Incidental Mutation 'R5715:Upf1'
| ID |
451114 |
| 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 |
043336-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.972)
|
| Stock # |
R5715 (G1)
|
| Quality Score |
190 |
|
Status
|
Not validated
|
| Chromosome |
8 |
| Chromosomal Location |
70784175-70805928 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 70805628 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Asparagine
at position 6
(Y6N)
|
| 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: Y6N
PolyPhen 2
Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: Y6N
| 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: Y6N
PolyPhen 2
Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)
|
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.7%
|
| Validation Efficiency |
|
| 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: 75 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 9930111J21Rik2 |
T |
A |
11: 48,910,777 (GRCm39) |
Y552F |
probably damaging |
Het |
| Asprv1 |
T |
A |
6: 86,605,596 (GRCm39) |
D147E |
probably benign |
Het |
| Atg4c |
G |
T |
4: 99,146,639 (GRCm39) |
L405F |
probably damaging |
Het |
| Birc6 |
C |
T |
17: 74,938,615 (GRCm39) |
L2670F |
probably damaging |
Het |
| Cdc20 |
T |
C |
4: 118,292,015 (GRCm39) |
D379G |
probably damaging |
Het |
| Chd6 |
T |
C |
2: 160,791,798 (GRCm39) |
M2520V |
probably benign |
Het |
| Clca4b |
A |
G |
3: 144,619,018 (GRCm39) |
V707A |
probably benign |
Het |
| Cmtm1 |
CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT |
CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT |
8: 105,036,102 (GRCm39) |
|
probably benign |
Het |
| Col12a1 |
A |
T |
9: 79,523,347 (GRCm39) |
C2743* |
probably null |
Het |
| Coq6 |
C |
A |
12: 84,413,681 (GRCm39) |
D70E |
probably benign |
Het |
| Cspg4 |
T |
A |
9: 56,798,335 (GRCm39) |
V1450D |
possibly damaging |
Het |
| Dnah7a |
A |
G |
1: 53,452,937 (GRCm39) |
L3847P |
probably damaging |
Het |
| Drd2 |
T |
A |
9: 49,316,189 (GRCm39) |
H316Q |
probably benign |
Het |
| Dusp19 |
T |
A |
2: 80,461,330 (GRCm39) |
N206K |
probably benign |
Het |
| Fam13c |
T |
G |
10: 70,370,670 (GRCm39) |
F270C |
probably damaging |
Het |
| Fam20a |
T |
C |
11: 109,569,257 (GRCm39) |
E246G |
probably damaging |
Het |
| Fbxo31 |
A |
G |
8: 122,305,302 (GRCm39) |
F65L |
probably damaging |
Het |
| Fshr |
T |
A |
17: 89,293,824 (GRCm39) |
|
probably null |
Het |
| Fstl4 |
T |
C |
11: 52,891,243 (GRCm39) |
V127A |
possibly damaging |
Het |
| Gdpd4 |
A |
T |
7: 97,610,804 (GRCm39) |
I75F |
probably benign |
Het |
| Grm5 |
C |
A |
7: 87,779,464 (GRCm39) |
A968E |
probably benign |
Het |
| Gucy2g |
A |
C |
19: 55,221,587 (GRCm39) |
F305V |
possibly damaging |
Het |
| Hivep3 |
T |
C |
4: 119,953,570 (GRCm39) |
F629L |
probably benign |
Het |
| Hoxb1 |
A |
G |
11: 96,257,152 (GRCm39) |
E167G |
probably benign |
Het |
| Hoxd4 |
T |
C |
2: 74,557,708 (GRCm39) |
L29P |
probably damaging |
Het |
| Ikbkb |
A |
G |
8: 23,168,866 (GRCm39) |
L211P |
probably damaging |
Het |
| Insc |
T |
C |
7: 114,449,076 (GRCm39) |
V499A |
probably benign |
Het |
| Irak3 |
A |
T |
10: 119,978,641 (GRCm39) |
H511Q |
possibly damaging |
Het |
| Itpripl1 |
T |
C |
2: 126,983,927 (GRCm39) |
E65G |
probably damaging |
Het |
| Lurap1l |
T |
A |
4: 80,871,958 (GRCm39) |
S150R |
possibly damaging |
Het |
| Mab21l3 |
C |
T |
3: 101,730,723 (GRCm39) |
R172Q |
probably benign |
Het |
| Macf1 |
T |
C |
4: 123,577,807 (GRCm39) |
D59G |
probably damaging |
Het |
| Mettl21a |
A |
T |
1: 64,654,314 (GRCm39) |
S68T |
probably benign |
Het |
| Mlxip |
T |
A |
5: 123,578,121 (GRCm39) |
W146R |
probably damaging |
Het |
| Mpp2 |
T |
A |
11: 101,953,087 (GRCm39) |
N285I |
probably damaging |
Het |
| Mrgprb4 |
T |
C |
7: 47,848,787 (GRCm39) |
N47S |
probably damaging |
Het |
| Msi2 |
A |
G |
11: 88,276,889 (GRCm39) |
Y237H |
probably damaging |
Het |
| Muc4 |
C |
T |
16: 32,570,734 (GRCm39) |
T598I |
possibly damaging |
Het |
| Musk |
A |
T |
4: 58,333,663 (GRCm39) |
I253F |
probably damaging |
Het |
| Myo5b |
G |
T |
18: 74,875,246 (GRCm39) |
C1550F |
possibly damaging |
Het |
| Nckap5l |
T |
C |
15: 99,321,457 (GRCm39) |
T1137A |
probably benign |
Het |
| Neb |
T |
C |
2: 52,141,780 (GRCm39) |
D3009G |
probably damaging |
Het |
| Nxph1 |
T |
A |
6: 9,247,740 (GRCm39) |
V237E |
probably damaging |
Het |
| Or52a33 |
A |
C |
7: 103,289,009 (GRCm39) |
S113A |
probably damaging |
Het |
| Pla2g12a |
A |
G |
3: 129,688,591 (GRCm39) |
K150E |
probably damaging |
Het |
| Potegl |
T |
C |
2: 23,097,989 (GRCm39) |
Y56H |
possibly damaging |
Het |
| Pramel30 |
A |
G |
4: 144,057,870 (GRCm39) |
D159G |
possibly damaging |
Het |
| Ptpn23 |
G |
A |
9: 110,216,143 (GRCm39) |
R1238W |
probably damaging |
Het |
| Pts |
C |
T |
9: 50,433,578 (GRCm39) |
G124R |
probably damaging |
Het |
| Rfk |
A |
T |
19: 17,376,002 (GRCm39) |
I99F |
probably benign |
Het |
| Rictor |
A |
T |
15: 6,780,197 (GRCm39) |
R151* |
probably null |
Het |
| Scn2a |
T |
A |
2: 65,547,928 (GRCm39) |
I1040N |
probably benign |
Het |
| Serinc5 |
A |
C |
13: 92,842,710 (GRCm39) |
T387P |
probably damaging |
Het |
| Sh3bp5l |
A |
G |
11: 58,236,841 (GRCm39) |
Q266R |
possibly damaging |
Het |
| Slc14a2 |
T |
C |
18: 78,201,551 (GRCm39) |
Y656C |
probably damaging |
Het |
| Slc26a3 |
T |
A |
12: 31,498,842 (GRCm39) |
|
probably null |
Het |
| Slc3a2 |
G |
T |
19: 8,685,594 (GRCm39) |
H168Q |
probably benign |
Het |
| Smarca2 |
A |
T |
19: 26,626,522 (GRCm39) |
I449L |
probably benign |
Het |
| Smarcc1 |
T |
C |
9: 110,025,435 (GRCm39) |
V704A |
possibly damaging |
Het |
| Sox13 |
A |
G |
1: 133,313,921 (GRCm39) |
|
probably null |
Het |
| Sptbn5 |
T |
C |
2: 119,902,985 (GRCm39) |
E7G |
probably damaging |
Het |
| Stard10 |
A |
G |
7: 100,971,110 (GRCm39) |
D26G |
probably damaging |
Het |
| Tap1 |
A |
T |
17: 34,411,868 (GRCm39) |
R91* |
probably null |
Het |
| Tgfbrap1 |
A |
T |
1: 43,099,097 (GRCm39) |
V239D |
possibly damaging |
Het |
| Tmem209 |
A |
T |
6: 30,497,922 (GRCm39) |
Y124* |
probably null |
Het |
| Tmprss2 |
T |
A |
16: 97,370,183 (GRCm39) |
E327V |
possibly damaging |
Het |
| Ttbk1 |
T |
C |
17: 46,790,133 (GRCm39) |
Y104C |
probably damaging |
Het |
| Ttll10 |
A |
T |
4: 156,129,848 (GRCm39) |
F154I |
probably damaging |
Het |
| Ubn2 |
T |
A |
6: 38,438,412 (GRCm39) |
Y40* |
probably null |
Het |
| Ubr5 |
A |
T |
15: 38,002,477 (GRCm39) |
S1519T |
probably benign |
Het |
| Ugt3a1 |
A |
C |
15: 9,306,430 (GRCm39) |
D193A |
probably damaging |
Het |
| Vmn2r103 |
A |
T |
17: 20,015,201 (GRCm39) |
D447V |
probably benign |
Het |
| Vps39 |
T |
C |
2: 120,155,717 (GRCm39) |
N519S |
possibly damaging |
Het |
| Zfp109 |
T |
C |
7: 23,928,995 (GRCm39) |
E138G |
possibly damaging |
Het |
| Znrf3 |
A |
C |
11: 5,236,239 (GRCm39) |
V157G |
possibly damaging |
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 |
|
R4152: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 |
|
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'- GGCTGGTTAACTGGGATCTAGC -3'
(R):5'- AACTCAGAGCTCAGAACCGG -3'
Sequencing Primer
(F):5'- AACTCACTTGTGCGTCGAG -3'
(R):5'- CTCAGAACCGGCGGCCC -3'
|
| Posted On |
2017-01-03 |
Incidental Mutation