transcript: ENSMUST00000034981
AA Change: Y545*

SMART Domains

Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: Y545*

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: Y545*

SMART Domains

Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: Y545*

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 null
Transcript: ENSMUST00000190665
AA Change: Y545*

SMART Domains

Protein: ENSMUSP00000139510
Gene: ENSMUSG00000032410
AA Change: Y545*

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

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 93.7%

Validation Efficiency

100% (43/43)

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: 43 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	G	A	11: 9,572,013 (GRCm39)		probably benign	Het
Acss2	T	A	2: 155,399,548 (GRCm39)	L529Q	probably damaging	Het
Adsl	T	C	15: 80,850,357 (GRCm39)	S359P	probably benign	Het
C1qtnf1	G	A	11: 118,337,365 (GRCm39)	G65D	probably benign	Het
Chd1l	A	T	3: 97,477,718 (GRCm39)	M679K	probably benign	Het
Cspg4	A	G	9: 56,794,601 (GRCm39)	T779A	probably benign	Het
Ddx18	T	C	1: 121,489,810 (GRCm39)	I200V	probably benign	Het
Dnah9	T	A	11: 65,725,290 (GRCm39)	M4288L	probably damaging	Het
F830045P16Rik	A	T	2: 129,305,467 (GRCm39)	N302K	probably damaging	Het
Gas1	T	G	13: 60,323,791 (GRCm39)	D322A	unknown	Het
Gfm2	T	A	13: 97,279,608 (GRCm39)		probably benign	Het
Gm5592	G	T	7: 40,938,934 (GRCm39)	V739L	probably benign	Het
Hbb-bh2	T	A	7: 103,489,416 (GRCm39)	H45L	probably benign	Het
Ifit2	G	T	19: 34,551,445 (GRCm39)	M328I	probably benign	Het
Igdcc4	T	C	9: 65,042,761 (GRCm39)	V1237A	probably benign	Het
Kat2b	G	A	17: 53,951,769 (GRCm39)		probably null	Het
Lmtk2	A	G	5: 144,112,697 (GRCm39)	N1139S	probably benign	Het
Map1a	G	A	2: 121,130,608 (GRCm39)	A475T	probably damaging	Het
Map3k20	G	A	2: 72,214,468 (GRCm39)		probably benign	Het
Mga	T	C	2: 119,762,261 (GRCm39)	V1084A	probably damaging	Het
Msantd5f6	T	C	4: 73,320,047 (GRCm39)	Y244C	probably damaging	Het
Myo3b	A	G	2: 69,926,720 (GRCm39)	I5V	probably benign	Het
Or10a3m	A	T	7: 108,313,366 (GRCm39)	I269L	probably benign	Het
Or10ag56	A	G	2: 87,139,555 (GRCm39)	I141V	probably benign	Het
Or10ag57	A	T	2: 87,218,924 (GRCm39)	I292F	possibly damaging	Het
Or56b1	A	G	7: 104,285,555 (GRCm39)	T225A	probably benign	Het
Or5h24	G	A	16: 58,919,124 (GRCm39)	T77I	unknown	Het
Or5v1	T	C	17: 37,810,382 (GRCm39)	V280A	possibly damaging	Het
Osmr	G	T	15: 6,854,014 (GRCm39)	R565S	probably benign	Het
Pcolce	G	T	5: 137,604,036 (GRCm39)	Q344K	probably benign	Het
Prdm11	A	G	2: 92,843,175 (GRCm39)	F95L	probably damaging	Het
Psd2	C	T	18: 36,120,300 (GRCm39)	T383I	probably benign	Het
Reg3a	G	A	6: 78,360,553 (GRCm39)	D164N	probably damaging	Het
Serpina3a	A	T	12: 104,084,902 (GRCm39)	D99V	probably benign	Het
Sgce	G	T	6: 4,691,563 (GRCm39)	Y301*	probably null	Het
Slc28a3	T	C	13: 58,714,064 (GRCm39)	K434E	probably benign	Het
Slc30a3	A	G	5: 31,244,203 (GRCm39)	F360L	probably damaging	Het
Tdpoz3	A	T	3: 93,733,550 (GRCm39)	Y75F	possibly damaging	Het
Trim65	A	G	11: 116,018,529 (GRCm39)	F249L	probably benign	Het
Tubgcp3	A	T	8: 12,689,634 (GRCm39)	L544*	probably null	Het
Vit	C	T	17: 78,842,121 (GRCm39)		probably benign	Het
Wdfy4	C	A	14: 32,824,637 (GRCm39)		probably benign	Het
Xpo6	T	C	7: 125,739,780 (GRCm39)	K431E	probably benign	Het

Other mutations in Xrn1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00487:Xrn1	APN	9	95,921,002 (GRCm39)	missense	probably benign	0.05
IGL00778:Xrn1	APN	9	95,855,500 (GRCm39)	splice site	probably benign
IGL01936:Xrn1	APN	9	95,930,397 (GRCm39)	missense	probably damaging	0.98
IGL01983:Xrn1	APN	9	95,855,421 (GRCm39)	critical splice donor site	probably null
IGL02106:Xrn1	APN	9	95,859,858 (GRCm39)	missense	probably benign	0.28
IGL02330:Xrn1	APN	9	95,855,401 (GRCm39)	nonsense	probably null
IGL02338:Xrn1	APN	9	95,859,880 (GRCm39)	missense	probably benign	0.42
IGL02830:Xrn1	APN	9	95,900,234 (GRCm39)	critical splice donor site	probably null
R0063:Xrn1	UTSW	9	95,851,588 (GRCm39)	missense	probably damaging	1.00
R0063:Xrn1	UTSW	9	95,851,588 (GRCm39)	missense	probably damaging	1.00
R0467:Xrn1	UTSW	9	95,906,244 (GRCm39)	missense	probably damaging	1.00
R0508:Xrn1	UTSW	9	95,933,789 (GRCm39)	missense	probably benign	0.00
R0605:Xrn1	UTSW	9	95,908,930 (GRCm39)	nonsense	probably null
R0670:Xrn1	UTSW	9	95,873,109 (GRCm39)	missense	probably damaging	1.00
R0691:Xrn1	UTSW	9	95,855,592 (GRCm39)	missense	probably damaging	0.96
R0781:Xrn1	UTSW	9	95,873,322 (GRCm39)	missense	probably benign	0.00
R0947:Xrn1	UTSW	9	95,880,316 (GRCm39)	missense	possibly damaging	0.60
R1034:Xrn1	UTSW	9	95,921,790 (GRCm39)	missense	probably damaging	1.00
R1124:Xrn1	UTSW	9	95,885,918 (GRCm39)	missense	probably benign	0.02
R1171:Xrn1	UTSW	9	95,873,064 (GRCm39)	missense	possibly damaging	0.47
R1199:Xrn1	UTSW	9	95,863,814 (GRCm39)	splice site	probably benign
R1609:Xrn1	UTSW	9	95,856,946 (GRCm39)	missense	probably benign	0.03
R1921:Xrn1	UTSW	9	95,881,550 (GRCm39)	missense	probably benign	0.04
R1953:Xrn1	UTSW	9	95,906,274 (GRCm39)	critical splice donor site	probably null
R2000:Xrn1	UTSW	9	95,927,616 (GRCm39)	nonsense	probably null
R2109:Xrn1	UTSW	9	95,861,273 (GRCm39)	missense	probably benign	0.13
R2111:Xrn1	UTSW	9	95,921,885 (GRCm39)	missense	probably benign	0.03
R2164:Xrn1	UTSW	9	95,888,873 (GRCm39)	missense	possibly damaging	0.95
R2266:Xrn1	UTSW	9	95,888,765 (GRCm39)	missense	possibly damaging	0.64
R3754:Xrn1	UTSW	9	95,849,841 (GRCm39)	missense	probably damaging	1.00
R3783:Xrn1	UTSW	9	95,851,338 (GRCm39)	missense	probably benign	0.10
R3921:Xrn1	UTSW	9	95,851,337 (GRCm39)	missense	probably benign	0.01
R3929:Xrn1	UTSW	9	95,870,926 (GRCm39)	missense	possibly damaging	0.89
R4082:Xrn1	UTSW	9	95,863,973 (GRCm39)	missense	probably benign	0.02
R4455:Xrn1	UTSW	9	95,855,698 (GRCm39)	intron	probably benign
R4736:Xrn1	UTSW	9	95,915,689 (GRCm39)	missense	probably damaging	1.00
R4756:Xrn1	UTSW	9	95,921,862 (GRCm39)	missense	probably benign	0.00
R4780:Xrn1	UTSW	9	95,856,797 (GRCm39)	intron	probably benign
R5152:Xrn1	UTSW	9	95,846,118 (GRCm39)	missense	probably benign	0.40
R5261:Xrn1	UTSW	9	95,927,596 (GRCm39)	missense	probably benign	0.00
R5741:Xrn1	UTSW	9	95,927,604 (GRCm39)	missense	probably benign	0.24
R6108:Xrn1	UTSW	9	95,856,480 (GRCm39)	missense	possibly damaging	0.91
R6127:Xrn1	UTSW	9	95,851,542 (GRCm39)	missense	probably damaging	0.99
R6268:Xrn1	UTSW	9	95,846,067 (GRCm39)	missense	probably damaging	1.00
R6418:Xrn1	UTSW	9	95,915,763 (GRCm39)	splice site	probably null
R7002:Xrn1	UTSW	9	95,929,843 (GRCm39)	missense	probably benign	0.00
R7067:Xrn1	UTSW	9	95,851,565 (GRCm39)	missense	probably damaging	0.98
R7155:Xrn1	UTSW	9	95,861,198 (GRCm39)	missense	possibly damaging	0.92
R7439:Xrn1	UTSW	9	95,933,682 (GRCm39)	missense	probably benign
R7447:Xrn1	UTSW	9	95,927,547 (GRCm39)	missense	probably benign
R7454:Xrn1	UTSW	9	95,930,411 (GRCm39)	missense	probably benign	0.03
R7473:Xrn1	UTSW	9	95,861,194 (GRCm39)	missense	probably benign	0.07
R7561:Xrn1	UTSW	9	95,881,511 (GRCm39)	missense	probably benign	0.18
R7580:Xrn1	UTSW	9	95,893,732 (GRCm39)	missense	not run
R7642:Xrn1	UTSW	9	95,903,906 (GRCm39)	missense	possibly damaging	0.95
R7763:Xrn1	UTSW	9	95,880,401 (GRCm39)	critical splice donor site	probably null
R8225:Xrn1	UTSW	9	95,917,720 (GRCm39)	missense	probably benign
R8372:Xrn1	UTSW	9	95,906,166 (GRCm39)	missense	probably benign	0.42
R8516:Xrn1	UTSW	9	95,930,444 (GRCm39)	nonsense	probably null
R8710:Xrn1	UTSW	9	95,884,285 (GRCm39)	missense
R8850:Xrn1	UTSW	9	95,920,732 (GRCm39)	missense	probably benign
R8865:Xrn1	UTSW	9	95,873,246 (GRCm39)	missense	probably benign	0.00
R8951:Xrn1	UTSW	9	95,870,999 (GRCm39)	missense	probably benign	0.00
R9013:Xrn1	UTSW	9	95,920,981 (GRCm39)	missense	probably benign	0.00
R9162:Xrn1	UTSW	9	95,915,660 (GRCm39)	missense	probably benign	0.01
R9163:Xrn1	UTSW	9	95,880,274 (GRCm39)	missense	probably benign	0.00
R9415:Xrn1	UTSW	9	95,851,527 (GRCm39)	missense	probably damaging	1.00
R9438:Xrn1	UTSW	9	95,893,287 (GRCm39)	missense	probably benign	0.30
R9544:Xrn1	UTSW	9	95,920,756 (GRCm39)	missense	probably benign
R9588:Xrn1	UTSW	9	95,920,756 (GRCm39)	missense	probably benign
R9674:Xrn1	UTSW	9	95,855,647 (GRCm39)	missense	possibly damaging	0.65
R9674:Xrn1	UTSW	9	95,855,645 (GRCm39)	missense	probably damaging	0.99
R9716:Xrn1	UTSW	9	95,927,632 (GRCm39)	missense	possibly damaging	0.71
Z1176:Xrn1	UTSW	9	95,846,243 (GRCm39)	missense	probably damaging	1.00
Z1177:Xrn1	UTSW	9	95,873,058 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- CAACAGTGGAGGCTAAGACC -3'
(R):5'- ACAAGGTGTCTGATGGTATCTG -3'

Sequencing Primer
(F):5'- CAGTGGAGGCTAAGACCAAGTG -3'
(R):5'- CTGATGGTATCTGAGGAATTACACC -3'

Posted On

2015-04-29