Incidental Mutation 'R1552:Upf1'
| ID |
170012 |
| 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 |
039591-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.972)
|
| Stock # |
R1552 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
70784175-70805928 bp(-) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
G to A
at 70785709 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamine to Stop codon
at position 1046
(Q1046*)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000148927
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000075666]
[ENSMUST00000140239]
[ENSMUST00000165819]
[ENSMUST00000207684]
[ENSMUST00000215817]
|
| AlphaFold |
Q9EPU0 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000075666
AA Change: Q1057*
|
| SMART Domains |
Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: Q1057*
| 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 benign
Transcript: ENSMUST00000140239
|
| SMART Domains |
Protein: ENSMUSP00000120598
Gene: ENSMUSG00000087408
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
49 |
68 |
N/A |
INTRINSIC |
|
TLC
|
97 |
311 |
1.24e-57 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000165819
|
| SMART Domains |
Protein: ENSMUSP00000128325
Gene: ENSMUSG00000087408
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Pfam:TGFb_propeptide
|
33 |
169 |
7e-16 |
PFAM |
|
low complexity region
|
225 |
237 |
N/A |
INTRINSIC |
|
TGFB
|
251 |
357 |
6.22e-56 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000207684
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000215817
AA Change: Q1046*
|
| Meta Mutation Damage Score |
0.9754 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.1%
- 20x: 91.7%
|
| Validation Efficiency |
97% (71/73) |
| 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: 68 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc5 |
T |
A |
16: 20,217,617 (GRCm39) |
I365F |
probably damaging |
Het |
| Abhd15 |
T |
C |
11: 77,406,233 (GRCm39) |
L70P |
probably damaging |
Het |
| Adam18 |
A |
C |
8: 25,136,377 (GRCm39) |
H381Q |
probably benign |
Het |
| Ankfy1 |
T |
C |
11: 72,645,321 (GRCm39) |
|
probably null |
Het |
| Arcn1 |
C |
T |
9: 44,670,291 (GRCm39) |
A112T |
probably damaging |
Het |
| Bltp3a |
T |
C |
17: 28,109,045 (GRCm39) |
F1088S |
possibly damaging |
Het |
| Calhm1 |
C |
T |
19: 47,129,640 (GRCm39) |
R294H |
probably benign |
Het |
| Ccdc121rt1 |
A |
G |
1: 181,338,556 (GRCm39) |
L132P |
probably damaging |
Het |
| Cdk5rap1 |
T |
C |
2: 154,212,615 (GRCm39) |
E81G |
probably benign |
Het |
| Cep170 |
T |
C |
1: 176,610,060 (GRCm39) |
|
probably benign |
Het |
| Cep350 |
C |
T |
1: 155,786,484 (GRCm39) |
R1454Q |
possibly damaging |
Het |
| Chrna3 |
C |
A |
9: 54,923,192 (GRCm39) |
E205D |
probably benign |
Het |
| Chst5 |
T |
C |
8: 112,616,912 (GRCm39) |
D236G |
probably damaging |
Het |
| Coro1a |
T |
C |
7: 126,299,124 (GRCm39) |
N367D |
probably benign |
Het |
| Cyp3a16 |
T |
C |
5: 145,373,346 (GRCm39) |
I474V |
probably benign |
Het |
| Cyth3 |
G |
A |
5: 143,683,505 (GRCm39) |
V87I |
probably benign |
Het |
| Dclk3 |
C |
A |
9: 111,317,647 (GRCm39) |
T761K |
probably damaging |
Het |
| Dvl2 |
T |
A |
11: 69,897,198 (GRCm39) |
M300K |
possibly damaging |
Het |
| Eefsec |
C |
T |
6: 88,353,182 (GRCm39) |
|
probably benign |
Het |
| Exog |
T |
C |
9: 119,274,176 (GRCm39) |
S54P |
unknown |
Het |
| Fasn |
A |
G |
11: 120,709,384 (GRCm39) |
S519P |
probably damaging |
Het |
| Gas8 |
G |
A |
8: 124,247,385 (GRCm39) |
A16T |
probably benign |
Het |
| Got2 |
A |
G |
8: 96,596,122 (GRCm39) |
S333P |
probably benign |
Het |
| Hadhb |
T |
A |
5: 30,381,931 (GRCm39) |
L287Q |
probably null |
Het |
| Ift57 |
A |
G |
16: 49,579,716 (GRCm39) |
T211A |
probably benign |
Het |
| Il1rap |
A |
G |
16: 26,541,184 (GRCm39) |
E475G |
possibly damaging |
Het |
| Ilkap |
A |
T |
1: 91,312,316 (GRCm39) |
D11E |
probably damaging |
Het |
| Impact |
T |
C |
18: 13,117,337 (GRCm39) |
S137P |
probably benign |
Het |
| Jarid2 |
T |
C |
13: 45,064,675 (GRCm39) |
V920A |
probably damaging |
Het |
| Kcnk18 |
A |
T |
19: 59,223,890 (GRCm39) |
H345L |
probably damaging |
Het |
| Kdm4d |
A |
T |
9: 14,375,325 (GRCm39) |
Y178N |
probably damaging |
Het |
| Klk1b1 |
A |
G |
7: 43,618,767 (GRCm39) |
Y48C |
probably damaging |
Het |
| Klra5 |
G |
T |
6: 129,886,848 (GRCm39) |
T60K |
probably damaging |
Het |
| Kng2 |
A |
T |
16: 22,806,270 (GRCm39) |
L643H |
probably damaging |
Het |
| Lamb3 |
A |
G |
1: 193,013,067 (GRCm39) |
|
probably null |
Het |
| Lingo2 |
A |
G |
4: 35,708,315 (GRCm39) |
V555A |
probably damaging |
Het |
| Mbd5 |
T |
C |
2: 49,162,946 (GRCm39) |
S251P |
probably damaging |
Het |
| Mc4r |
T |
C |
18: 66,992,766 (GRCm39) |
S116G |
probably benign |
Het |
| Mipol1 |
T |
C |
12: 57,352,874 (GRCm39) |
V71A |
possibly damaging |
Het |
| Myo15b |
A |
C |
11: 115,757,461 (GRCm39) |
S1104R |
probably benign |
Het |
| Nek1 |
T |
A |
8: 61,459,771 (GRCm39) |
D26E |
probably damaging |
Het |
| Neu1 |
C |
T |
17: 35,151,089 (GRCm39) |
|
probably benign |
Het |
| Npffr2 |
T |
C |
5: 89,730,975 (GRCm39) |
S302P |
possibly damaging |
Het |
| Or8b48 |
T |
C |
9: 38,492,675 (GRCm39) |
M34T |
probably benign |
Het |
| Palmd |
T |
A |
3: 116,741,689 (GRCm39) |
|
probably benign |
Het |
| Pcdh8 |
A |
T |
14: 80,008,047 (GRCm39) |
V172E |
probably benign |
Het |
| Pnpla6 |
C |
A |
8: 3,572,403 (GRCm39) |
Q291K |
probably damaging |
Het |
| Pou2af2 |
T |
A |
9: 51,202,870 (GRCm39) |
S95C |
probably damaging |
Het |
| Prkch |
T |
C |
12: 73,749,320 (GRCm39) |
F357L |
probably benign |
Het |
| Ptprj |
A |
T |
2: 90,301,497 (GRCm39) |
Y212N |
probably damaging |
Het |
| Reln |
G |
T |
5: 22,165,376 (GRCm39) |
H2061N |
probably benign |
Het |
| Rint1 |
T |
A |
5: 24,005,656 (GRCm39) |
S113T |
probably benign |
Het |
| Rnf38 |
G |
C |
4: 44,142,468 (GRCm39) |
|
probably null |
Het |
| Slc30a4 |
T |
A |
2: 122,527,936 (GRCm39) |
I374L |
probably benign |
Het |
| Slfn10-ps |
T |
C |
11: 82,920,676 (GRCm39) |
|
noncoding transcript |
Het |
| Smcp |
A |
T |
3: 92,491,710 (GRCm39) |
C46S |
unknown |
Het |
| Smu1 |
A |
C |
4: 40,748,570 (GRCm39) |
V240G |
probably damaging |
Het |
| Srsf5 |
A |
G |
12: 80,996,519 (GRCm39) |
|
probably benign |
Het |
| Stn1 |
T |
C |
19: 47,524,812 (GRCm39) |
|
probably null |
Het |
| Stx18 |
A |
G |
5: 38,262,335 (GRCm39) |
E63G |
probably damaging |
Het |
| Tas2r130 |
A |
G |
6: 131,607,130 (GRCm39) |
Y222H |
probably benign |
Het |
| Tescl |
G |
T |
7: 24,032,758 (GRCm39) |
P189Q |
probably benign |
Het |
| Tlr1 |
A |
G |
5: 65,084,203 (GRCm39) |
S125P |
probably damaging |
Het |
| Ugt2a2 |
G |
T |
5: 87,609,880 (GRCm39) |
D566E |
possibly damaging |
Het |
| Unc13b |
A |
T |
4: 43,237,144 (GRCm39) |
T3405S |
probably damaging |
Het |
| Wwox |
T |
A |
8: 115,172,090 (GRCm39) |
Y61* |
probably null |
Het |
| Zfhx4 |
C |
T |
3: 5,468,170 (GRCm39) |
T2776M |
probably damaging |
Het |
| Zranb3 |
G |
A |
1: 127,888,488 (GRCm39) |
|
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 |
|
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 |
|
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'- TCATTCACCCTTCAGAAAGGCAGC -3'
(R):5'- GCCCTCGAACATGTACTTCCAGAC -3'
Sequencing Primer
(F):5'- TTCTCTGCTGTAGGATGCAG -3'
(R):5'- TTAGTATGATCAGCGCAGGC -3'
|
| Posted On |
2014-04-13 |
Incidental Mutation