Incidental Mutation 'R0103:Psd2'
| ID |
17391 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Psd2
|
| Ensembl Gene |
ENSMUSG00000024347 |
| Gene Name |
pleckstrin and Sec7 domain containing 2 |
| Synonyms |
EFA6C, 6330404E20Rik |
| MMRRC Submission |
038389-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R0103 (G1)
|
| Quality Score |
|
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
36097883-36147768 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 36137770 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Serine
at position 455
(N455S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000135616
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000115716]
[ENSMUST00000175734]
[ENSMUST00000176472]
[ENSMUST00000176873]
[ENSMUST00000177432]
|
| AlphaFold |
Q6P1I6 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000115716
AA Change: N454S
PolyPhen 2
Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000111381
Gene: ENSMUSG00000024347
AA Change: N454S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
153 |
169 |
N/A |
INTRINSIC |
|
low complexity region
|
216 |
234 |
N/A |
INTRINSIC |
|
low complexity region
|
247 |
264 |
N/A |
INTRINSIC |
|
Sec7
|
270 |
461 |
4.69e-56 |
SMART |
|
PH
|
510 |
624 |
4.35e-14 |
SMART |
|
Blast:Sec7
|
653 |
705 |
4e-24 |
BLAST |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000175720
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000175734
AA Change: N455S
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000135795
Gene: ENSMUSG00000024347
AA Change: N455S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
153 |
169 |
N/A |
INTRINSIC |
|
low complexity region
|
216 |
234 |
N/A |
INTRINSIC |
|
low complexity region
|
247 |
264 |
N/A |
INTRINSIC |
|
Sec7
|
270 |
462 |
4.1e-55 |
SMART |
|
PH
|
511 |
625 |
1.9e-16 |
SMART |
|
Blast:Sec7
|
654 |
706 |
4e-24 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000176472
AA Change: N454S
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
| SMART Domains |
Protein: ENSMUSP00000135285
Gene: ENSMUSG00000024347
AA Change: N454S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
153 |
169 |
N/A |
INTRINSIC |
|
low complexity region
|
216 |
234 |
N/A |
INTRINSIC |
|
low complexity region
|
247 |
264 |
N/A |
INTRINSIC |
|
Sec7
|
270 |
461 |
4.69e-56 |
SMART |
|
Pfam:PH_9
|
511 |
553 |
4.5e-12 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000176873
AA Change: N455S
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000135616
Gene: ENSMUSG00000024347
AA Change: N455S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
153 |
169 |
N/A |
INTRINSIC |
|
low complexity region
|
216 |
234 |
N/A |
INTRINSIC |
|
low complexity region
|
247 |
264 |
N/A |
INTRINSIC |
|
Sec7
|
270 |
462 |
4.2e-55 |
SMART |
|
PH
|
511 |
625 |
1.9e-16 |
SMART |
|
Blast:Sec7
|
654 |
706 |
4e-24 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000177432
AA Change: N454S
PolyPhen 2
Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000135431
Gene: ENSMUSG00000024347
AA Change: N454S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
153 |
169 |
N/A |
INTRINSIC |
|
low complexity region
|
216 |
234 |
N/A |
INTRINSIC |
|
low complexity region
|
247 |
264 |
N/A |
INTRINSIC |
|
Sec7
|
270 |
461 |
4.69e-56 |
SMART |
|
PH
|
510 |
621 |
5.36e-14 |
SMART |
|
Blast:Sec7
|
650 |
702 |
4e-24 |
BLAST |
|
| Meta Mutation Damage Score |
0.1036 |
| Coding Region Coverage |
- 1x: 89.4%
- 3x: 86.4%
- 10x: 77.8%
- 20x: 63.0%
|
| Validation Efficiency |
91% (89/98) |
| Allele List at MGI |
All alleles(2) : Targeted, other(2) |
| Other mutations in this stock |
Total: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca13 |
A |
C |
11: 9,223,951 (GRCm39) |
R443S |
probably damaging |
Het |
| Adgrl3 |
A |
G |
5: 81,940,194 (GRCm39) |
|
probably benign |
Het |
| Anapc1 |
T |
C |
2: 128,522,372 (GRCm39) |
|
probably benign |
Het |
| Aqr |
T |
A |
2: 113,979,497 (GRCm39) |
I313F |
probably damaging |
Het |
| Arfgap3 |
A |
T |
15: 83,206,922 (GRCm39) |
|
probably benign |
Het |
| Asah2 |
G |
T |
19: 31,996,377 (GRCm39) |
H374N |
probably benign |
Het |
| Catspere2 |
A |
G |
1: 177,943,771 (GRCm39) |
N703D |
unknown |
Het |
| Ccdc106 |
C |
A |
7: 5,060,544 (GRCm39) |
Q35K |
probably benign |
Het |
| Ccm2l |
G |
T |
2: 152,909,839 (GRCm39) |
E64* |
probably null |
Het |
| Cep85l |
A |
T |
10: 53,154,270 (GRCm39) |
D776E |
possibly damaging |
Het |
| Cfap52 |
T |
A |
11: 67,815,951 (GRCm39) |
I611F |
possibly damaging |
Het |
| Cldn22 |
C |
T |
8: 48,277,589 (GRCm39) |
T9M |
probably benign |
Het |
| Coa7 |
T |
C |
4: 108,195,338 (GRCm39) |
L89P |
possibly damaging |
Het |
| Cox7a2l |
A |
T |
17: 83,821,701 (GRCm39) |
Y2N |
probably damaging |
Het |
| Cyp27a1 |
A |
C |
1: 74,775,074 (GRCm39) |
E301A |
probably benign |
Het |
| Dennd4c |
A |
G |
4: 86,730,683 (GRCm39) |
Y860C |
probably benign |
Het |
| Dhx58 |
T |
C |
11: 100,586,096 (GRCm39) |
T642A |
probably damaging |
Het |
| Dlg4 |
A |
G |
11: 69,922,019 (GRCm39) |
Y87C |
probably damaging |
Het |
| Dnah6 |
C |
T |
6: 73,069,155 (GRCm39) |
E2511K |
probably damaging |
Het |
| Entpd5 |
C |
A |
12: 84,443,717 (GRCm39) |
E9* |
probably null |
Het |
| Fbln2 |
A |
C |
6: 91,248,532 (GRCm39) |
I1066L |
probably benign |
Het |
| Fhl2 |
C |
T |
1: 43,192,381 (GRCm39) |
R4H |
probably benign |
Het |
| Frmpd1 |
T |
A |
4: 45,229,884 (GRCm39) |
I17K |
probably damaging |
Het |
| Gbp7 |
T |
A |
3: 142,252,299 (GRCm39) |
N627K |
probably benign |
Het |
| Gnptab |
A |
G |
10: 88,265,381 (GRCm39) |
Y331C |
probably damaging |
Het |
| Hibadh |
T |
A |
6: 52,534,862 (GRCm39) |
M173L |
probably benign |
Het |
| Itga1 |
T |
C |
13: 115,152,790 (GRCm39) |
I211V |
probably benign |
Het |
| Keg1 |
A |
T |
19: 12,696,280 (GRCm39) |
I155F |
possibly damaging |
Het |
| Ltb |
A |
G |
17: 35,414,016 (GRCm39) |
|
probably benign |
Het |
| Manea |
A |
T |
4: 26,329,080 (GRCm39) |
|
probably null |
Het |
| Ms4a4a |
T |
A |
19: 11,370,048 (GRCm39) |
M202K |
possibly damaging |
Het |
| Myo3a |
T |
G |
2: 22,436,360 (GRCm39) |
|
probably benign |
Het |
| Myo9b |
C |
T |
8: 71,776,493 (GRCm39) |
|
probably benign |
Het |
| Nanos3 |
C |
T |
8: 84,902,763 (GRCm39) |
R133Q |
probably damaging |
Het |
| Ncor1 |
G |
T |
11: 62,233,871 (GRCm39) |
Q444K |
possibly damaging |
Het |
| Nek7 |
A |
T |
1: 138,471,980 (GRCm39) |
C53* |
probably null |
Het |
| Obscn |
G |
T |
11: 58,953,522 (GRCm39) |
Y4044* |
probably null |
Het |
| Pcsk6 |
T |
C |
7: 65,578,845 (GRCm39) |
|
probably benign |
Het |
| Phax |
T |
A |
18: 56,695,785 (GRCm39) |
V7D |
probably benign |
Het |
| Phxr4 |
T |
C |
9: 13,343,087 (GRCm39) |
|
probably benign |
Het |
| Pkhd1 |
T |
A |
1: 20,593,583 (GRCm39) |
D1510V |
probably benign |
Het |
| Pkhd1l1 |
T |
C |
15: 44,460,537 (GRCm39) |
C4249R |
probably benign |
Het |
| Prpf39 |
T |
C |
12: 65,102,057 (GRCm39) |
V378A |
possibly damaging |
Het |
| Ptpro |
T |
A |
6: 137,420,592 (GRCm39) |
V1007D |
probably damaging |
Het |
| Rab4b |
A |
G |
7: 26,873,927 (GRCm39) |
I117T |
probably benign |
Het |
| Rad9b |
A |
T |
5: 122,469,590 (GRCm39) |
V348E |
probably damaging |
Het |
| Rcor1 |
T |
C |
12: 111,076,212 (GRCm39) |
|
probably benign |
Het |
| Rhoc |
A |
T |
3: 104,699,307 (GRCm39) |
E32V |
possibly damaging |
Het |
| Rnf40 |
T |
G |
7: 127,199,743 (GRCm39) |
V925G |
probably damaging |
Het |
| Slc25a32 |
A |
T |
15: 38,963,292 (GRCm39) |
Y176* |
probably null |
Het |
| Slc7a1 |
T |
A |
5: 148,289,236 (GRCm39) |
K4* |
probably null |
Het |
| Taar2 |
G |
A |
10: 23,817,393 (GRCm39) |
R311H |
probably benign |
Het |
| Taar4 |
A |
T |
10: 23,837,304 (GRCm39) |
N305Y |
probably damaging |
Het |
| Tcaf1 |
G |
T |
6: 42,663,324 (GRCm39) |
D185E |
probably benign |
Het |
| Tmem138 |
T |
C |
19: 10,552,316 (GRCm39) |
N62S |
possibly damaging |
Het |
| Tnfrsf25 |
C |
T |
4: 152,201,405 (GRCm39) |
P65S |
possibly damaging |
Het |
| Trp53bp1 |
A |
T |
2: 121,067,240 (GRCm39) |
S495R |
possibly damaging |
Het |
| Trpv3 |
T |
C |
11: 73,184,805 (GRCm39) |
F597S |
probably damaging |
Het |
| Ugt2a3 |
A |
G |
5: 87,484,577 (GRCm39) |
V149A |
possibly damaging |
Het |
| Ush2a |
T |
G |
1: 188,051,267 (GRCm39) |
I251R |
possibly damaging |
Het |
| Vamp4 |
T |
C |
1: 162,417,108 (GRCm39) |
C114R |
possibly damaging |
Het |
| Zc3h13 |
T |
A |
14: 75,567,908 (GRCm39) |
V1067E |
probably damaging |
Het |
| Zcwpw1 |
G |
A |
5: 137,808,375 (GRCm39) |
W274* |
probably null |
Het |
|
| Other mutations in Psd2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01486:Psd2
|
APN |
18 |
36,113,388 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01578:Psd2
|
APN |
18 |
36,112,838 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02086:Psd2
|
APN |
18 |
36,138,959 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02132:Psd2
|
APN |
18 |
36,137,809 (GRCm39) |
splice site |
probably benign |
|
|
IGL02480:Psd2
|
APN |
18 |
36,139,136 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02726:Psd2
|
APN |
18 |
36,120,355 (GRCm39) |
critical splice donor site |
probably null |
|
|
recluse
|
UTSW |
18 |
36,112,764 (GRCm39) |
missense |
probably damaging |
1.00 |
|
widow
|
UTSW |
18 |
36,113,478 (GRCm39) |
missense |
probably damaging |
0.99 |
|
3-1:Psd2
|
UTSW |
18 |
36,117,454 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0103:Psd2
|
UTSW |
18 |
36,137,770 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0320:Psd2
|
UTSW |
18 |
36,112,697 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0573:Psd2
|
UTSW |
18 |
36,113,546 (GRCm39) |
splice site |
probably benign |
|
|
R0685:Psd2
|
UTSW |
18 |
36,136,044 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R0698:Psd2
|
UTSW |
18 |
36,145,764 (GRCm39) |
missense |
probably benign |
0.22 |
|
R0730:Psd2
|
UTSW |
18 |
36,111,627 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R0971:Psd2
|
UTSW |
18 |
36,112,839 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1085:Psd2
|
UTSW |
18 |
36,145,830 (GRCm39) |
missense |
probably benign |
0.10 |
|
R1535:Psd2
|
UTSW |
18 |
36,138,843 (GRCm39) |
missense |
probably benign |
0.31 |
|
R2056:Psd2
|
UTSW |
18 |
36,139,744 (GRCm39) |
missense |
possibly damaging |
0.60 |
|
R4011:Psd2
|
UTSW |
18 |
36,120,300 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4246:Psd2
|
UTSW |
18 |
36,139,172 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4335:Psd2
|
UTSW |
18 |
36,140,583 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R4584:Psd2
|
UTSW |
18 |
36,145,881 (GRCm39) |
missense |
probably benign |
|
|
R4942:Psd2
|
UTSW |
18 |
36,111,717 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5120:Psd2
|
UTSW |
18 |
36,112,863 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R5373:Psd2
|
UTSW |
18 |
36,140,556 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5374:Psd2
|
UTSW |
18 |
36,140,556 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5839:Psd2
|
UTSW |
18 |
36,140,577 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R6200:Psd2
|
UTSW |
18 |
36,139,776 (GRCm39) |
splice site |
probably null |
|
|
R6925:Psd2
|
UTSW |
18 |
36,112,764 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6967:Psd2
|
UTSW |
18 |
36,113,385 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R7074:Psd2
|
UTSW |
18 |
36,143,737 (GRCm39) |
missense |
probably benign |
0.03 |
|
R7142:Psd2
|
UTSW |
18 |
36,113,097 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R7239:Psd2
|
UTSW |
18 |
36,113,472 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7348:Psd2
|
UTSW |
18 |
36,113,389 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R7581:Psd2
|
UTSW |
18 |
36,113,050 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7793:Psd2
|
UTSW |
18 |
36,136,032 (GRCm39) |
missense |
probably benign |
0.37 |
|
R8221:Psd2
|
UTSW |
18 |
36,113,478 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8310:Psd2
|
UTSW |
18 |
36,112,766 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8939:Psd2
|
UTSW |
18 |
36,121,292 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R9463:Psd2
|
UTSW |
18 |
36,143,798 (GRCm39) |
missense |
probably damaging |
0.98 |
|
X0065:Psd2
|
UTSW |
18 |
36,135,995 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
Z1177:Psd2
|
UTSW |
18 |
36,111,333 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
| Posted On |
2013-01-31 |
Incidental Mutation