Incidental Mutation 'R6401:Smg7'
| ID |
516147 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smg7
|
| Ensembl Gene |
ENSMUSG00000042772 |
| Gene Name |
SMG7 nonsense mediated mRNA decay factor |
| Synonyms |
9430023P16Rik, Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans) |
| MMRRC Submission |
044548-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.923)
|
| Stock # |
R6401 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
152712746-152778397 bp(-) (GRCm39) |
| Type of Mutation |
splice site (3145 bp from exon) |
| DNA Base Change (assembly) |
A to G
at 152715887 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000140404
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000027754]
[ENSMUST00000043560]
[ENSMUST00000073441]
[ENSMUST00000111836]
[ENSMUST00000186568]
|
| AlphaFold |
Q5RJH6 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000027754
|
| SMART Domains |
Protein: ENSMUSP00000027754
Gene: ENSMUSG00000026480
| Domain | Start | End | E-Value | Type |
|---|
|
TPR
|
37 |
70 |
1.42e0 |
SMART |
|
TPR
|
71 |
104 |
3.58e-6 |
SMART |
|
TPR
|
121 |
154 |
1.05e1 |
SMART |
|
SH3
|
243 |
298 |
1.02e-13 |
SMART |
|
low complexity region
|
312 |
326 |
N/A |
INTRINSIC |
|
PB1
|
350 |
428 |
2.6e-10 |
SMART |
|
SH3
|
459 |
514 |
8.36e-19 |
SMART |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000043560
AA Change: S1076P
PolyPhen 2
Score 0.676 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000041241
Gene: ENSMUSG00000042772
AA Change: S1076P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:EST1
|
63 |
177 |
3.4e-30 |
PFAM |
|
Pfam:EST1_DNA_bind
|
179 |
438 |
3.3e-64 |
PFAM |
|
low complexity region
|
457 |
465 |
N/A |
INTRINSIC |
|
low complexity region
|
615 |
633 |
N/A |
INTRINSIC |
|
low complexity region
|
682 |
710 |
N/A |
INTRINSIC |
|
low complexity region
|
711 |
729 |
N/A |
INTRINSIC |
|
low complexity region
|
874 |
898 |
N/A |
INTRINSIC |
|
low complexity region
|
906 |
922 |
N/A |
INTRINSIC |
|
low complexity region
|
931 |
947 |
N/A |
INTRINSIC |
|
low complexity region
|
1008 |
1034 |
N/A |
INTRINSIC |
|
low complexity region
|
1126 |
1140 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000073441
AA Change: S1064P
PolyPhen 2
Score 0.051 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000073144
Gene: ENSMUSG00000042772
AA Change: S1064P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:EST1
|
52 |
172 |
2.3e-26 |
PFAM |
|
Pfam:EST1_DNA_bind
|
171 |
430 |
3.6e-66 |
PFAM |
|
low complexity region
|
449 |
457 |
N/A |
INTRINSIC |
|
low complexity region
|
653 |
671 |
N/A |
INTRINSIC |
|
low complexity region
|
720 |
748 |
N/A |
INTRINSIC |
|
low complexity region
|
749 |
767 |
N/A |
INTRINSIC |
|
low complexity region
|
919 |
935 |
N/A |
INTRINSIC |
|
low complexity region
|
996 |
1022 |
N/A |
INTRINSIC |
|
low complexity region
|
1114 |
1128 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111836
AA Change: S1068P
PolyPhen 2
Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000107467
Gene: ENSMUSG00000042772
AA Change: S1068P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:EST1
|
52 |
172 |
2.3e-26 |
PFAM |
|
Pfam:EST1_DNA_bind
|
171 |
430 |
3.7e-66 |
PFAM |
|
low complexity region
|
449 |
457 |
N/A |
INTRINSIC |
|
low complexity region
|
607 |
625 |
N/A |
INTRINSIC |
|
low complexity region
|
674 |
702 |
N/A |
INTRINSIC |
|
low complexity region
|
703 |
721 |
N/A |
INTRINSIC |
|
low complexity region
|
866 |
890 |
N/A |
INTRINSIC |
|
low complexity region
|
898 |
914 |
N/A |
INTRINSIC |
|
low complexity region
|
923 |
939 |
N/A |
INTRINSIC |
|
low complexity region
|
1000 |
1026 |
N/A |
INTRINSIC |
|
low complexity region
|
1118 |
1132 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000186568
|
| SMART Domains |
Protein: ENSMUSP00000140404
Gene: ENSMUSG00000026480
| Domain | Start | End | E-Value | Type |
|---|
|
TPR
|
37 |
70 |
1.42e0 |
SMART |
|
TPR
|
71 |
104 |
3.58e-6 |
SMART |
|
TPR
|
121 |
154 |
1.05e1 |
SMART |
|
SH3
|
243 |
298 |
1.02e-13 |
SMART |
|
low complexity region
|
312 |
326 |
N/A |
INTRINSIC |
|
PB1
|
350 |
428 |
2.6e-10 |
SMART |
|
SH3
|
459 |
514 |
8.36e-19 |
SMART |
|
| Meta Mutation Damage Score |
0.3286 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.4%
- 20x: 97.9%
|
| Validation Efficiency |
93% (41/44) |
| 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 essential for nonsense-mediated mRNA decay (NMD); a process whereby transcripts with premature termination codons are targeted for rapid degradation by a mRNA decay complex. The mRNA decay complex consists, in part, of this protein along with proteins SMG5 and UPF1. The N-terminal domain of this protein is thought to mediate its association with SMG5 or UPF1 while the C-terminal domain interacts with the mRNA decay complex. This protein may therefore couple changes in UPF1 phosphorylation state to the degradation of NMD-candidate transcripts. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Aug 2011]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 41 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ano3 |
T |
A |
2: 110,605,459 (GRCm39) |
N249I |
probably benign |
Het |
| Ap3s1 |
A |
C |
18: 46,891,074 (GRCm39) |
I56L |
probably benign |
Het |
| Ccn5 |
T |
C |
2: 163,670,946 (GRCm39) |
I151T |
probably benign |
Het |
| Cngb1 |
A |
G |
8: 96,030,367 (GRCm39) |
|
probably benign |
Het |
| Col2a1 |
T |
C |
15: 97,883,773 (GRCm39) |
T570A |
unknown |
Het |
| Cyp3a16 |
T |
C |
5: 145,377,174 (GRCm39) |
E471G |
probably damaging |
Het |
| D930020B18Rik |
A |
G |
10: 121,477,762 (GRCm39) |
N14D |
possibly damaging |
Het |
| Ext1 |
T |
C |
15: 52,969,493 (GRCm39) |
E365G |
possibly damaging |
Het |
| Fbn1 |
C |
A |
2: 125,188,370 (GRCm39) |
V1490F |
probably damaging |
Het |
| Fsip2 |
A |
G |
2: 82,820,430 (GRCm39) |
T5388A |
possibly damaging |
Het |
| Gm5431 |
T |
A |
11: 48,779,536 (GRCm39) |
N740I |
probably benign |
Het |
| Ifi209 |
T |
C |
1: 173,472,269 (GRCm39) |
M370T |
probably damaging |
Het |
| Ighv2-4 |
G |
T |
12: 113,617,082 (GRCm39) |
P60Q |
probably damaging |
Het |
| Kif19b |
A |
T |
5: 140,442,698 (GRCm39) |
T80S |
possibly damaging |
Het |
| Ldb3 |
A |
T |
14: 34,299,291 (GRCm39) |
L111Q |
probably benign |
Het |
| Mcmbp |
G |
T |
7: 128,308,783 (GRCm39) |
L413I |
possibly damaging |
Het |
| Mib1 |
T |
A |
18: 10,795,802 (GRCm39) |
M721K |
probably benign |
Het |
| Nos3 |
A |
G |
5: 24,584,809 (GRCm39) |
T738A |
probably benign |
Het |
| Notch3 |
T |
A |
17: 32,377,597 (GRCm39) |
I160L |
probably benign |
Het |
| Nrxn3 |
C |
A |
12: 89,221,770 (GRCm39) |
N516K |
possibly damaging |
Het |
| Nt5c2 |
A |
G |
19: 46,878,250 (GRCm39) |
Y496H |
probably benign |
Het |
| Or13f5 |
A |
C |
4: 52,826,242 (GRCm39) |
T282P |
probably damaging |
Het |
| Or1n1 |
A |
T |
2: 36,750,177 (GRCm39) |
L61* |
probably null |
Het |
| Or5b111 |
T |
C |
19: 13,290,878 (GRCm39) |
Y257C |
probably damaging |
Het |
| Polm |
A |
T |
11: 5,779,491 (GRCm39) |
W436R |
probably damaging |
Het |
| Prex2 |
T |
A |
1: 11,256,951 (GRCm39) |
I1221N |
probably benign |
Het |
| Rfpl4b |
T |
C |
10: 38,696,941 (GRCm39) |
H220R |
possibly damaging |
Het |
| Rgs12 |
T |
C |
5: 35,177,676 (GRCm39) |
F79L |
probably damaging |
Het |
| Rxfp2 |
A |
G |
5: 149,966,595 (GRCm39) |
D111G |
probably benign |
Het |
| Spata22 |
T |
C |
11: 73,224,180 (GRCm39) |
S34P |
probably damaging |
Het |
| St7 |
T |
A |
6: 17,855,317 (GRCm39) |
|
probably null |
Het |
| Stk31 |
A |
G |
6: 49,400,372 (GRCm39) |
E399G |
probably damaging |
Het |
| Tcp10b |
C |
A |
17: 13,292,466 (GRCm39) |
N296K |
probably damaging |
Het |
| Tonsl |
T |
C |
15: 76,517,866 (GRCm39) |
Y645C |
probably damaging |
Het |
| Ttn |
A |
T |
2: 76,800,206 (GRCm39) |
M334K |
probably benign |
Het |
| Vcpkmt |
C |
A |
12: 69,629,619 (GRCm39) |
V48F |
probably damaging |
Het |
| Vmn2r112 |
T |
A |
17: 22,822,532 (GRCm39) |
Y403* |
probably null |
Het |
| Vwa7 |
G |
A |
17: 35,236,286 (GRCm39) |
|
probably null |
Het |
| Wscd2 |
A |
T |
5: 113,726,206 (GRCm39) |
*572C |
probably null |
Het |
| Xpo7 |
A |
G |
14: 70,919,787 (GRCm39) |
L676P |
probably damaging |
Het |
| Zbtb32 |
A |
C |
7: 30,291,244 (GRCm39) |
L17W |
probably damaging |
Het |
|
| Other mutations in Smg7 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01751:Smg7
|
APN |
1 |
152,719,812 (GRCm39) |
missense |
possibly damaging |
0.68 |
|
IGL02320:Smg7
|
APN |
1 |
152,744,088 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
IGL02336:Smg7
|
APN |
1 |
152,719,030 (GRCm39) |
missense |
probably benign |
|
|
IGL02680:Smg7
|
APN |
1 |
152,721,145 (GRCm39) |
missense |
probably benign |
0.15 |
|
IGL03232:Smg7
|
APN |
1 |
152,715,907 (GRCm39) |
missense |
probably damaging |
1.00 |
|
chill
|
UTSW |
1 |
152,715,887 (GRCm39) |
splice site |
probably null |
|
|
R0322:Smg7
|
UTSW |
1 |
152,725,624 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0540:Smg7
|
UTSW |
1 |
152,731,713 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0685:Smg7
|
UTSW |
1 |
152,742,399 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0707:Smg7
|
UTSW |
1 |
152,746,508 (GRCm39) |
splice site |
probably null |
|
|
R1109:Smg7
|
UTSW |
1 |
152,721,334 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1118:Smg7
|
UTSW |
1 |
152,742,326 (GRCm39) |
splice site |
probably benign |
|
|
R1119:Smg7
|
UTSW |
1 |
152,742,326 (GRCm39) |
splice site |
probably benign |
|
|
R1458:Smg7
|
UTSW |
1 |
152,731,594 (GRCm39) |
splice site |
probably null |
|
|
R1759:Smg7
|
UTSW |
1 |
152,724,597 (GRCm39) |
missense |
probably benign |
0.20 |
|
R1846:Smg7
|
UTSW |
1 |
152,724,601 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2015:Smg7
|
UTSW |
1 |
152,736,259 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2155:Smg7
|
UTSW |
1 |
152,716,064 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R2199:Smg7
|
UTSW |
1 |
152,730,079 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2234:Smg7
|
UTSW |
1 |
152,744,064 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2235:Smg7
|
UTSW |
1 |
152,744,064 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3861:Smg7
|
UTSW |
1 |
152,728,349 (GRCm39) |
missense |
probably null |
1.00 |
|
R4597:Smg7
|
UTSW |
1 |
152,716,052 (GRCm39) |
critical splice donor site |
probably null |
|
|
R4672:Smg7
|
UTSW |
1 |
152,721,164 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4851:Smg7
|
UTSW |
1 |
152,720,020 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5486:Smg7
|
UTSW |
1 |
152,721,927 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5607:Smg7
|
UTSW |
1 |
152,718,985 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6131:Smg7
|
UTSW |
1 |
152,720,962 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6396:Smg7
|
UTSW |
1 |
152,724,351 (GRCm39) |
missense |
probably benign |
0.33 |
|
R6905:Smg7
|
UTSW |
1 |
152,725,757 (GRCm39) |
splice site |
probably null |
|
|
R6961:Smg7
|
UTSW |
1 |
152,717,334 (GRCm39) |
nonsense |
probably null |
|
|
R7051:Smg7
|
UTSW |
1 |
152,724,601 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7124:Smg7
|
UTSW |
1 |
152,753,831 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7146:Smg7
|
UTSW |
1 |
152,737,576 (GRCm39) |
missense |
probably benign |
0.34 |
|
R7573:Smg7
|
UTSW |
1 |
152,735,240 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7578:Smg7
|
UTSW |
1 |
152,721,181 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7621:Smg7
|
UTSW |
1 |
152,717,295 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R7956:Smg7
|
UTSW |
1 |
152,719,953 (GRCm39) |
missense |
probably benign |
0.02 |
|
R8167:Smg7
|
UTSW |
1 |
152,720,123 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R8751:Smg7
|
UTSW |
1 |
152,719,129 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8905:Smg7
|
UTSW |
1 |
152,715,817 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9082:Smg7
|
UTSW |
1 |
152,715,928 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R9229:Smg7
|
UTSW |
1 |
152,720,971 (GRCm39) |
missense |
possibly damaging |
0.72 |
|
R9260:Smg7
|
UTSW |
1 |
152,737,549 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9262:Smg7
|
UTSW |
1 |
152,721,262 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9323:Smg7
|
UTSW |
1 |
152,731,753 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9519:Smg7
|
UTSW |
1 |
152,735,196 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9732:Smg7
|
UTSW |
1 |
152,736,212 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTGGATGCCCTGACAACACAC -3'
(R):5'- CTCCAGATAACAGGGATAGGCG -3'
Sequencing Primer
(F):5'- CTCAAGACGCCTCTCAATCCGG -3'
(R):5'- CCTGCAGATAGGTGGAAAACTG -3'
|
| Posted On |
2018-05-04 |
Incidental Mutation