Incidental Mutation 'R2199:Smg7'
| ID |
238536 |
| 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 |
040201-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.924)
|
| Stock # |
R2199 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
1 |
| Chromosomal Location |
152712746-152778397 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 152730079 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Tyrosine
at position 405
(D405Y)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000107467
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000043560]
[ENSMUST00000073441]
[ENSMUST00000111836]
|
| AlphaFold |
Q5RJH6 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000043560
AA Change: D413Y
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000041241
Gene: ENSMUSG00000042772
AA Change: D413Y
| 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 damaging
Transcript: ENSMUST00000073441
AA Change: D405Y
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000073144
Gene: ENSMUSG00000042772
AA Change: D405Y
| 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 damaging
Transcript: ENSMUST00000111836
AA Change: D405Y
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000107467
Gene: ENSMUSG00000042772
AA Change: D405Y
| 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 |
noncoding transcript
Transcript: ENSMUST00000186692
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.6%
|
| 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 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: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca17 |
T |
C |
17: 24,554,598 (GRCm39) |
I119V |
probably benign |
Het |
| Arfgap2 |
T |
A |
2: 91,096,037 (GRCm39) |
|
probably null |
Het |
| Ccm2 |
T |
C |
11: 6,540,790 (GRCm39) |
V216A |
probably damaging |
Het |
| Ctdspl2 |
T |
C |
2: 121,817,510 (GRCm39) |
|
probably null |
Het |
| Dmxl2 |
T |
C |
9: 54,283,527 (GRCm39) |
T2769A |
probably benign |
Het |
| Dnah3 |
C |
T |
7: 119,550,792 (GRCm39) |
V3165M |
possibly damaging |
Het |
| Dnajc1 |
A |
C |
2: 18,313,710 (GRCm39) |
F137C |
probably damaging |
Het |
| Gli2 |
A |
T |
1: 118,765,378 (GRCm39) |
D924E |
possibly damaging |
Het |
| Gnrhr |
T |
C |
5: 86,345,677 (GRCm39) |
N3S |
probably benign |
Het |
| Grhl1 |
G |
T |
12: 24,662,169 (GRCm39) |
R536L |
probably damaging |
Het |
| Hormad1 |
T |
C |
3: 95,475,033 (GRCm39) |
|
probably null |
Het |
| Il20 |
T |
A |
1: 130,838,476 (GRCm39) |
I74L |
probably benign |
Het |
| Ints11 |
A |
G |
4: 155,959,738 (GRCm39) |
K115R |
probably benign |
Het |
| Irx4 |
A |
T |
13: 73,413,720 (GRCm39) |
E63D |
probably benign |
Het |
| Itch |
A |
C |
2: 155,044,141 (GRCm39) |
Q482P |
probably benign |
Het |
| Kctd8 |
C |
A |
5: 69,498,588 (GRCm39) |
M19I |
probably benign |
Het |
| Klhl31 |
T |
C |
9: 77,557,383 (GRCm39) |
L33P |
probably damaging |
Het |
| Lrp1 |
A |
T |
10: 127,382,709 (GRCm39) |
C3691S |
probably damaging |
Het |
| Lrrc39 |
A |
G |
3: 116,364,610 (GRCm39) |
D167G |
probably damaging |
Het |
| Lrrd1 |
A |
T |
5: 3,916,478 (GRCm39) |
I832L |
possibly damaging |
Het |
| Lrriq1 |
A |
G |
10: 102,904,774 (GRCm39) |
V1620A |
probably damaging |
Het |
| Ltbr |
T |
C |
6: 125,289,024 (GRCm39) |
K213E |
probably benign |
Het |
| Megf8 |
T |
A |
7: 25,039,039 (GRCm39) |
D883E |
possibly damaging |
Het |
| Nherf2 |
T |
C |
17: 24,859,570 (GRCm39) |
E174G |
probably null |
Het |
| Nmt1 |
T |
A |
11: 102,954,682 (GRCm39) |
S405T |
probably damaging |
Het |
| Nsd3 |
G |
T |
8: 26,156,073 (GRCm39) |
V547F |
probably damaging |
Het |
| Or4c110 |
A |
G |
2: 88,831,894 (GRCm39) |
V246A |
probably damaging |
Het |
| Or7g16 |
C |
A |
9: 18,727,219 (GRCm39) |
V124F |
probably damaging |
Het |
| Otud7a |
A |
G |
7: 63,407,404 (GRCm39) |
K569R |
possibly damaging |
Het |
| Otud7b |
A |
G |
3: 96,063,089 (GRCm39) |
Y776C |
probably damaging |
Het |
| Pcdh15 |
T |
C |
10: 74,006,341 (GRCm39) |
I73T |
probably damaging |
Het |
| Rnf213 |
A |
T |
11: 119,350,835 (GRCm39) |
H3890L |
probably benign |
Het |
| Sall3 |
T |
C |
18: 81,015,085 (GRCm39) |
T948A |
probably benign |
Het |
| Slc44a3 |
T |
C |
3: 121,307,393 (GRCm39) |
I198V |
probably benign |
Het |
| Synpo2l |
A |
G |
14: 20,711,987 (GRCm39) |
L211S |
probably benign |
Het |
| Thsd7b |
A |
G |
1: 130,145,895 (GRCm39) |
Y1601C |
probably benign |
Het |
| Traf4 |
T |
C |
11: 78,050,806 (GRCm39) |
Y450C |
probably damaging |
Het |
| Trpv1 |
A |
G |
11: 73,131,077 (GRCm39) |
K239E |
probably damaging |
Het |
| Ttn |
C |
T |
2: 76,585,150 (GRCm39) |
G20302S |
probably damaging |
Het |
| Ube2o |
A |
G |
11: 116,435,571 (GRCm39) |
S406P |
probably benign |
Het |
| Xrn2 |
C |
T |
2: 146,866,670 (GRCm39) |
A80V |
probably damaging |
Het |
| Zfp616 |
C |
T |
11: 73,975,456 (GRCm39) |
T575I |
possibly 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 |
|
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 |
|
R6401:Smg7
|
UTSW |
1 |
152,715,887 (GRCm39) |
splice site |
probably null |
|
|
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'- TGAGTATCAGGGGTACTTCAGG -3'
(R):5'- GATTTACATAGCCTTGAAGATGGC -3'
Sequencing Primer
(F):5'- GGTACTTCAGGAGAATTACCCAC -3'
(R):5'- GCCTTGAAGATGGCTGAGG -3'
|
| Posted On |
2014-10-02 |
Incidental Mutation