Incidental Mutation 'R4152:Upf1'
| ID |
314955 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Upf1
|
| Ensembl Gene |
ENSMUSG00000058301 |
| Gene Name |
UPF1 regulator of nonsense transcripts homolog (yeast) |
| Synonyms |
B430202H16Rik, Rent1, PNORF-1 |
| MMRRC Submission |
040996-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.972)
|
| Stock # |
R4152 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
70784175-70805928 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 70791110 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Histidine
at position 544
(R544H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000148927
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000075666]
[ENSMUST00000215817]
|
| AlphaFold |
Q9EPU0 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000075666
AA Change: R555H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: R555H
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
47 |
67 |
N/A |
INTRINSIC |
|
low complexity region
|
101 |
110 |
N/A |
INTRINSIC |
|
Pfam:UPF1_Zn_bind
|
116 |
267 |
4.1e-78 |
PFAM |
|
Pfam:ResIII
|
475 |
617 |
1.3e-6 |
PFAM |
|
Pfam:AAA_11
|
476 |
600 |
4.5e-24 |
PFAM |
|
Pfam:AAA_30
|
476 |
688 |
5.6e-13 |
PFAM |
|
Pfam:AAA_19
|
483 |
559 |
3.8e-16 |
PFAM |
|
Pfam:AAA_11
|
576 |
679 |
7.7e-30 |
PFAM |
|
Pfam:AAA_12
|
686 |
883 |
3.3e-64 |
PFAM |
|
low complexity region
|
995 |
1001 |
N/A |
INTRINSIC |
|
low complexity region
|
1013 |
1028 |
N/A |
INTRINSIC |
|
low complexity region
|
1066 |
1081 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000215817
AA Change: R544H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| Meta Mutation Damage Score |
0.8963 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.7%
|
| Validation Efficiency |
96% (45/47) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein is located only in the cytoplasm. When translation ends, it interacts with the protein that is a functional homolog of yeast Upf2p to trigger mRNA decapping. Use of multiple polyadenylation sites has been noted for this gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
PHENOTYPE: Mice homozygous for a targeted null mutation are viable in the pre-implantation period but resorb in the early post-implantation period. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 41 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acaca |
T |
G |
11: 84,183,752 (GRCm39) |
M31R |
possibly damaging |
Het |
| Akap6 |
A |
C |
12: 53,187,190 (GRCm39) |
S1535R |
probably benign |
Het |
| Ap3b2 |
A |
G |
7: 81,127,765 (GRCm39) |
I137T |
probably damaging |
Het |
| Cdc16 |
A |
G |
8: 13,812,857 (GRCm39) |
S36G |
probably damaging |
Het |
| Clcn4 |
T |
C |
7: 7,297,833 (GRCm39) |
N67D |
probably benign |
Het |
| Col4a1 |
T |
C |
8: 11,267,227 (GRCm39) |
|
probably null |
Het |
| Crem |
G |
T |
18: 3,288,055 (GRCm39) |
N179K |
probably damaging |
Het |
| Fam78b |
T |
C |
1: 166,906,369 (GRCm39) |
M176T |
probably benign |
Het |
| Fcgbpl1 |
T |
A |
7: 27,856,322 (GRCm39) |
H2036Q |
possibly damaging |
Het |
| Gcn1 |
A |
G |
5: 115,751,413 (GRCm39) |
|
probably null |
Het |
| Gm6483 |
T |
C |
8: 19,737,926 (GRCm39) |
|
noncoding transcript |
Het |
| Klk14 |
G |
A |
7: 43,341,501 (GRCm39) |
C51Y |
probably damaging |
Het |
| Klk1b16 |
T |
C |
7: 43,789,973 (GRCm39) |
F81S |
probably benign |
Het |
| Lpgat1 |
C |
A |
1: 191,451,600 (GRCm39) |
Y36* |
probably null |
Het |
| Mavs |
A |
G |
2: 131,088,528 (GRCm39) |
D444G |
probably benign |
Het |
| Ndst3 |
T |
C |
3: 123,465,876 (GRCm39) |
Y32C |
probably damaging |
Het |
| Nemp2 |
A |
G |
1: 52,680,210 (GRCm39) |
S145G |
probably benign |
Het |
| Or52b1 |
T |
C |
7: 104,978,592 (GRCm39) |
N269S |
probably damaging |
Het |
| Or7g20 |
T |
A |
9: 18,946,816 (GRCm39) |
Y132* |
probably null |
Het |
| Or8g52 |
A |
C |
9: 39,631,296 (GRCm39) |
M258L |
probably benign |
Het |
| Pds5a |
A |
T |
5: 65,823,514 (GRCm39) |
C92* |
probably null |
Het |
| Pgk2 |
A |
G |
17: 40,519,149 (GRCm39) |
V93A |
probably damaging |
Het |
| Phf3 |
C |
T |
1: 30,870,539 (GRCm39) |
V116I |
probably benign |
Het |
| Prl8a2 |
T |
C |
13: 27,534,985 (GRCm39) |
Y86H |
possibly damaging |
Het |
| Rab4b |
T |
C |
7: 26,875,551 (GRCm39) |
|
probably benign |
Het |
| Rsad1 |
T |
C |
11: 94,439,449 (GRCm39) |
|
probably benign |
Het |
| Sim1 |
G |
A |
10: 50,859,950 (GRCm39) |
C604Y |
probably damaging |
Het |
| Slc5a3 |
T |
A |
16: 91,874,696 (GRCm39) |
L251* |
probably null |
Het |
| Slit3 |
A |
G |
11: 35,589,147 (GRCm39) |
N1234S |
probably damaging |
Het |
| Sntg1 |
A |
T |
1: 8,653,569 (GRCm39) |
|
probably null |
Het |
| Snx31 |
T |
C |
15: 36,525,785 (GRCm39) |
N305D |
probably benign |
Het |
| St14 |
T |
C |
9: 31,001,802 (GRCm39) |
I768V |
probably benign |
Het |
| Tep1 |
G |
A |
14: 51,075,051 (GRCm39) |
H1755Y |
possibly damaging |
Het |
| Tlr6 |
A |
C |
5: 65,110,555 (GRCm39) |
F784C |
probably damaging |
Het |
| Tmem132a |
A |
G |
19: 10,836,427 (GRCm39) |
V701A |
probably benign |
Het |
| Tspan15 |
A |
T |
10: 62,025,621 (GRCm39) |
M197K |
possibly damaging |
Het |
| Vegfb |
T |
C |
19: 6,963,446 (GRCm39) |
Y106C |
probably damaging |
Het |
| Vmn2r100 |
AAAACAGGAGTATTGATTGGAAAC |
AAAAC |
17: 19,743,681 (GRCm39) |
|
probably null |
Het |
| Vmn2r18 |
T |
A |
5: 151,485,730 (GRCm39) |
Q588L |
probably damaging |
Het |
| Vmn2r66 |
T |
C |
7: 84,654,800 (GRCm39) |
D503G |
probably benign |
Het |
| Zc3h15 |
T |
C |
2: 83,488,913 (GRCm39) |
V161A |
probably benign |
Het |
|
| Other mutations in Upf1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01113:Upf1
|
APN |
8 |
70,790,934 (GRCm39) |
missense |
probably benign |
|
|
IGL01890:Upf1
|
APN |
8 |
70,786,880 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
IGL02534:Upf1
|
APN |
8 |
70,788,302 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL03142:Upf1
|
APN |
8 |
70,785,977 (GRCm39) |
missense |
probably benign |
0.04 |
|
IGL03151:Upf1
|
APN |
8 |
70,788,037 (GRCm39) |
missense |
probably damaging |
0.98 |
|
Nanosphere
|
UTSW |
8 |
70,796,912 (GRCm39) |
missense |
probably benign |
0.01 |
|
Particulate
|
UTSW |
8 |
70,789,675 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R0270:Upf1
|
UTSW |
8 |
70,788,295 (GRCm39) |
splice site |
probably benign |
|
|
R0477:Upf1
|
UTSW |
8 |
70,786,730 (GRCm39) |
missense |
probably benign |
|
|
R0755:Upf1
|
UTSW |
8 |
70,786,779 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1018:Upf1
|
UTSW |
8 |
70,791,556 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R1067:Upf1
|
UTSW |
8 |
70,791,053 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1445:Upf1
|
UTSW |
8 |
70,794,174 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1458:Upf1
|
UTSW |
8 |
70,796,904 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1511:Upf1
|
UTSW |
8 |
70,791,155 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1552:Upf1
|
UTSW |
8 |
70,785,709 (GRCm39) |
nonsense |
probably null |
|
|
R1560:Upf1
|
UTSW |
8 |
70,791,092 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1562:Upf1
|
UTSW |
8 |
70,796,017 (GRCm39) |
nonsense |
probably null |
|
|
R2082:Upf1
|
UTSW |
8 |
70,794,222 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2143:Upf1
|
UTSW |
8 |
70,792,004 (GRCm39) |
missense |
probably null |
1.00 |
|
R2423:Upf1
|
UTSW |
8 |
70,791,110 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2425:Upf1
|
UTSW |
8 |
70,791,110 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3031:Upf1
|
UTSW |
8 |
70,791,110 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3032:Upf1
|
UTSW |
8 |
70,791,110 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3123:Upf1
|
UTSW |
8 |
70,790,133 (GRCm39) |
splice site |
probably benign |
|
|
R3508:Upf1
|
UTSW |
8 |
70,791,110 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3747:Upf1
|
UTSW |
8 |
70,786,000 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R3748:Upf1
|
UTSW |
8 |
70,786,000 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R3750:Upf1
|
UTSW |
8 |
70,786,000 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R3754:Upf1
|
UTSW |
8 |
70,792,464 (GRCm39) |
missense |
probably benign |
0.30 |
|
R3964:Upf1
|
UTSW |
8 |
70,791,110 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3965:Upf1
|
UTSW |
8 |
70,791,110 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4505:Upf1
|
UTSW |
8 |
70,790,216 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4506:Upf1
|
UTSW |
8 |
70,790,216 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4838:Upf1
|
UTSW |
8 |
70,792,018 (GRCm39) |
missense |
probably benign |
0.03 |
|
R5001:Upf1
|
UTSW |
8 |
70,787,350 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5715:Upf1
|
UTSW |
8 |
70,805,628 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R5748:Upf1
|
UTSW |
8 |
70,791,167 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5856:Upf1
|
UTSW |
8 |
70,787,412 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R5930:Upf1
|
UTSW |
8 |
70,796,912 (GRCm39) |
missense |
probably benign |
0.01 |
|
R6010:Upf1
|
UTSW |
8 |
70,789,675 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6056:Upf1
|
UTSW |
8 |
70,785,687 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6870:Upf1
|
UTSW |
8 |
70,794,211 (GRCm39) |
missense |
probably benign |
0.11 |
|
R7205:Upf1
|
UTSW |
8 |
70,792,695 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R7385:Upf1
|
UTSW |
8 |
70,793,268 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7464:Upf1
|
UTSW |
8 |
70,786,073 (GRCm39) |
missense |
probably benign |
|
|
R7759:Upf1
|
UTSW |
8 |
70,786,730 (GRCm39) |
missense |
probably benign |
|
|
R7783:Upf1
|
UTSW |
8 |
70,805,508 (GRCm39) |
missense |
probably benign |
0.11 |
|
R8079:Upf1
|
UTSW |
8 |
70,791,534 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8192:Upf1
|
UTSW |
8 |
70,793,294 (GRCm39) |
missense |
probably benign |
0.03 |
|
R8544:Upf1
|
UTSW |
8 |
70,789,702 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8738:Upf1
|
UTSW |
8 |
70,785,973 (GRCm39) |
missense |
probably benign |
0.06 |
|
R8738:Upf1
|
UTSW |
8 |
70,785,972 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8826:Upf1
|
UTSW |
8 |
70,790,930 (GRCm39) |
missense |
probably benign |
|
|
R8876:Upf1
|
UTSW |
8 |
70,796,918 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R8906:Upf1
|
UTSW |
8 |
70,786,815 (GRCm39) |
nonsense |
probably null |
|
|
R8911:Upf1
|
UTSW |
8 |
70,791,087 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
R9163:Upf1
|
UTSW |
8 |
70,792,674 (GRCm39) |
missense |
probably benign |
|
|
R9425:Upf1
|
UTSW |
8 |
70,792,003 (GRCm39) |
missense |
probably benign |
0.06 |
|
| Predicted Primers |
PCR Primer
(F):5'- ATCTGCAGATGACAGCTCGC -3'
(R):5'- CATGGCTGTACCTGCCTATTAC -3'
Sequencing Primer
(F):5'- GTCTCATCCTTTAGCTGCTGCAG -3'
(R):5'- TGCCTATTACAGCTGTGCAG -3'
|
| Posted On |
2015-05-14 |
Incidental Mutation