Incidental Mutation 'R3861:Smg7'
| ID |
276321 |
| 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 |
040788-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.924)
|
| Stock # |
R3861 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
152712746-152778397 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 152728349 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Lysine
at position 439
(R439K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000041241
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000043560]
[ENSMUST00000073441]
[ENSMUST00000111836]
|
| AlphaFold |
Q5RJH6 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000043560
AA Change: R439K
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000041241
Gene: ENSMUSG00000042772
AA Change: R439K
| 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 null
Transcript: ENSMUST00000073441
AA Change: R431K
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000073144
Gene: ENSMUSG00000042772
AA Change: R431K
| 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 null
Transcript: ENSMUST00000111836
AA Change: R431K
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000107467
Gene: ENSMUSG00000042772
AA Change: R431K
| 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
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000186900
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000188937
|
| Meta Mutation Damage Score |
0.3063 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.8%
|
| Validation Efficiency |
100% (55/55) |
| 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: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 5730507C01Rik |
G |
A |
12: 18,583,411 (GRCm39) |
S157N |
probably benign |
Het |
| A830018L16Rik |
T |
C |
1: 11,658,778 (GRCm39) |
|
probably benign |
Het |
| Akip1 |
C |
T |
7: 109,306,613 (GRCm39) |
|
probably benign |
Het |
| Anxa5 |
T |
C |
3: 36,504,807 (GRCm39) |
T252A |
probably benign |
Het |
| Arhgef10l |
A |
G |
4: 140,242,798 (GRCm39) |
F1072L |
possibly damaging |
Het |
| Armc1 |
C |
T |
3: 19,189,196 (GRCm39) |
R186Q |
probably damaging |
Het |
| Atxn2l |
A |
T |
7: 126,101,123 (GRCm39) |
|
probably null |
Het |
| Cadps2 |
A |
G |
6: 23,355,860 (GRCm39) |
I849T |
probably damaging |
Het |
| Ccdc28a |
T |
A |
10: 18,100,743 (GRCm39) |
Q28L |
probably damaging |
Het |
| Cdh4 |
T |
A |
2: 179,515,890 (GRCm39) |
V356D |
probably damaging |
Het |
| Chd8 |
T |
A |
14: 52,474,578 (GRCm39) |
Q151L |
probably benign |
Het |
| Chgb |
T |
A |
2: 132,635,064 (GRCm39) |
H335Q |
probably damaging |
Het |
| Col19a1 |
G |
A |
1: 24,365,098 (GRCm39) |
P506S |
probably damaging |
Het |
| Col5a2 |
T |
C |
1: 45,419,397 (GRCm39) |
T1228A |
probably damaging |
Het |
| Cpxm2 |
A |
G |
7: 131,656,648 (GRCm39) |
V538A |
probably benign |
Het |
| Cramp1 |
A |
T |
17: 25,216,588 (GRCm39) |
|
probably benign |
Het |
| Cttnbp2 |
T |
C |
6: 18,423,832 (GRCm39) |
R831G |
probably benign |
Het |
| Cyp4f17 |
A |
G |
17: 32,747,078 (GRCm39) |
D436G |
probably damaging |
Het |
| Dcaf6 |
A |
T |
1: 165,256,838 (GRCm39) |
N48K |
probably damaging |
Het |
| Ddx50 |
C |
A |
10: 62,478,725 (GRCm39) |
V154L |
possibly damaging |
Het |
| Dnah9 |
T |
C |
11: 65,943,820 (GRCm39) |
|
probably benign |
Het |
| Dnm3 |
T |
A |
1: 162,138,974 (GRCm39) |
I395L |
possibly damaging |
Het |
| Elp2 |
C |
T |
18: 24,739,977 (GRCm39) |
R68C |
probably benign |
Het |
| Frg1 |
A |
T |
8: 41,860,820 (GRCm39) |
|
probably null |
Het |
| Fsip2 |
G |
T |
2: 82,815,120 (GRCm39) |
D3618Y |
probably damaging |
Het |
| Gabra2 |
T |
C |
5: 71,130,886 (GRCm39) |
D314G |
probably damaging |
Het |
| Gramd1a |
A |
C |
7: 30,835,365 (GRCm39) |
D407E |
possibly damaging |
Het |
| Grm5 |
T |
A |
7: 87,779,202 (GRCm39) |
S881T |
possibly damaging |
Het |
| Ikbkb |
T |
A |
8: 23,168,852 (GRCm39) |
I216F |
possibly damaging |
Het |
| Kif3a |
T |
C |
11: 53,488,805 (GRCm39) |
V634A |
probably benign |
Het |
| Ltbp1 |
A |
T |
17: 75,666,333 (GRCm39) |
Y1342F |
possibly damaging |
Het |
| Mia2 |
G |
T |
12: 59,155,807 (GRCm39) |
V508L |
probably benign |
Het |
| Mtus2 |
C |
T |
5: 148,250,223 (GRCm39) |
T155M |
probably damaging |
Het |
| Napepld |
A |
T |
5: 21,888,287 (GRCm39) |
V54E |
probably benign |
Het |
| Nlrc4 |
T |
C |
17: 74,752,616 (GRCm39) |
E589G |
probably benign |
Het |
| Nphp3 |
G |
T |
9: 103,916,525 (GRCm39) |
|
probably benign |
Het |
| Nr2f1 |
T |
A |
13: 78,343,794 (GRCm39) |
R10* |
probably null |
Het |
| Nsfl1c |
C |
A |
2: 151,352,824 (GRCm39) |
|
probably null |
Het |
| Or14a258 |
A |
G |
7: 86,035,331 (GRCm39) |
V179A |
possibly damaging |
Het |
| Pcdhgc3 |
A |
G |
18: 37,941,581 (GRCm39) |
T661A |
probably damaging |
Het |
| Pdzrn3 |
A |
G |
6: 101,149,332 (GRCm39) |
V332A |
possibly damaging |
Het |
| Pip4p2 |
A |
G |
4: 14,902,506 (GRCm39) |
N169S |
probably damaging |
Het |
| Pkhd1 |
C |
T |
1: 20,271,151 (GRCm39) |
C3134Y |
probably damaging |
Het |
| Ptprz1 |
T |
C |
6: 23,036,894 (GRCm39) |
V1131A |
probably damaging |
Het |
| Rccd1 |
T |
C |
7: 79,970,116 (GRCm39) |
E167G |
probably benign |
Het |
| Ror1 |
T |
C |
4: 100,265,120 (GRCm39) |
I198T |
possibly damaging |
Het |
| Rpl31-ps17 |
C |
T |
12: 54,748,397 (GRCm39) |
|
noncoding transcript |
Het |
| Scly |
C |
T |
1: 91,230,573 (GRCm39) |
|
probably benign |
Het |
| Scn4a |
T |
C |
11: 106,216,950 (GRCm39) |
|
probably benign |
Het |
| Sh3rf2 |
T |
C |
18: 42,286,384 (GRCm39) |
S594P |
probably damaging |
Het |
| Slc19a1 |
G |
A |
10: 76,877,809 (GRCm39) |
V115M |
possibly damaging |
Het |
| Slc26a6 |
A |
T |
9: 108,731,395 (GRCm39) |
|
probably benign |
Het |
| Spata31e3 |
T |
C |
13: 50,400,887 (GRCm39) |
K480E |
probably benign |
Het |
| Syne2 |
A |
G |
12: 76,013,253 (GRCm39) |
R2815G |
probably damaging |
Het |
| Trim75 |
G |
A |
8: 65,435,479 (GRCm39) |
R324C |
probably damaging |
Het |
| Ucp3 |
T |
C |
7: 100,129,458 (GRCm39) |
S98P |
probably benign |
Het |
| Zscan29 |
G |
C |
2: 120,991,212 (GRCm39) |
R859G |
probably benign |
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 |
|
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'- ACTTACATGGAGTGAACTGTGG -3'
(R):5'- AATGGACATGACACATTCTTCCC -3'
Sequencing Primer
(F):5'- AGCCTTATTCCCTTGAGACAGGG -3'
(R):5'- TGGACATGACACATTCTTCCCATACC -3'
|
| Posted On |
2015-04-06 |
Incidental Mutation