Incidental Mutation 'R7116:Psd3'
| ID |
551777 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Psd3
|
| Ensembl Gene |
ENSMUSG00000030465 |
| Gene Name |
pleckstrin and Sec7 domain containing 3 |
| Synonyms |
EFA6D, 4931420C21Rik |
| MMRRC Submission |
045207-MU
|
| Accession Numbers |
Ncbi RefSeq: NM_030263.5, NM_027626.1; MGI:1918215
|
| Essential gene? |
Probably non essential
(E-score: 0.077)
|
| Stock # |
R7116 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
8 |
| Chromosomal Location |
67689082-68212027 bp(-) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 67713738 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 915
(V915A)
|
| 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 |
probably benign
Transcript: ENSMUST00000038959
AA Change: V916A
PolyPhen 2
Score 0.075 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000041339
Gene: ENSMUSG00000030465
AA Change: V916A
| 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 |
possibly damaging
Transcript: ENSMUST00000059374
AA Change: V287A
PolyPhen 2
Score 0.745 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000060306
Gene: ENSMUSG00000030465
AA Change: V287A
| 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: V429A
PolyPhen 2
Score 0.849 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000091178
Gene: ENSMUSG00000030465
AA Change: V429A
| 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 |
probably benign
Transcript: ENSMUST00000093469
AA Change: V915A
PolyPhen 2
Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000091179
Gene: ENSMUSG00000030465
AA Change: V915A
| 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 benign
Transcript: ENSMUST00000098696
AA Change: V915A
PolyPhen 2
Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000096293
Gene: ENSMUSG00000030465
AA Change: V915A
| 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 benign
Transcript: ENSMUST00000120071
AA Change: V287A
PolyPhen 2
Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
|
| SMART Domains |
Protein: ENSMUSP00000112545
Gene: ENSMUSG00000030465
AA Change: V287A
| Domain | Start | End | E-Value | Type |
|---|
|
PH
|
114 |
228 |
3.85e-15 |
SMART |
|
Blast:Sec7
|
247 |
309 |
3e-11 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000212505
AA Change: V946A
PolyPhen 2
Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000212960
AA Change: V1200A
PolyPhen 2
Score 0.052 (Sensitivity: 0.94; Specificity: 0.83)
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.8%
|
| Validation Efficiency |
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 59 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Actn1 |
A |
G |
12: 80,204,977 (GRCm38) |
S109P |
probably damaging |
Het |
| Afg3l1 |
T |
G |
8: 123,489,862 (GRCm38) |
L280R |
probably damaging |
Het |
| Akap13 |
T |
A |
7: 75,720,195 (GRCm38) |
S129T |
probably benign |
Het |
| Ankrd11 |
A |
G |
8: 122,896,130 (GRCm38) |
S328P |
probably damaging |
Het |
| Aox3 |
A |
T |
1: 58,153,530 (GRCm38) |
E554D |
probably benign |
Het |
| Bcl11a |
T |
C |
11: 24,163,839 (GRCm38) |
V394A |
probably damaging |
Het |
| Cass4 |
A |
G |
2: 172,427,969 (GRCm38) |
Y657C |
unknown |
Het |
| Ccdc88a |
C |
T |
11: 29,504,051 (GRCm38) |
A1738V |
probably benign |
Het |
| Cfap74 |
T |
C |
4: 155,455,061 (GRCm38) |
F948L |
unknown |
Het |
| Chgb |
A |
T |
2: 132,781,317 (GRCm38) |
|
probably benign |
Het |
| Coro1c |
C |
T |
5: 113,852,206 (GRCm38) |
W138* |
probably null |
Het |
| Dgkb |
A |
G |
12: 37,981,990 (GRCm38) |
Q17R |
probably benign |
Het |
| Esco2 |
A |
G |
14: 65,826,557 (GRCm38) |
Y393H |
probably damaging |
Het |
| Eya3 |
T |
A |
4: 132,694,799 (GRCm38) |
D228E |
probably benign |
Het |
| Fat2 |
T |
C |
11: 55,282,336 (GRCm38) |
D2517G |
probably damaging |
Het |
| Fry |
T |
A |
5: 150,395,869 (GRCm38) |
|
probably null |
Het |
| Gal3st2b |
A |
T |
1: 93,940,776 (GRCm38) |
Q243L |
possibly damaging |
Het |
| Gimap9 |
C |
T |
6: 48,678,055 (GRCm38) |
A192V |
probably benign |
Het |
| Glg1 |
T |
A |
8: 111,178,957 (GRCm38) |
Q564L |
probably benign |
Het |
| H2-Aa |
A |
T |
17: 34,283,627 (GRCm38) |
Y188* |
probably null |
Het |
| Hira |
T |
C |
16: 18,912,114 (GRCm38) |
Y188H |
probably damaging |
Het |
| Ighv8-8 |
C |
T |
12: 115,294,194 (GRCm38) |
D76N |
probably benign |
Het |
| Irf6 |
T |
C |
1: 193,167,597 (GRCm38) |
F276L |
probably damaging |
Het |
| Itpr1 |
T |
C |
6: 108,481,268 (GRCm38) |
C2000R |
probably damaging |
Het |
| Jakmip3 |
T |
C |
7: 139,020,250 (GRCm38) |
V293A |
possibly damaging |
Het |
| Kcnh7 |
A |
G |
2: 62,877,270 (GRCm38) |
V132A |
probably benign |
Het |
| Kcnj1 |
A |
G |
9: 32,396,981 (GRCm38) |
T234A |
possibly damaging |
Het |
| Kpna3 |
T |
A |
14: 61,368,186 (GRCm38) |
N470I |
probably benign |
Het |
| Lamb2 |
T |
C |
9: 108,487,323 (GRCm38) |
F1121L |
probably damaging |
Het |
| Lingo1 |
T |
C |
9: 56,620,627 (GRCm38) |
D232G |
probably benign |
Het |
| Lpxn |
T |
A |
19: 12,811,258 (GRCm38) |
N70K |
probably benign |
Het |
| Ltbp4 |
T |
A |
7: 27,305,427 (GRCm38) |
H1657L |
probably damaging |
Het |
| Luzp2 |
C |
A |
7: 55,265,330 (GRCm38) |
F334L |
possibly damaging |
Het |
| Mgat5b |
A |
T |
11: 116,944,959 (GRCm38) |
S142C |
possibly damaging |
Het |
| Mroh7 |
G |
A |
4: 106,711,320 (GRCm38) |
T396I |
probably benign |
Het |
| Muc5b |
T |
C |
7: 141,863,750 (GRCm38) |
S3478P |
probably benign |
Het |
| Nfatc2 |
A |
T |
2: 168,507,349 (GRCm38) |
M626K |
probably benign |
Het |
| Nlrp14 |
A |
G |
7: 107,183,048 (GRCm38) |
D484G |
possibly damaging |
Het |
| Npc1 |
T |
C |
18: 12,211,544 (GRCm38) |
Y423C |
probably damaging |
Het |
| Nrsn1 |
A |
G |
13: 25,253,405 (GRCm38) |
I180T |
probably damaging |
Het |
| Olfr570 |
T |
A |
7: 102,900,635 (GRCm38) |
N89K |
probably benign |
Het |
| Olfr741 |
A |
T |
14: 50,485,568 (GRCm38) |
I37F |
probably benign |
Het |
| Osbpl6 |
A |
T |
2: 76,595,881 (GRCm38) |
I935F |
probably benign |
Het |
| Otog |
T |
C |
7: 46,298,265 (GRCm38) |
F96L |
probably damaging |
Het |
| Pde1b |
T |
C |
15: 103,528,318 (GRCm38) |
L534P |
possibly damaging |
Het |
| Pdzd8 |
C |
T |
19: 59,299,693 (GRCm38) |
E1092K |
probably damaging |
Het |
| Pfkl |
T |
C |
10: 78,001,415 (GRCm38) |
H108R |
probably benign |
Het |
| Pkhd1l1 |
G |
A |
15: 44,557,976 (GRCm38) |
V3047I |
probably benign |
Het |
| Plag1 |
A |
T |
4: 3,904,812 (GRCm38) |
C126* |
probably null |
Het |
| Pphln1 |
T |
A |
15: 93,455,525 (GRCm38) |
S229T |
probably benign |
Het |
| Pramel5 |
C |
T |
4: 144,273,881 (GRCm38) |
D42N |
possibly damaging |
Het |
| Ptdss1 |
T |
A |
13: 66,945,327 (GRCm38) |
I77N |
probably benign |
Het |
| Rsbn1 |
T |
A |
3: 103,914,576 (GRCm38) |
C3* |
probably null |
Het |
| Shank1 |
C |
T |
7: 44,327,161 (GRCm38) |
A561V |
unknown |
Het |
| Stip1 |
C |
T |
19: 7,021,810 (GRCm38) |
G467S |
possibly damaging |
Het |
| Sv2c |
A |
T |
13: 95,976,644 (GRCm38) |
V599E |
probably damaging |
Het |
| Vmn2r37 |
T |
C |
7: 9,217,899 (GRCm38) |
T322A |
probably benign |
Het |
| Vmn2r60 |
T |
A |
7: 42,137,063 (GRCm38) |
M430K |
probably benign |
Het |
| Wipf3 |
T |
A |
6: 54,481,919 (GRCm38) |
|
probably null |
Het |
|
| Other mutations in Psd3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00769:Psd3
|
APN |
8 |
67,908,679 (GRCm38) |
splice site |
probably benign |
|
|
IGL01095:Psd3
|
APN |
8 |
67,908,513 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL01139:Psd3
|
APN |
8 |
67,908,535 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL01330:Psd3
|
APN |
8 |
67,697,178 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL01350:Psd3
|
APN |
8 |
67,720,892 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL01487:Psd3
|
APN |
8 |
67,697,114 (GRCm38) |
missense |
probably benign |
0.01 |
|
IGL01780:Psd3
|
APN |
8 |
67,963,869 (GRCm38) |
missense |
probably benign |
|
|
IGL02020:Psd3
|
APN |
8 |
67,974,170 (GRCm38) |
intron |
probably benign |
|
|
IGL02232:Psd3
|
APN |
8 |
67,904,145 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL02350:Psd3
|
APN |
8 |
67,963,869 (GRCm38) |
missense |
probably benign |
|
|
IGL02357:Psd3
|
APN |
8 |
67,963,869 (GRCm38) |
missense |
probably benign |
|
|
PIT4495001:Psd3
|
UTSW |
8 |
67,963,913 (GRCm38) |
missense |
probably benign |
0.00 |
|
R0052:Psd3
|
UTSW |
8 |
67,882,979 (GRCm38) |
critical splice donor site |
probably null |
|
|
R0052:Psd3
|
UTSW |
8 |
67,882,979 (GRCm38) |
critical splice donor site |
probably null |
|
|
R0242:Psd3
|
UTSW |
8 |
67,758,086 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R0242:Psd3
|
UTSW |
8 |
67,758,086 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R0581:Psd3
|
UTSW |
8 |
67,720,946 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0655:Psd3
|
UTSW |
8 |
67,963,689 (GRCm38) |
missense |
probably benign |
0.19 |
|
R1740:Psd3
|
UTSW |
8 |
68,120,839 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1789:Psd3
|
UTSW |
8 |
67,960,565 (GRCm38) |
missense |
probably benign |
0.26 |
|
R1847:Psd3
|
UTSW |
8 |
67,720,004 (GRCm38) |
missense |
possibly damaging |
0.93 |
|
R1951:Psd3
|
UTSW |
8 |
67,963,487 (GRCm38) |
missense |
probably benign |
0.00 |
|
R1954:Psd3
|
UTSW |
8 |
67,697,075 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R2143:Psd3
|
UTSW |
8 |
67,964,351 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4387:Psd3
|
UTSW |
8 |
68,000,761 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4801:Psd3
|
UTSW |
8 |
68,121,148 (GRCm38) |
missense |
probably benign |
|
|
R4802:Psd3
|
UTSW |
8 |
68,121,148 (GRCm38) |
missense |
probably benign |
|
|
R4913:Psd3
|
UTSW |
8 |
68,121,169 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R5045:Psd3
|
UTSW |
8 |
67,713,825 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R5173:Psd3
|
UTSW |
8 |
67,696,989 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5264:Psd3
|
UTSW |
8 |
67,713,725 (GRCm38) |
missense |
probably benign |
0.23 |
|
R5350:Psd3
|
UTSW |
8 |
67,908,861 (GRCm38) |
missense |
probably benign |
0.00 |
|
R5816:Psd3
|
UTSW |
8 |
67,960,510 (GRCm38) |
missense |
possibly damaging |
0.90 |
|
R5994:Psd3
|
UTSW |
8 |
67,719,968 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R6157:Psd3
|
UTSW |
8 |
68,121,527 (GRCm38) |
start codon destroyed |
probably benign |
0.14 |
|
R6241:Psd3
|
UTSW |
8 |
67,818,139 (GRCm38) |
intron |
probably benign |
|
|
R6586:Psd3
|
UTSW |
8 |
67,963,545 (GRCm38) |
missense |
probably damaging |
0.96 |
|
R6735:Psd3
|
UTSW |
8 |
68,120,746 (GRCm38) |
critical splice donor site |
probably null |
|
|
R6908:Psd3
|
UTSW |
8 |
67,964,177 (GRCm38) |
missense |
probably benign |
0.00 |
|
R6984:Psd3
|
UTSW |
8 |
67,818,045 (GRCm38) |
missense |
possibly damaging |
0.85 |
|
R7082:Psd3
|
UTSW |
8 |
67,904,148 (GRCm38) |
missense |
probably benign |
0.03 |
|
R7297:Psd3
|
UTSW |
8 |
68,121,034 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R7334:Psd3
|
UTSW |
8 |
67,908,705 (GRCm38) |
missense |
possibly damaging |
0.94 |
|
R7348:Psd3
|
UTSW |
8 |
67,790,931 (GRCm38) |
missense |
possibly damaging |
0.65 |
|
R7357:Psd3
|
UTSW |
8 |
68,121,497 (GRCm38) |
missense |
probably benign |
0.01 |
|
R7369:Psd3
|
UTSW |
8 |
67,904,166 (GRCm38) |
missense |
possibly damaging |
0.95 |
|
R7385:Psd3
|
UTSW |
8 |
68,000,756 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7733:Psd3
|
UTSW |
8 |
68,120,916 (GRCm38) |
missense |
possibly damaging |
0.75 |
|
R7873:Psd3
|
UTSW |
8 |
67,882,982 (GRCm38) |
missense |
possibly damaging |
0.95 |
|
R8110:Psd3
|
UTSW |
8 |
68,121,056 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R8765:Psd3
|
UTSW |
8 |
67,963,441 (GRCm38) |
missense |
possibly damaging |
0.69 |
|
R8768:Psd3
|
UTSW |
8 |
67,964,351 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R8817:Psd3
|
UTSW |
8 |
67,960,483 (GRCm38) |
missense |
possibly damaging |
0.95 |
|
R8837:Psd3
|
UTSW |
8 |
67,719,944 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R8878:Psd3
|
UTSW |
8 |
67,758,098 (GRCm38) |
missense |
probably benign |
0.28 |
|
R8903:Psd3
|
UTSW |
8 |
67,713,293 (GRCm38) |
missense |
unknown |
|
|
R8955:Psd3
|
UTSW |
8 |
67,963,809 (GRCm38) |
missense |
probably benign |
0.08 |
|
R9216:Psd3
|
UTSW |
8 |
68,120,887 (GRCm38) |
missense |
probably benign |
0.00 |
|
R9241:Psd3
|
UTSW |
8 |
67,963,315 (GRCm38) |
missense |
probably benign |
0.00 |
|
R9351:Psd3
|
UTSW |
8 |
67,960,649 (GRCm38) |
missense |
probably benign |
0.18 |
|
R9449:Psd3
|
UTSW |
8 |
67,713,181 (GRCm38) |
missense |
unknown |
|
|
R9451:Psd3
|
UTSW |
8 |
67,910,835 (GRCm38) |
missense |
unknown |
|
|
R9709:Psd3
|
UTSW |
8 |
67,741,762 (GRCm38) |
missense |
probably null |
0.99 |
|
R9797:Psd3
|
UTSW |
8 |
67,758,126 (GRCm38) |
missense |
probably damaging |
0.99 |
|
Z1088:Psd3
|
UTSW |
8 |
67,906,260 (GRCm38) |
splice site |
silent |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GGGCTCCTGTCATATTAGGATGTC -3'
(R):5'- TTGGAAGGACTTAGGACCAATG -3'
Sequencing Primer
(F):5'- TGTCCTAAATTGGAGCCAGGAC -3'
(R):5'- GGACTTAGGACCAATGATAAATGTTG -3'
|
| Posted On |
2019-05-15 |
Incidental Mutation