Incidental Mutation 'PIT4802001:Smg6'
| ID |
556745 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smg6
|
| Ensembl Gene |
ENSMUSG00000038290 |
| Gene Name |
SMG6 nonsense mediated mRNA decay factor |
| Synonyms |
Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans) |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
PIT4802001 (G1)
|
| Quality Score |
209.009 |
|
Status
|
Not validated
|
| Chromosome |
11 |
| Chromosomal Location |
74816665-75055274 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 75046991 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Aspartic acid
at position 1228
(V1228D)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000043555
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000045281]
|
| AlphaFold |
P61406 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000045281
AA Change: V1228D
PolyPhen 2
Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000043555
Gene: ENSMUSG00000038290
AA Change: V1228D
| Domain | Start | End | E-Value | Type |
|---|
|
internal_repeat_1
|
42 |
99 |
7.68e-6 |
PROSPERO |
|
internal_repeat_1
|
135 |
188 |
7.68e-6 |
PROSPERO |
|
low complexity region
|
212 |
227 |
N/A |
INTRINSIC |
|
low complexity region
|
257 |
271 |
N/A |
INTRINSIC |
|
low complexity region
|
376 |
390 |
N/A |
INTRINSIC |
|
low complexity region
|
417 |
426 |
N/A |
INTRINSIC |
|
low complexity region
|
436 |
453 |
N/A |
INTRINSIC |
|
low complexity region
|
538 |
549 |
N/A |
INTRINSIC |
|
coiled coil region
|
574 |
600 |
N/A |
INTRINSIC |
|
Pfam:EST1
|
637 |
742 |
1.8e-18 |
PFAM |
|
Pfam:EST1_DNA_bind
|
750 |
1106 |
1.6e-78 |
PFAM |
|
coiled coil region
|
1197 |
1234 |
N/A |
INTRINSIC |
|
PINc
|
1245 |
1396 |
2.85e-25 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000130145
|
| SMART Domains |
Protein: ENSMUSP00000120229
Gene: ENSMUSG00000038290
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
35 |
61 |
N/A |
INTRINSIC |
|
Pfam:EST1
|
99 |
204 |
1.3e-19 |
PFAM |
|
Pfam:EST1_DNA_bind
|
212 |
339 |
7.3e-37 |
PFAM |
|
| Coding Region Coverage |
- 1x: 93.6%
- 3x: 91.0%
- 10x: 85.4%
- 20x: 73.7%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a component of the telomerase ribonucleoprotein complex responsible for the replication and maintenance of chromosome ends. The encoded protein also plays a role in the nonsense-mediated mRNA decay (NMD) pathway, providing the endonuclease activity near the premature translation termination codon that is needed to initiate NMD. Alternatively spliced transcript variants encoding distinct protein isoforms have been described. [provided by RefSeq, Feb 2014]
PHENOTYPE: Homozygosity for insertion of a transgene into intron 6 of the gene results in embryonic lethality. Mice homozygous for a knock-out allele exhibit prenatal lethality. Mice homozygous for a conditional allele activated in embryonic stem cells exhibit defective telomere maintenance and NMD. [provided by MGI curators]
|
| Allele List at MGI |
All alleles(52) : Gene trapped(52)
|
| Other mutations in this stock |
Total: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aatk |
A |
T |
11: 119,902,172 (GRCm39) |
D741E |
probably benign |
Het |
| Abca16 |
A |
G |
7: 120,139,351 (GRCm39) |
D1461G |
probably benign |
Het |
| Adam6a |
G |
T |
12: 113,509,078 (GRCm39) |
D484Y |
probably damaging |
Het |
| Akap5 |
T |
C |
12: 76,376,706 (GRCm39) |
Y713H |
probably damaging |
Het |
| AW554918 |
A |
G |
18: 25,473,132 (GRCm39) |
E312G |
possibly damaging |
Het |
| Car4 |
G |
A |
11: 84,855,231 (GRCm39) |
A157T |
probably damaging |
Het |
| Chst9 |
A |
T |
18: 15,585,849 (GRCm39) |
M238K |
probably benign |
Het |
| Ctbp2 |
G |
A |
7: 132,589,974 (GRCm39) |
H397Y |
possibly damaging |
Het |
| Cyp3a59 |
A |
G |
5: 146,039,611 (GRCm39) |
M295V |
probably benign |
Het |
| Daglb |
T |
C |
5: 143,488,803 (GRCm39) |
Y586H |
probably benign |
Het |
| Ehbp1l1 |
G |
T |
19: 5,769,603 (GRCm39) |
P567T |
possibly damaging |
Het |
| Emilin2 |
A |
G |
17: 71,580,464 (GRCm39) |
I754T |
probably damaging |
Het |
| Esyt2 |
G |
A |
12: 116,329,457 (GRCm39) |
A672T |
probably benign |
Het |
| Evx1 |
G |
T |
6: 52,291,175 (GRCm39) |
E116* |
probably null |
Het |
| Exph5 |
T |
C |
9: 53,286,278 (GRCm39) |
S1120P |
probably damaging |
Het |
| Fam184a |
A |
T |
10: 53,560,450 (GRCm39) |
L515* |
probably null |
Het |
| Flt4 |
T |
A |
11: 49,523,996 (GRCm39) |
D525E |
probably benign |
Het |
| Galt |
T |
C |
4: 41,756,764 (GRCm39) |
W135R |
probably damaging |
Het |
| Ifitm6 |
A |
T |
7: 140,596,648 (GRCm39) |
C42S |
probably damaging |
Het |
| Ift172 |
A |
G |
5: 31,442,610 (GRCm39) |
S186P |
probably benign |
Het |
| Kcnk3 |
A |
G |
5: 30,779,712 (GRCm39) |
E254G |
probably damaging |
Het |
| Kmt2b |
A |
G |
7: 30,278,996 (GRCm39) |
S1509P |
probably damaging |
Het |
| Ky |
T |
A |
9: 102,414,972 (GRCm39) |
S295T |
probably benign |
Het |
| Lrba |
T |
A |
3: 86,571,801 (GRCm39) |
Y2368* |
probably null |
Het |
| Mtmr4 |
T |
A |
11: 87,501,953 (GRCm39) |
V669E |
probably benign |
Het |
| Myh10 |
C |
T |
11: 68,655,918 (GRCm39) |
R471C |
probably damaging |
Het |
| Nav1 |
G |
A |
1: 135,380,671 (GRCm39) |
T1416I |
unknown |
Het |
| Nrip1 |
A |
C |
16: 76,090,157 (GRCm39) |
S467A |
probably damaging |
Het |
| Ntrk1 |
T |
A |
3: 87,695,941 (GRCm39) |
N190Y |
probably damaging |
Het |
| Or14a256 |
A |
T |
7: 86,265,763 (GRCm39) |
L30Q |
probably null |
Het |
| Or5h25 |
A |
C |
16: 58,930,964 (GRCm39) |
M3R |
probably benign |
Het |
| Pdxp |
A |
G |
15: 78,802,611 (GRCm39) |
S282G |
probably damaging |
Het |
| Phtf2 |
A |
T |
5: 21,006,904 (GRCm39) |
S220T |
probably damaging |
Het |
| Piezo2 |
A |
T |
18: 63,157,540 (GRCm39) |
V2390E |
probably damaging |
Het |
| Pop1 |
T |
G |
15: 34,529,229 (GRCm39) |
L783R |
probably benign |
Het |
| Prf1 |
G |
A |
10: 61,135,972 (GRCm39) |
A83T |
probably benign |
Het |
| Rab4b |
A |
G |
7: 26,875,267 (GRCm39) |
V50A |
probably benign |
Het |
| Rtn1 |
T |
A |
12: 72,351,100 (GRCm39) |
T370S |
probably benign |
Het |
| Sdr16c5 |
T |
A |
4: 4,012,423 (GRCm39) |
I123F |
probably damaging |
Het |
| Smim19 |
A |
G |
8: 22,963,539 (GRCm39) |
V23A |
probably benign |
Het |
| Sox13 |
A |
T |
1: 133,313,996 (GRCm39) |
I346N |
probably damaging |
Het |
| Tap1 |
T |
A |
17: 34,412,165 (GRCm39) |
Y457N |
probably damaging |
Het |
| Tbck |
C |
T |
3: 132,458,427 (GRCm39) |
P686S |
probably damaging |
Het |
| Tcof1 |
A |
G |
18: 60,965,010 (GRCm39) |
S570P |
unknown |
Het |
| Tmc5 |
A |
T |
7: 118,271,449 (GRCm39) |
M921L |
probably benign |
Het |
| Ttc6 |
A |
G |
12: 57,772,462 (GRCm39) |
Y1594C |
possibly damaging |
Het |
| Virma |
T |
A |
4: 11,546,008 (GRCm39) |
H1615Q |
probably damaging |
Het |
| Vmn1r19 |
T |
A |
6: 57,382,037 (GRCm39) |
Y197N |
probably damaging |
Het |
| Vps13c |
T |
C |
9: 67,845,068 (GRCm39) |
F2051L |
probably damaging |
Het |
| Wdr6 |
C |
T |
9: 108,451,765 (GRCm39) |
C706Y |
probably damaging |
Het |
| Zfand4 |
A |
G |
6: 116,261,736 (GRCm39) |
N100D |
probably damaging |
Het |
|
| Other mutations in Smg6 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00952:Smg6
|
APN |
11 |
74,819,974 (GRCm39) |
missense |
probably benign |
|
|
IGL01146:Smg6
|
APN |
11 |
74,821,254 (GRCm39) |
nonsense |
probably null |
|
|
IGL01505:Smg6
|
APN |
11 |
75,047,117 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01541:Smg6
|
APN |
11 |
74,816,770 (GRCm39) |
missense |
probably benign |
0.43 |
|
IGL01636:Smg6
|
APN |
11 |
74,825,929 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL02379:Smg6
|
APN |
11 |
74,944,751 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02794:Smg6
|
APN |
11 |
74,944,760 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02964:Smg6
|
APN |
11 |
74,821,576 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL03057:Smg6
|
APN |
11 |
74,826,260 (GRCm39) |
nonsense |
probably null |
|
|
1mM(1):Smg6
|
UTSW |
11 |
74,825,815 (GRCm39) |
splice site |
probably benign |
|
|
IGL03097:Smg6
|
UTSW |
11 |
74,823,252 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0269:Smg6
|
UTSW |
11 |
75,053,757 (GRCm39) |
missense |
probably benign |
|
|
R0344:Smg6
|
UTSW |
11 |
74,820,647 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0437:Smg6
|
UTSW |
11 |
74,820,527 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0452:Smg6
|
UTSW |
11 |
74,821,039 (GRCm39) |
missense |
probably benign |
|
|
R0511:Smg6
|
UTSW |
11 |
74,819,884 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0617:Smg6
|
UTSW |
11 |
75,053,757 (GRCm39) |
missense |
probably benign |
|
|
R0737:Smg6
|
UTSW |
11 |
75,050,662 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1715:Smg6
|
UTSW |
11 |
74,820,256 (GRCm39) |
missense |
probably benign |
|
|
R1780:Smg6
|
UTSW |
11 |
74,836,942 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1927:Smg6
|
UTSW |
11 |
75,033,674 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2073:Smg6
|
UTSW |
11 |
74,821,120 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2171:Smg6
|
UTSW |
11 |
74,929,472 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2513:Smg6
|
UTSW |
11 |
74,820,502 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3943:Smg6
|
UTSW |
11 |
74,820,367 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3944:Smg6
|
UTSW |
11 |
74,820,367 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4275:Smg6
|
UTSW |
11 |
74,884,700 (GRCm39) |
intron |
probably benign |
|
|
R4369:Smg6
|
UTSW |
11 |
74,823,269 (GRCm39) |
nonsense |
probably null |
|
|
R4452:Smg6
|
UTSW |
11 |
74,880,967 (GRCm39) |
missense |
probably benign |
0.14 |
|
R4864:Smg6
|
UTSW |
11 |
74,820,988 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R4885:Smg6
|
UTSW |
11 |
74,932,744 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5043:Smg6
|
UTSW |
11 |
74,820,721 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R5189:Smg6
|
UTSW |
11 |
74,932,822 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5378:Smg6
|
UTSW |
11 |
74,932,820 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
R5518:Smg6
|
UTSW |
11 |
74,944,724 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5725:Smg6
|
UTSW |
11 |
74,821,439 (GRCm39) |
missense |
probably benign |
0.45 |
|
R5746:Smg6
|
UTSW |
11 |
75,030,113 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6151:Smg6
|
UTSW |
11 |
75,047,033 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6319:Smg6
|
UTSW |
11 |
75,047,048 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6349:Smg6
|
UTSW |
11 |
74,944,600 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R6500:Smg6
|
UTSW |
11 |
74,821,331 (GRCm39) |
missense |
possibly damaging |
0.74 |
|
R6619:Smg6
|
UTSW |
11 |
74,823,279 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6820:Smg6
|
UTSW |
11 |
74,932,790 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6923:Smg6
|
UTSW |
11 |
74,820,169 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
R7361:Smg6
|
UTSW |
11 |
74,820,979 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7494:Smg6
|
UTSW |
11 |
74,820,449 (GRCm39) |
missense |
probably benign |
|
|
R7498:Smg6
|
UTSW |
11 |
74,819,932 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7681:Smg6
|
UTSW |
11 |
74,822,531 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7710:Smg6
|
UTSW |
11 |
74,821,445 (GRCm39) |
missense |
probably benign |
0.26 |
|
R7770:Smg6
|
UTSW |
11 |
74,884,687 (GRCm39) |
missense |
unknown |
|
|
R8159:Smg6
|
UTSW |
11 |
74,929,465 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8381:Smg6
|
UTSW |
11 |
74,822,566 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8463:Smg6
|
UTSW |
11 |
74,820,886 (GRCm39) |
missense |
probably benign |
0.14 |
|
R8509:Smg6
|
UTSW |
11 |
74,932,702 (GRCm39) |
missense |
probably benign |
0.04 |
|
R8557:Smg6
|
UTSW |
11 |
75,047,064 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8743:Smg6
|
UTSW |
11 |
74,820,859 (GRCm39) |
missense |
probably benign |
|
|
R9240:Smg6
|
UTSW |
11 |
74,825,884 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9312:Smg6
|
UTSW |
11 |
74,820,877 (GRCm39) |
missense |
probably benign |
0.27 |
|
X0018:Smg6
|
UTSW |
11 |
74,820,812 (GRCm39) |
missense |
possibly damaging |
0.76 |
|
Z1186:Smg6
|
UTSW |
11 |
75,047,092 (GRCm39) |
missense |
probably benign |
0.06 |
|
Z1187:Smg6
|
UTSW |
11 |
75,047,092 (GRCm39) |
missense |
probably benign |
0.06 |
|
Z1188:Smg6
|
UTSW |
11 |
75,047,092 (GRCm39) |
missense |
probably benign |
0.06 |
|
Z1189:Smg6
|
UTSW |
11 |
75,047,092 (GRCm39) |
missense |
probably benign |
0.06 |
|
Z1190:Smg6
|
UTSW |
11 |
75,047,092 (GRCm39) |
missense |
probably benign |
0.06 |
|
Z1191:Smg6
|
UTSW |
11 |
75,047,092 (GRCm39) |
missense |
probably benign |
0.06 |
|
Z1192:Smg6
|
UTSW |
11 |
75,047,092 (GRCm39) |
missense |
probably benign |
0.06 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTAGTGAGACTTCAGGCCTGG -3'
(R):5'- CATGTCTAGGGTTGCTCTGTCC -3'
Sequencing Primer
(F):5'- GCCTGGGCCATTTGGTC -3'
(R):5'- GGGTTGCTCTGTCCTCCCG -3'
|
| Posted On |
2019-06-07 |
Incidental Mutation