Mutagenetix > Incidental Mutation

Incidental Mutation 'R0947:Xrn1'

81674

Institutional Source

Beutler Lab

Gene Symbol

Xrn1

Ensembl Gene

ENSMUSG00000032410

Gene Name

5'-3' exoribonuclease 1

Synonyms

mXrn1, Dhm2

MMRRC Submission

039086-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.917) question?

Stock #

R0947 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

95836813-95939856 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 95880316 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Isoleucine at position 752 (K752I)

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: K752I

PolyPhen 2 Score 0.109 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: K752I

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

possibly damaging
Transcript: ENSMUST00000185633
AA Change: K752I

PolyPhen 2 Score 0.598 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: K752I

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 benign
Transcript: ENSMUST00000190665
AA Change: K644I

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000139510
Gene: ENSMUSG00000032410
AA Change: K644I

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: 99.2%
3x: 98.2%
10x: 95.4%
20x: 89.2%

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: 36 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aldh7a1	A	T	18: 56,693,910 (GRCm39)		probably null	Het
Atm	A	G	9: 53,415,392 (GRCm39)	V833A	probably benign	Het
Atp6v1b1	A	T	6: 83,730,814 (GRCm39)	I180F	probably damaging	Het
Cwf19l2	T	C	9: 3,421,286 (GRCm39)	S188P	probably benign	Het
Gdpd1	T	G	11: 86,928,707 (GRCm39)	E240D	probably benign	Het
Hsh2d	G	A	8: 72,954,304 (GRCm39)	D229N	probably benign	Het
Htt	T	C	5: 35,056,268 (GRCm39)	S2681P	probably damaging	Het
Itgad	A	G	7: 127,774,865 (GRCm39)	D40G	probably benign	Het
Krt18	A	G	15: 101,939,163 (GRCm39)	Y249C	possibly damaging	Het
Lrp2	G	T	2: 69,318,182 (GRCm39)	P2090T	probably damaging	Het
Lrrc32	A	G	7: 98,148,090 (GRCm39)	D290G	probably benign	Het
Man1a	A	T	10: 53,809,619 (GRCm39)	Y486*	probably null	Het
Mcm9	CCTGTCCCTGCTGTCCCTGCTGTCCCTGCTGTCCCTGCTGTCC	CCTGTCCCTGCTGTCCCTGCTGTCCCTGCTGTCC	10: 53,413,597 (GRCm39)		probably benign	Het
Nin	A	T	12: 70,107,960 (GRCm39)	C211S	probably damaging	Het
Npat	A	C	9: 53,481,624 (GRCm39)	I1111L	probably benign	Het
Or5p79	A	G	7: 108,221,879 (GRCm39)	I287V	probably benign	Het
Or9i1b	T	A	19: 13,896,535 (GRCm39)	H50Q	probably benign	Het
Pbx1	A	G	1: 168,030,935 (GRCm39)	S228P	probably damaging	Het
Pcsk7	G	T	9: 45,822,470 (GRCm39)	R230L	probably damaging	Het
Prom2	G	T	2: 127,380,183 (GRCm39)	Q350K	possibly damaging	Het
Racgap1	C	T	15: 99,522,195 (GRCm39)	A458T	possibly damaging	Het
Rsf1	T	A	7: 97,318,985 (GRCm39)	C912S	probably damaging	Het
Setd2	G	A	9: 110,377,579 (GRCm39)	E465K	possibly damaging	Het
Sgk2	T	A	2: 162,848,758 (GRCm39)	D269E	probably benign	Het
Spsb1	T	C	4: 149,991,536 (GRCm39)	T11A	probably benign	Het
Tln2	A	T	9: 67,203,095 (GRCm39)	S509T	probably benign	Het
Trim5	A	T	7: 103,914,958 (GRCm39)	D370E	probably damaging	Het
Ttn	T	A	2: 76,715,574 (GRCm39)		probably benign	Het
Ubr2	C	A	17: 47,252,038 (GRCm39)	G1501C	probably damaging	Het
Ugcg	C	T	4: 59,207,798 (GRCm39)	P46S	probably benign	Het
Vmn2r93	A	T	17: 18,524,343 (GRCm39)	R112S	probably benign	Het
Vps26b	T	C	9: 26,924,077 (GRCm39)	Y222C	probably damaging	Het
Wdr64	T	A	1: 175,603,315 (GRCm39)	Y198N	probably benign	Het
Zbtb14	C	A	17: 69,695,497 (GRCm39)	F398L	probably damaging	Het
Zfp386	T	C	12: 116,023,398 (GRCm39)	I372T	probably benign	Het
Zfp804a	T	C	2: 82,089,062 (GRCm39)	Y964H	possibly 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
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
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'- cgcccggcGTTATTCTCTTAGTTTT -3'
(R):5'- AGTTCCAGCCCTGGCCCTC -3'

Sequencing Primer
(F):5'- TGGGGTTTTGCAATTGTACC -3'
(R):5'- ctcacaatcctcctgcctc -3'

Posted On

2013-11-08