Incidental Mutation 'R1951:Psd3'
| ID |
217302 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Psd3
|
| Ensembl Gene |
ENSMUSG00000030465 |
| Gene Name |
pleckstrin and Sec7 domain containing 3 |
| Synonyms |
EFA6D, 4931420C21Rik |
| MMRRC Submission |
039965-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.093)
|
| Stock # |
R1951 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
68141734-68664679 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 68416139 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Phenylalanine
at position 586
(C586F)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000148783
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000038959]
[ENSMUST00000093469]
[ENSMUST00000098696]
[ENSMUST00000212505]
[ENSMUST00000212960]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000038959
AA Change: C300F
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000041339
Gene: ENSMUSG00000030465
AA Change: C300F
| 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 benign
Transcript: ENSMUST00000093469
AA Change: C300F
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000091179
Gene: ENSMUSG00000030465
AA Change: C300F
| 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: C300F
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000096293
Gene: ENSMUSG00000030465
AA Change: C300F
| 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 |
noncoding transcript
Transcript: ENSMUST00000127631
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150169
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000212123
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000212505
AA Change: C333F
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000212960
AA Change: C586F
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.2%
|
| Validation Efficiency |
98% (84/86) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 82 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca15 |
C |
T |
7: 119,960,655 (GRCm39) |
R706C |
probably damaging |
Het |
| Adcy3 |
T |
C |
12: 4,258,624 (GRCm39) |
F847S |
probably benign |
Het |
| Alyref |
C |
G |
11: 120,486,758 (GRCm39) |
V168L |
probably damaging |
Het |
| Arhgap28 |
G |
A |
17: 68,208,336 (GRCm39) |
A44V |
probably benign |
Het |
| Asap3 |
C |
T |
4: 135,954,767 (GRCm39) |
R60* |
probably null |
Het |
| Baz1b |
T |
A |
5: 135,245,593 (GRCm39) |
N347K |
probably benign |
Het |
| Best2 |
T |
A |
8: 85,737,858 (GRCm39) |
N179I |
possibly damaging |
Het |
| Bfar |
C |
T |
16: 13,519,970 (GRCm39) |
S276L |
probably damaging |
Het |
| Bloc1s3 |
A |
G |
7: 19,241,483 (GRCm39) |
V15A |
possibly damaging |
Het |
| Borcs5 |
A |
G |
6: 134,687,230 (GRCm39) |
H196R |
unknown |
Het |
| Calhm3 |
A |
G |
19: 47,140,256 (GRCm39) |
L279P |
probably benign |
Het |
| Cand1 |
A |
T |
10: 119,043,925 (GRCm39) |
|
probably benign |
Het |
| Car15 |
T |
C |
16: 17,655,269 (GRCm39) |
D57G |
possibly damaging |
Het |
| Casp12 |
G |
A |
9: 5,348,959 (GRCm39) |
|
probably null |
Het |
| Cd93 |
T |
C |
2: 148,283,778 (GRCm39) |
T523A |
probably benign |
Het |
| Ces4a |
G |
A |
8: 105,864,729 (GRCm39) |
G69S |
probably damaging |
Het |
| Ckap5 |
A |
G |
2: 91,386,837 (GRCm39) |
|
probably benign |
Het |
| Col6a5 |
G |
A |
9: 105,814,156 (GRCm39) |
R619W |
unknown |
Het |
| Colec12 |
G |
A |
18: 9,859,975 (GRCm39) |
|
probably null |
Het |
| Crmp1 |
G |
A |
5: 37,430,699 (GRCm39) |
V222I |
possibly damaging |
Het |
| Crnkl1 |
G |
A |
2: 145,770,120 (GRCm39) |
A241V |
probably damaging |
Het |
| Ctbp2 |
A |
G |
7: 132,616,756 (GRCm39) |
S60P |
probably benign |
Het |
| Cyp2c68 |
T |
C |
19: 39,700,972 (GRCm39) |
Y282C |
probably benign |
Het |
| Dhx36 |
T |
C |
3: 62,391,694 (GRCm39) |
I551V |
probably damaging |
Het |
| Dlg5 |
T |
A |
14: 24,206,537 (GRCm39) |
|
probably benign |
Het |
| Dlgap1 |
A |
T |
17: 71,068,306 (GRCm39) |
I300F |
probably damaging |
Het |
| Dmd |
T |
A |
X: 82,874,123 (GRCm39) |
I1342N |
probably damaging |
Het |
| Dnah6 |
T |
A |
6: 73,061,704 (GRCm39) |
R2794* |
probably null |
Het |
| Fcgr1 |
G |
A |
3: 96,194,386 (GRCm39) |
T167I |
probably damaging |
Het |
| Fgl1 |
G |
T |
8: 41,650,387 (GRCm39) |
F187L |
probably benign |
Het |
| Fras1 |
T |
A |
5: 96,860,242 (GRCm39) |
V2096E |
probably benign |
Het |
| Gm10647 |
A |
G |
9: 66,705,762 (GRCm39) |
|
probably benign |
Het |
| Gm14226 |
G |
A |
2: 154,866,255 (GRCm39) |
D71N |
possibly damaging |
Het |
| Grip2 |
A |
T |
6: 91,760,829 (GRCm39) |
I284N |
probably damaging |
Het |
| Hirip3 |
A |
G |
7: 126,462,038 (GRCm39) |
R19G |
probably damaging |
Het |
| Ift70b |
A |
G |
2: 75,767,586 (GRCm39) |
L389P |
probably damaging |
Het |
| Irx5 |
A |
G |
8: 93,086,438 (GRCm39) |
N174D |
probably damaging |
Het |
| Itgal |
A |
G |
7: 126,929,317 (GRCm39) |
D1078G |
probably damaging |
Het |
| Khdc3 |
T |
C |
9: 73,010,519 (GRCm39) |
V123A |
possibly damaging |
Het |
| Klhl13 |
A |
G |
X: 23,127,820 (GRCm39) |
|
probably benign |
Het |
| Klhl42 |
T |
C |
6: 146,993,321 (GRCm39) |
S98P |
probably damaging |
Het |
| Lrp5 |
T |
C |
19: 3,670,298 (GRCm39) |
N602S |
possibly damaging |
Het |
| Lrrd1 |
A |
T |
5: 3,901,488 (GRCm39) |
I598F |
probably damaging |
Het |
| Ltbp1 |
A |
G |
17: 75,458,372 (GRCm39) |
T318A |
probably benign |
Het |
| Mfsd6 |
A |
G |
1: 52,748,517 (GRCm39) |
F116S |
probably damaging |
Het |
| Ncam1 |
T |
C |
9: 49,456,492 (GRCm39) |
I486V |
probably benign |
Het |
| Nptx1 |
A |
G |
11: 119,434,006 (GRCm39) |
|
probably null |
Het |
| Nrg1 |
T |
C |
8: 32,408,221 (GRCm39) |
Y4C |
probably damaging |
Het |
| Nsf |
G |
A |
11: 103,773,702 (GRCm39) |
R271* |
probably null |
Het |
| Or5d39 |
A |
G |
2: 87,979,641 (GRCm39) |
S241P |
possibly damaging |
Het |
| Or8g24 |
T |
A |
9: 38,989,580 (GRCm39) |
I154F |
probably benign |
Het |
| Or8k18 |
G |
C |
2: 86,085,440 (GRCm39) |
T199S |
probably benign |
Het |
| Or8k21 |
T |
A |
2: 86,145,504 (GRCm39) |
N42I |
probably damaging |
Het |
| Or8k24 |
A |
T |
2: 86,215,855 (GRCm39) |
H302Q |
probably benign |
Het |
| Pax2 |
A |
G |
19: 44,777,271 (GRCm39) |
T155A |
probably benign |
Het |
| Pdia4 |
A |
G |
6: 47,780,813 (GRCm39) |
Y212H |
probably damaging |
Het |
| Pgr |
A |
G |
9: 8,946,954 (GRCm39) |
|
probably benign |
Het |
| Pitpnm3 |
G |
T |
11: 71,965,450 (GRCm39) |
H112N |
possibly damaging |
Het |
| Ppargc1b |
G |
T |
18: 61,431,848 (GRCm39) |
T1000K |
possibly damaging |
Het |
| Ptprm |
A |
T |
17: 67,247,575 (GRCm39) |
S587T |
probably benign |
Het |
| Rabep2 |
A |
T |
7: 126,037,736 (GRCm39) |
R169S |
possibly damaging |
Het |
| Rad21l |
T |
C |
2: 151,497,179 (GRCm39) |
R309G |
probably benign |
Het |
| Rbm12 |
T |
C |
2: 155,939,133 (GRCm39) |
R380G |
probably damaging |
Het |
| Selp |
A |
G |
1: 163,954,081 (GRCm39) |
N127S |
probably benign |
Het |
| Slc12a2 |
A |
G |
18: 58,012,467 (GRCm39) |
T197A |
possibly damaging |
Het |
| Slc22a18 |
C |
T |
7: 143,029,984 (GRCm39) |
T17I |
probably damaging |
Het |
| Sptbn4 |
T |
C |
7: 27,065,868 (GRCm39) |
E2026G |
possibly damaging |
Het |
| Srf |
A |
T |
17: 46,862,633 (GRCm39) |
M285K |
possibly damaging |
Het |
| Tanc1 |
T |
C |
2: 59,622,156 (GRCm39) |
V425A |
possibly damaging |
Het |
| Tle4 |
A |
T |
19: 14,493,721 (GRCm39) |
|
probably null |
Het |
| Tmem132e |
A |
G |
11: 82,335,908 (GRCm39) |
R905G |
possibly damaging |
Het |
| Tmem200c |
A |
T |
17: 69,147,983 (GRCm39) |
I189F |
probably damaging |
Het |
| Trappc13 |
T |
C |
13: 104,311,150 (GRCm39) |
Q87R |
probably benign |
Het |
| Trpm7 |
A |
T |
2: 126,673,219 (GRCm39) |
D511E |
probably damaging |
Het |
| Ttn |
A |
T |
2: 76,632,634 (GRCm39) |
I14140N |
possibly damaging |
Het |
| Virma |
A |
G |
4: 11,513,907 (GRCm39) |
D587G |
probably benign |
Het |
| Vmn1r72 |
A |
G |
7: 11,403,731 (GRCm39) |
L239P |
probably damaging |
Het |
| Vmn2r68 |
A |
G |
7: 84,883,102 (GRCm39) |
F217L |
probably damaging |
Het |
| Vps13c |
T |
C |
9: 67,881,041 (GRCm39) |
|
probably null |
Het |
| Vrtn |
T |
C |
12: 84,695,973 (GRCm39) |
V241A |
probably damaging |
Het |
| Xdh |
T |
C |
17: 74,214,653 (GRCm39) |
E764G |
probably damaging |
Het |
| Zranb3 |
A |
T |
1: 127,927,136 (GRCm39) |
V343D |
probably damaging |
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 |
|
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 |
|
R7348:Psd3
|
UTSW |
8 |
68,243,583 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
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'- TAGCAAAGTTCTCCTCAAGGTG -3'
(R):5'- TGCTTTAAGAGAGCAGAGGTCTG -3'
Sequencing Primer
(F):5'- AAAGTTCTCCTCAAGGTGTTCTTTG -3'
(R):5'- GAGCACCCTAGAGGCTATGATC -3'
|
| Posted On |
2014-08-01 |
Incidental Mutation