Incidental Mutation 'IGL02106:Xrn1'
| ID |
280001 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Xrn1
|
| Ensembl Gene |
ENSMUSG00000032410 |
| Gene Name |
5'-3' exoribonuclease 1 |
| Synonyms |
mXrn1, Dhm2 |
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.917)
|
| Stock # |
IGL02106
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
9 |
| Chromosomal Location |
95836813-95939856 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 95859858 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Lysine
at position 417
(E417K)
|
| 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 benign
Transcript: ENSMUST00000034981
AA Change: E417K
PolyPhen 2
Score 0.137 (Sensitivity: 0.92; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000034981
Gene: ENSMUSG00000032410
AA Change: E417K
| 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: E417K
PolyPhen 2
Score 0.064 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000140278
Gene: ENSMUSG00000032410
AA Change: E417K
| 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: E417K
PolyPhen 2
Score 0.279 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000139510
Gene: ENSMUSG00000032410
AA Change: E417K
| 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 |
|
| 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: 44 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Bcl9l |
A |
G |
9: 44,420,496 (GRCm39) |
N1264D |
probably benign |
Het |
| Bmyc |
A |
G |
2: 25,597,082 (GRCm39) |
K49E |
probably damaging |
Het |
| Cdc45 |
C |
T |
16: 18,617,479 (GRCm39) |
M200I |
probably benign |
Het |
| Ceacam2 |
A |
G |
7: 25,230,166 (GRCm39) |
S147P |
probably benign |
Het |
| Cep152 |
G |
T |
2: 125,444,856 (GRCm39) |
|
probably null |
Het |
| Cnbd1 |
G |
T |
4: 18,894,993 (GRCm39) |
P250T |
possibly damaging |
Het |
| Col6a4 |
A |
G |
9: 105,940,304 (GRCm39) |
C1209R |
possibly damaging |
Het |
| Coro1c |
T |
C |
5: 113,990,334 (GRCm39) |
T116A |
probably benign |
Het |
| Ddx46 |
A |
G |
13: 55,825,416 (GRCm39) |
|
probably benign |
Het |
| Dnaaf5 |
T |
C |
5: 139,137,268 (GRCm39) |
I207T |
probably damaging |
Het |
| Erap1 |
A |
G |
13: 74,794,758 (GRCm39) |
D139G |
probably benign |
Het |
| Fbxw22 |
A |
T |
9: 109,231,087 (GRCm39) |
I121N |
possibly damaging |
Het |
| Fcmr |
T |
C |
1: 130,802,872 (GRCm39) |
S162P |
probably benign |
Het |
| Gadl1 |
A |
G |
9: 115,766,225 (GRCm39) |
|
probably benign |
Het |
| Gli2 |
T |
A |
1: 118,764,465 (GRCm39) |
S1229C |
probably benign |
Het |
| Gm10717 |
A |
T |
9: 3,026,287 (GRCm39) |
Y195F |
probably damaging |
Het |
| Gne |
T |
C |
4: 44,037,306 (GRCm39) |
N692D |
probably damaging |
Het |
| Knl1 |
A |
G |
2: 118,902,489 (GRCm39) |
T1397A |
possibly damaging |
Het |
| Lama3 |
C |
A |
18: 12,601,371 (GRCm39) |
A1016E |
probably damaging |
Het |
| Lhfpl2 |
A |
G |
13: 94,328,419 (GRCm39) |
D160G |
probably benign |
Het |
| Lmtk2 |
T |
A |
5: 144,112,769 (GRCm39) |
V1163E |
probably benign |
Het |
| Lrrtm2 |
G |
T |
18: 35,345,868 (GRCm39) |
S478* |
probably null |
Het |
| Nfatc2ip |
T |
C |
7: 125,989,736 (GRCm39) |
|
probably null |
Het |
| Nlrp12 |
A |
G |
7: 3,282,574 (GRCm39) |
I775T |
probably benign |
Het |
| Npr1 |
A |
G |
3: 90,372,165 (GRCm39) |
F216L |
probably benign |
Het |
| Or4m1 |
A |
T |
14: 50,557,617 (GRCm39) |
L225H |
probably damaging |
Het |
| Or5ac24 |
T |
A |
16: 59,165,387 (GRCm39) |
N226Y |
probably benign |
Het |
| Or5b99 |
G |
T |
19: 12,976,929 (GRCm39) |
S193I |
possibly damaging |
Het |
| Pkd1l1 |
C |
A |
11: 8,783,800 (GRCm39) |
G2052C |
probably damaging |
Het |
| Ppp1r16b |
A |
G |
2: 158,588,451 (GRCm39) |
N112S |
possibly damaging |
Het |
| Prr11 |
A |
G |
11: 86,994,141 (GRCm39) |
|
probably benign |
Het |
| Scap |
A |
G |
9: 110,210,724 (GRCm39) |
|
probably benign |
Het |
| Sirt1 |
C |
T |
10: 63,171,608 (GRCm39) |
R191Q |
probably damaging |
Het |
| Slc38a6 |
A |
C |
12: 73,397,320 (GRCm39) |
S321R |
possibly damaging |
Het |
| Sp140 |
T |
C |
1: 85,570,940 (GRCm39) |
V460A |
probably benign |
Het |
| Spdye4c |
A |
T |
2: 128,434,586 (GRCm39) |
K54N |
possibly damaging |
Het |
| Spta1 |
T |
A |
1: 174,030,860 (GRCm39) |
N947K |
probably benign |
Het |
| Srgap1 |
A |
G |
10: 121,621,598 (GRCm39) |
V965A |
possibly damaging |
Het |
| Tmem209 |
A |
C |
6: 30,508,659 (GRCm39) |
|
probably null |
Het |
| Trim37 |
A |
T |
11: 87,092,230 (GRCm39) |
K123* |
probably null |
Het |
| Trio |
T |
C |
15: 27,744,244 (GRCm39) |
T2563A |
possibly damaging |
Het |
| Utrn |
A |
T |
10: 12,289,717 (GRCm39) |
S734T |
possibly damaging |
Het |
| Vars2 |
A |
G |
17: 35,975,513 (GRCm39) |
|
probably benign |
Het |
| Yeats2 |
T |
A |
16: 20,011,970 (GRCm39) |
V515E |
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 |
|
|
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 |
|
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 |
|
| Posted On |
2015-04-16 |
Incidental Mutation