Incidental Mutation 'R7348:Psd3'
ID |
570359 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Psd3
|
Ensembl Gene |
ENSMUSG00000030465 |
Gene Name |
pleckstrin and Sec7 domain containing 3 |
Synonyms |
EFA6D, 4931420C21Rik |
MMRRC Submission |
045380-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.093)
|
Stock # |
R7348 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
8 |
Chromosomal Location |
68141734-68664679 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 68243583 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Asparagine to Serine
at position 685
(N685S)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000096293
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000038959]
[ENSMUST00000059374]
[ENSMUST00000093468]
[ENSMUST00000093469]
[ENSMUST00000098696]
[ENSMUST00000120071]
[ENSMUST00000212505]
[ENSMUST00000212960]
|
AlphaFold |
no structure available at present |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000038959
AA Change: N686S
PolyPhen 2
Score 0.700 (Sensitivity: 0.86; Specificity: 0.92)
|
SMART Domains |
Protein: ENSMUSP00000041339 Gene: ENSMUSG00000030465 AA Change: N686S
Domain | Start | End | E-Value | Type |
low complexity region
|
204 |
218 |
N/A |
INTRINSIC |
Blast:Sec7
|
431 |
496 |
5e-28 |
BLAST |
Sec7
|
502 |
693 |
3.9e-53 |
SMART |
PH
|
743 |
857 |
3.85e-15 |
SMART |
Blast:Sec7
|
876 |
938 |
2e-10 |
BLAST |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000059374
AA Change: N57S
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
SMART Domains |
Protein: ENSMUSP00000060306 Gene: ENSMUSG00000030465 AA Change: N57S
Domain | Start | End | E-Value | Type |
PH
|
114 |
228 |
3.85e-15 |
SMART |
Blast:Sec7
|
247 |
305 |
1e-8 |
BLAST |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000093468
AA Change: N199S
PolyPhen 2
Score 0.865 (Sensitivity: 0.83; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000091178 Gene: ENSMUSG00000030465 AA Change: N199S
Domain | Start | End | E-Value | Type |
Sec7
|
17 |
206 |
1.35e-56 |
SMART |
PH
|
256 |
370 |
3.85e-15 |
SMART |
Blast:Sec7
|
389 |
451 |
1e-10 |
BLAST |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000093469
AA Change: N685S
PolyPhen 2
Score 0.651 (Sensitivity: 0.87; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000091179 Gene: ENSMUSG00000030465 AA Change: N685S
Domain | Start | End | E-Value | Type |
low complexity region
|
204 |
218 |
N/A |
INTRINSIC |
Blast:Sec7
|
431 |
496 |
5e-28 |
BLAST |
Sec7
|
502 |
692 |
2.4e-53 |
SMART |
PH
|
742 |
856 |
3.85e-15 |
SMART |
Blast:Sec7
|
875 |
937 |
2e-10 |
BLAST |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000098696
AA Change: N685S
PolyPhen 2
Score 0.651 (Sensitivity: 0.87; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000096293 Gene: ENSMUSG00000030465 AA Change: N685S
Domain | Start | End | E-Value | Type |
low complexity region
|
204 |
218 |
N/A |
INTRINSIC |
Blast:Sec7
|
431 |
496 |
5e-28 |
BLAST |
Sec7
|
502 |
692 |
2.4e-53 |
SMART |
PH
|
742 |
856 |
3.85e-15 |
SMART |
Blast:Sec7
|
875 |
937 |
2e-10 |
BLAST |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000120071
AA Change: N57S
PolyPhen 2
Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000112545 Gene: ENSMUSG00000030465 AA Change: N57S
Domain | Start | End | E-Value | Type |
PH
|
114 |
228 |
3.85e-15 |
SMART |
Blast:Sec7
|
247 |
309 |
3e-11 |
BLAST |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000212505
AA Change: N716S
PolyPhen 2
Score 0.651 (Sensitivity: 0.87; Specificity: 0.91)
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000212960
AA Change: N970S
PolyPhen 2
Score 0.401 (Sensitivity: 0.89; Specificity: 0.89)
|
Meta Mutation Damage Score |
0.0657 |
Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 98.8%
|
Validation Efficiency |
99% (80/81) |
Allele List at MGI |
|
Other mutations in this stock |
Total: 79 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abra |
G |
A |
15: 41,729,555 (GRCm39) |
R282C |
probably damaging |
Het |
Adcy2 |
T |
A |
13: 68,882,794 (GRCm39) |
E314D |
possibly damaging |
Het |
Adgrl2 |
A |
T |
3: 148,523,402 (GRCm39) |
I274N |
|
Het |
Adpgk |
A |
G |
9: 59,221,069 (GRCm39) |
I292V |
probably benign |
Het |
Agtrap |
G |
T |
4: 148,165,054 (GRCm39) |
F124L |
probably benign |
Het |
Ankrd26 |
A |
G |
6: 118,485,525 (GRCm39) |
Y1450H |
probably damaging |
Het |
Ap4e1 |
A |
T |
2: 126,903,896 (GRCm39) |
S933C |
probably damaging |
Het |
Ap4e1 |
G |
T |
2: 126,903,897 (GRCm39) |
S933I |
possibly damaging |
Het |
Ap5s1 |
A |
T |
2: 131,054,572 (GRCm39) |
T128S |
possibly damaging |
Het |
Arih1 |
T |
C |
9: 59,393,341 (GRCm39) |
Y97C |
probably damaging |
Het |
Atp1a3 |
A |
G |
7: 24,678,251 (GRCm39) |
F1034S |
unknown |
Het |
Bmp6 |
T |
C |
13: 38,669,879 (GRCm39) |
S388P |
probably benign |
Het |
Ccdc39 |
A |
G |
3: 33,886,825 (GRCm39) |
V261A |
possibly damaging |
Het |
Ccdc66 |
C |
T |
14: 27,222,293 (GRCm39) |
C150Y |
probably damaging |
Het |
Cep89 |
G |
A |
7: 35,129,353 (GRCm39) |
R630H |
probably damaging |
Het |
Cln6 |
A |
G |
9: 62,756,458 (GRCm39) |
S201G |
probably benign |
Het |
Cntnap4 |
T |
C |
8: 113,391,909 (GRCm39) |
Y125H |
probably damaging |
Het |
Copa |
A |
G |
1: 171,929,790 (GRCm39) |
T286A |
possibly damaging |
Het |
Cul9 |
A |
T |
17: 46,821,919 (GRCm39) |
I1852K |
possibly damaging |
Het |
Cyp2j8 |
C |
A |
4: 96,332,877 (GRCm39) |
A490S |
probably benign |
Het |
Cyp2t4 |
A |
G |
7: 26,856,676 (GRCm39) |
I239V |
probably benign |
Het |
Dpcd |
A |
G |
19: 45,560,905 (GRCm39) |
Y111C |
probably damaging |
Het |
E2f7 |
C |
T |
10: 110,616,836 (GRCm39) |
T692I |
probably damaging |
Het |
Fastkd5 |
A |
G |
2: 130,457,055 (GRCm39) |
Y512H |
probably damaging |
Het |
Fastkd5 |
A |
C |
2: 130,458,359 (GRCm39) |
M77R |
probably benign |
Het |
Fhod3 |
A |
G |
18: 25,223,524 (GRCm39) |
R957G |
possibly damaging |
Het |
H6pd |
C |
A |
4: 150,068,359 (GRCm39) |
|
probably null |
Het |
Haus5 |
G |
T |
7: 30,356,391 (GRCm39) |
P544Q |
possibly damaging |
Het |
Ifi207 |
CTGTTGATGAAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATACAGTTGCTTGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATAGAGTTGCATATGGAGCCAGGAGGATGCTATATGTTGTTGATGAAGTTGCATGTGGAGCCAGGAG |
CTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATACAGTTGCTTGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATAGAGTTGCATATGGAGCCAGGAGGATGCTATATGTTGTTGATGAAGTTGCATGTGGAGCCAGGAG |
1: 173,556,762 (GRCm39) |
|
probably benign |
Het |
Igf2r |
A |
G |
17: 12,922,371 (GRCm39) |
Y1248H |
probably damaging |
Het |
Izumo3 |
T |
C |
4: 92,035,455 (GRCm39) |
N6S |
possibly damaging |
Het |
Lrp6 |
G |
T |
6: 134,427,781 (GRCm39) |
P1604T |
probably damaging |
Het |
Map3k8 |
T |
A |
18: 4,340,561 (GRCm39) |
H251L |
probably damaging |
Het |
Mapre3 |
T |
C |
5: 31,019,173 (GRCm39) |
Y6H |
probably benign |
Het |
Mlh3 |
G |
T |
12: 85,314,215 (GRCm39) |
P657Q |
probably damaging |
Het |
Mrgpra1 |
T |
C |
7: 46,985,157 (GRCm39) |
Y174C |
probably benign |
Het |
Ms4a6d |
G |
A |
19: 11,567,437 (GRCm39) |
Q155* |
probably null |
Het |
Myh1 |
C |
A |
11: 67,093,365 (GRCm39) |
P152Q |
probably damaging |
Het |
Myh6 |
A |
T |
14: 55,189,716 (GRCm39) |
L1110Q |
probably damaging |
Het |
Nf1 |
T |
A |
11: 79,427,676 (GRCm39) |
S1778T |
probably benign |
Het |
Nkpd1 |
G |
A |
7: 19,258,341 (GRCm39) |
E707K |
probably damaging |
Het |
Nlrp4a |
A |
G |
7: 26,143,698 (GRCm39) |
E21G |
probably damaging |
Het |
Nr4a3 |
T |
G |
4: 48,051,290 (GRCm39) |
S15A |
possibly damaging |
Het |
Or2f1 |
T |
C |
6: 42,721,790 (GRCm39) |
L273S |
possibly damaging |
Het |
Or5p1 |
T |
C |
7: 107,916,920 (GRCm39) |
V273A |
possibly damaging |
Het |
Or5p64 |
T |
C |
7: 107,855,330 (GRCm39) |
D5G |
probably benign |
Het |
Or7a38 |
A |
G |
10: 78,753,396 (GRCm39) |
T241A |
probably damaging |
Het |
Parg |
G |
A |
14: 31,972,036 (GRCm39) |
R677Q |
possibly damaging |
Het |
Pcsk5 |
A |
T |
19: 17,434,182 (GRCm39) |
C1395* |
probably null |
Het |
Psd2 |
G |
A |
18: 36,113,389 (GRCm39) |
S287N |
possibly damaging |
Het |
Pygb |
C |
T |
2: 150,628,903 (GRCm39) |
T39M |
probably benign |
Het |
Rbfox1 |
C |
A |
16: 7,225,888 (GRCm39) |
Y351* |
probably null |
Het |
Rftn1 |
A |
G |
17: 50,311,351 (GRCm39) |
L396P |
probably damaging |
Het |
S1pr1 |
A |
G |
3: 115,505,710 (GRCm39) |
Y295H |
probably damaging |
Het |
Scn5a |
T |
C |
9: 119,364,899 (GRCm39) |
M440V |
probably benign |
Het |
Sel1l2 |
T |
C |
2: 140,107,644 (GRCm39) |
N240S |
probably benign |
Het |
Skic3 |
T |
C |
13: 76,331,003 (GRCm39) |
F1478L |
possibly damaging |
Het |
Skint1 |
T |
C |
4: 111,878,770 (GRCm39) |
L234P |
probably damaging |
Het |
Skint11 |
T |
A |
4: 114,101,919 (GRCm39) |
Y311N |
probably benign |
Het |
Slc6a5 |
A |
T |
7: 49,559,915 (GRCm39) |
|
probably benign |
Het |
Tas2r134 |
T |
C |
2: 51,518,414 (GRCm39) |
S298P |
possibly damaging |
Het |
Tbcd |
C |
A |
11: 121,485,137 (GRCm39) |
A773D |
probably benign |
Het |
Tgoln1 |
G |
C |
6: 72,593,261 (GRCm39) |
T73R |
probably benign |
Het |
Tmem184a |
T |
C |
5: 139,799,809 (GRCm39) |
E24G |
probably null |
Het |
Tmem207 |
C |
A |
16: 26,335,577 (GRCm39) |
W53C |
possibly damaging |
Het |
Tns1 |
T |
A |
1: 73,956,076 (GRCm39) |
H549L |
possibly damaging |
Het |
Ttc41 |
G |
T |
10: 86,586,212 (GRCm39) |
E839* |
probably null |
Het |
Ufd1 |
T |
G |
16: 18,634,635 (GRCm39) |
|
probably benign |
Het |
Usp28 |
A |
G |
9: 48,942,177 (GRCm39) |
E713G |
probably benign |
Het |
Utrn |
A |
G |
10: 12,623,762 (GRCm39) |
W159R |
probably damaging |
Het |
Vcl |
C |
T |
14: 21,053,218 (GRCm39) |
A411V |
probably benign |
Het |
Vcl |
T |
A |
14: 21,059,020 (GRCm39) |
C545* |
probably null |
Het |
Vmn1r120 |
A |
T |
7: 20,787,377 (GRCm39) |
S111R |
probably damaging |
Het |
Wwox |
T |
A |
8: 115,199,392 (GRCm39) |
C146S |
probably benign |
Het |
Zbtb2 |
T |
C |
10: 4,324,574 (GRCm39) |
T57A |
possibly damaging |
Het |
Zfp362 |
T |
C |
4: 128,671,010 (GRCm39) |
D336G |
possibly damaging |
Het |
Zfp628 |
G |
A |
7: 4,924,817 (GRCm39) |
G1013E |
probably damaging |
Het |
Zfp704 |
A |
G |
3: 9,539,658 (GRCm39) |
S231P |
probably damaging |
Het |
Zhx3 |
G |
T |
2: 160,624,038 (GRCm39) |
S43* |
probably null |
Het |
|
Other mutations in Psd3 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00769:Psd3
|
APN |
8 |
68,361,331 (GRCm39) |
splice site |
probably benign |
|
IGL01095:Psd3
|
APN |
8 |
68,361,165 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01139:Psd3
|
APN |
8 |
68,361,187 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01330:Psd3
|
APN |
8 |
68,149,830 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01350:Psd3
|
APN |
8 |
68,173,544 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01487:Psd3
|
APN |
8 |
68,149,766 (GRCm39) |
missense |
probably benign |
0.01 |
IGL01780:Psd3
|
APN |
8 |
68,416,521 (GRCm39) |
missense |
probably benign |
|
IGL02020:Psd3
|
APN |
8 |
68,426,822 (GRCm39) |
intron |
probably benign |
|
IGL02232:Psd3
|
APN |
8 |
68,356,797 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL02350:Psd3
|
APN |
8 |
68,416,521 (GRCm39) |
missense |
probably benign |
|
IGL02357:Psd3
|
APN |
8 |
68,416,521 (GRCm39) |
missense |
probably benign |
|
PIT4495001:Psd3
|
UTSW |
8 |
68,416,565 (GRCm39) |
missense |
probably benign |
0.00 |
R0052:Psd3
|
UTSW |
8 |
68,335,631 (GRCm39) |
critical splice donor site |
probably null |
|
R0052:Psd3
|
UTSW |
8 |
68,335,631 (GRCm39) |
critical splice donor site |
probably null |
|
R0242:Psd3
|
UTSW |
8 |
68,210,738 (GRCm39) |
missense |
probably damaging |
0.99 |
R0242:Psd3
|
UTSW |
8 |
68,210,738 (GRCm39) |
missense |
probably damaging |
0.99 |
R0581:Psd3
|
UTSW |
8 |
68,173,598 (GRCm39) |
missense |
probably damaging |
1.00 |
R0655:Psd3
|
UTSW |
8 |
68,416,341 (GRCm39) |
missense |
probably benign |
0.19 |
R1740:Psd3
|
UTSW |
8 |
68,573,491 (GRCm39) |
missense |
probably damaging |
1.00 |
R1789:Psd3
|
UTSW |
8 |
68,413,217 (GRCm39) |
missense |
probably benign |
0.26 |
R1847:Psd3
|
UTSW |
8 |
68,172,656 (GRCm39) |
missense |
possibly damaging |
0.93 |
R1951:Psd3
|
UTSW |
8 |
68,416,139 (GRCm39) |
missense |
probably benign |
0.00 |
R1954:Psd3
|
UTSW |
8 |
68,149,727 (GRCm39) |
missense |
probably damaging |
1.00 |
R2143:Psd3
|
UTSW |
8 |
68,417,003 (GRCm39) |
missense |
probably damaging |
1.00 |
R4387:Psd3
|
UTSW |
8 |
68,453,413 (GRCm39) |
missense |
probably damaging |
1.00 |
R4801:Psd3
|
UTSW |
8 |
68,573,800 (GRCm39) |
missense |
probably benign |
|
R4802:Psd3
|
UTSW |
8 |
68,573,800 (GRCm39) |
missense |
probably benign |
|
R4913:Psd3
|
UTSW |
8 |
68,573,821 (GRCm39) |
missense |
probably damaging |
0.99 |
R5045:Psd3
|
UTSW |
8 |
68,166,477 (GRCm39) |
missense |
probably damaging |
0.99 |
R5173:Psd3
|
UTSW |
8 |
68,149,641 (GRCm39) |
missense |
probably damaging |
1.00 |
R5264:Psd3
|
UTSW |
8 |
68,166,377 (GRCm39) |
missense |
probably benign |
0.23 |
R5350:Psd3
|
UTSW |
8 |
68,361,513 (GRCm39) |
missense |
probably benign |
0.00 |
R5816:Psd3
|
UTSW |
8 |
68,413,162 (GRCm39) |
missense |
possibly damaging |
0.90 |
R5994:Psd3
|
UTSW |
8 |
68,172,620 (GRCm39) |
missense |
probably damaging |
1.00 |
R6157:Psd3
|
UTSW |
8 |
68,574,179 (GRCm39) |
start codon destroyed |
probably benign |
0.14 |
R6241:Psd3
|
UTSW |
8 |
68,270,791 (GRCm39) |
intron |
probably benign |
|
R6586:Psd3
|
UTSW |
8 |
68,416,197 (GRCm39) |
missense |
probably damaging |
0.96 |
R6735:Psd3
|
UTSW |
8 |
68,573,398 (GRCm39) |
critical splice donor site |
probably null |
|
R6908:Psd3
|
UTSW |
8 |
68,416,829 (GRCm39) |
missense |
probably benign |
0.00 |
R6984:Psd3
|
UTSW |
8 |
68,270,697 (GRCm39) |
missense |
possibly damaging |
0.85 |
R7082:Psd3
|
UTSW |
8 |
68,356,800 (GRCm39) |
missense |
probably benign |
0.03 |
R7116:Psd3
|
UTSW |
8 |
68,166,390 (GRCm39) |
missense |
probably benign |
0.12 |
R7297:Psd3
|
UTSW |
8 |
68,573,686 (GRCm39) |
missense |
probably damaging |
0.98 |
R7334:Psd3
|
UTSW |
8 |
68,361,357 (GRCm39) |
missense |
possibly damaging |
0.94 |
R7357:Psd3
|
UTSW |
8 |
68,574,149 (GRCm39) |
missense |
probably benign |
0.01 |
R7369:Psd3
|
UTSW |
8 |
68,356,818 (GRCm39) |
missense |
possibly damaging |
0.95 |
R7385:Psd3
|
UTSW |
8 |
68,453,408 (GRCm39) |
missense |
probably damaging |
1.00 |
R7733:Psd3
|
UTSW |
8 |
68,573,568 (GRCm39) |
missense |
possibly damaging |
0.75 |
R7873:Psd3
|
UTSW |
8 |
68,335,634 (GRCm39) |
missense |
possibly damaging |
0.95 |
R8110:Psd3
|
UTSW |
8 |
68,573,708 (GRCm39) |
missense |
probably damaging |
1.00 |
R8765:Psd3
|
UTSW |
8 |
68,416,093 (GRCm39) |
missense |
possibly damaging |
0.69 |
R8768:Psd3
|
UTSW |
8 |
68,417,003 (GRCm39) |
missense |
probably damaging |
1.00 |
R8817:Psd3
|
UTSW |
8 |
68,413,135 (GRCm39) |
missense |
possibly damaging |
0.95 |
R8837:Psd3
|
UTSW |
8 |
68,172,596 (GRCm39) |
missense |
probably damaging |
0.99 |
R8878:Psd3
|
UTSW |
8 |
68,210,750 (GRCm39) |
missense |
probably benign |
0.28 |
R8903:Psd3
|
UTSW |
8 |
68,165,945 (GRCm39) |
missense |
unknown |
|
R8955:Psd3
|
UTSW |
8 |
68,416,461 (GRCm39) |
missense |
probably benign |
0.08 |
R9216:Psd3
|
UTSW |
8 |
68,573,539 (GRCm39) |
missense |
probably benign |
0.00 |
R9241:Psd3
|
UTSW |
8 |
68,415,967 (GRCm39) |
missense |
probably benign |
0.00 |
R9351:Psd3
|
UTSW |
8 |
68,413,301 (GRCm39) |
missense |
probably benign |
0.18 |
R9449:Psd3
|
UTSW |
8 |
68,165,833 (GRCm39) |
missense |
unknown |
|
R9451:Psd3
|
UTSW |
8 |
68,363,487 (GRCm39) |
missense |
unknown |
|
R9709:Psd3
|
UTSW |
8 |
68,194,414 (GRCm39) |
missense |
probably null |
0.99 |
R9797:Psd3
|
UTSW |
8 |
68,210,778 (GRCm39) |
missense |
probably damaging |
0.99 |
Z1088:Psd3
|
UTSW |
8 |
68,358,912 (GRCm39) |
splice site |
silent |
|
|
Predicted Primers |
PCR Primer
(F):5'- GGGTTTCACACAAAGCAGGTC -3'
(R):5'- AAACTAAGTTTTGCCTCCCCTG -3'
Sequencing Primer
(F):5'- ACAAAGCAGGTCAGACAACTG -3'
(R):5'- TCTAGAGTTGTGCAGCCCAAC -3'
|
Posted On |
2019-09-13 |