Mutagenetix > Incidental Mutation

Incidental Mutation 'R1609:Xrn1'

176682

Institutional Source

Beutler Lab

Gene Symbol

Xrn1

Ensembl Gene

ENSMUSG00000032410

Gene Name

5'-3' exoribonuclease 1

Synonyms

mXrn1, Dhm2

MMRRC Submission

039646-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.917) question?

Stock #

R1609 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

95836813-95939856 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 95856946 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Asparagine at position 389 (K389N)

Ref Sequence

ENSEMBL: ENSMUSP00000140278 (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: K389N

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: K389N

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: K389N

PolyPhen 2 Score 0.028 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: K389N

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: ENSMUST00000185759

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000187175

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189612

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189806

Predicted Effect

probably benign
Transcript: ENSMUST00000190665
AA Change: K389N

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000139510
Gene: ENSMUSG00000032410
AA Change: K389N

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

0.0898

Coding Region Coverage

1x: 98.9%
3x: 98.0%
10x: 95.1%
20x: 88.1%

Validation Efficiency

96% (49/51)

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: 38 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acot2	C	T	12: 84,039,630 (GRCm39)	R380C	possibly damaging	Het
Allc	A	T	12: 28,603,993 (GRCm39)	D363E	probably damaging	Het
Anxa2	TCCC	TCC	9: 69,397,036 (GRCm39)		probably null	Het
App	C	A	16: 84,876,837 (GRCm39)	V185L	probably damaging	Het
Atp5if1	T	C	4: 132,258,078 (GRCm39)	D47G	probably benign	Het
Auh	G	A	13: 52,989,532 (GRCm39)	P308L	probably benign	Het
Cbr4	T	A	8: 61,956,192 (GRCm39)	Y220N	probably damaging	Het
Ccdc6	C	A	10: 70,002,877 (GRCm39)	Q203K	probably damaging	Het
Cntnap2	T	C	6: 45,992,264 (GRCm39)	V397A	probably benign	Het
Dmxl2	A	G	9: 54,316,547 (GRCm39)	I1613T	possibly damaging	Het
Dnah14	T	C	1: 181,577,742 (GRCm39)	S3020P	probably damaging	Het
Dnah7b	T	C	1: 46,392,126 (GRCm39)	L3829P	probably damaging	Het
Fbxw25	C	T	9: 109,492,578 (GRCm39)	C53Y	probably benign	Het
Fndc1	G	T	17: 7,991,598 (GRCm39)	H699Q	unknown	Het
Gnaq	G	A	19: 16,360,618 (GRCm39)	V314M	possibly damaging	Het
Gpr158	A	G	2: 21,788,104 (GRCm39)	T582A	possibly damaging	Het
Mapk1	T	C	16: 16,856,170 (GRCm39)		probably benign	Het
Med1	T	A	11: 98,051,996 (GRCm39)	H456L	possibly damaging	Het
Myo6	G	A	9: 80,195,499 (GRCm39)		probably null	Het
Nipbl	A	G	15: 8,396,148 (GRCm39)	Y142H	probably damaging	Het
Or4c113	A	T	2: 88,885,688 (GRCm39)	F27L	probably benign	Het
Or8k24	A	G	2: 86,215,838 (GRCm39)	I308T	probably benign	Het
Or8k33	A	C	2: 86,383,949 (GRCm39)	V173G	probably damaging	Het
Pgbd5	T	C	8: 125,160,750 (GRCm39)	D39G	probably benign	Het
Pnisr	G	T	4: 21,871,440 (GRCm39)	G387*	probably null	Het
Pnpla6	T	C	8: 3,567,135 (GRCm39)	L61P	probably damaging	Het
Prkra	A	T	2: 76,463,936 (GRCm39)	I242N	probably benign	Het
Rp1	A	G	1: 4,419,424 (GRCm39)	S563P	probably damaging	Het
Rtp3	A	G	9: 110,815,085 (GRCm39)		probably benign	Het
Sema3d	A	G	5: 12,591,023 (GRCm39)	T301A	probably damaging	Het
Setmar	A	G	6: 108,053,076 (GRCm39)	D190G	probably benign	Het
Sf3b2	A	G	19: 5,345,061 (GRCm39)		probably benign	Het
Taf4b	A	G	18: 14,968,938 (GRCm39)	K692E	probably damaging	Het
Tktl2	A	G	8: 66,965,504 (GRCm39)	E354G	probably benign	Het
Tspan4	A	G	7: 141,071,557 (GRCm39)	T135A	probably damaging	Het
Vmn1r22	G	T	6: 57,877,733 (GRCm39)	Y81*	probably null	Het
Vmn2r31	T	C	7: 7,387,888 (GRCm39)	E561G	probably damaging	Het
Zfp277	A	T	12: 40,378,719 (GRCm39)	N379K	probably damaging	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
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
R4011:Xrn1	UTSW	9	95,867,278 (GRCm39)	nonsense	probably null
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'- TGTTAATGGTTGGAAATGTGGAAGCCT -3'
(R):5'- GCCCCTGAAACCTAAGGAAAATGAAGAA -3'

Sequencing Primer
(F):5'- ACCTCGATTTGAGAGATACCTTGTG -3'
(R):5'- GTTTTACTGCTACAGTT -3'

Posted On

2014-04-24