Incidental Mutation 'R4246:Psd2'
| ID |
320443 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Psd2
|
| Ensembl Gene |
ENSMUSG00000024347 |
| Gene Name |
pleckstrin and Sec7 domain containing 2 |
| Synonyms |
EFA6C, 6330404E20Rik |
| MMRRC Submission |
041062-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4246 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
36097883-36147768 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 36139172 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Proline
at position 540
(L540P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000135431
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000115716]
[ENSMUST00000175734]
[ENSMUST00000176472]
[ENSMUST00000176873]
[ENSMUST00000177432]
|
| AlphaFold |
Q6P1I6 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000115716
AA Change: L543P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000111381
Gene: ENSMUSG00000024347
AA Change: L543P
| 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: L544P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000135795
Gene: ENSMUSG00000024347
AA Change: L544P
| 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 damaging
Transcript: ENSMUST00000176472
AA Change: L543P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000135285
Gene: ENSMUSG00000024347
AA Change: L543P
| 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: L544P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000135616
Gene: ENSMUSG00000024347
AA Change: L544P
| 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 damaging
Transcript: ENSMUST00000177432
AA Change: L540P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000135431
Gene: ENSMUSG00000024347
AA Change: L540P
| 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 |
|
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.9%
|
| Validation Efficiency |
|
| Allele List at MGI |
All alleles(2) : Targeted, other(2) |
| Other mutations in this stock |
Total: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2700062C07Rik |
A |
G |
18: 24,606,013 (GRCm39) |
N36S |
possibly damaging |
Het |
| Ak1 |
A |
G |
2: 32,523,384 (GRCm39) |
T151A |
possibly damaging |
Het |
| Asxl3 |
A |
G |
18: 22,658,557 (GRCm39) |
D2189G |
probably damaging |
Het |
| Ccdc91 |
C |
T |
6: 147,493,646 (GRCm39) |
A346V |
unknown |
Het |
| Dnah6 |
C |
T |
6: 73,106,431 (GRCm39) |
E1769K |
probably benign |
Het |
| Dock6 |
A |
T |
9: 21,750,786 (GRCm39) |
|
probably null |
Het |
| Fhod3 |
A |
G |
18: 25,123,123 (GRCm39) |
K271R |
probably null |
Het |
| Glyatl3 |
T |
A |
17: 41,220,989 (GRCm39) |
D126V |
probably benign |
Het |
| Gnal |
C |
G |
18: 67,221,654 (GRCm39) |
P19R |
unknown |
Het |
| Igkv8-21 |
T |
A |
6: 70,292,436 (GRCm39) |
M1L |
possibly damaging |
Het |
| Itih4 |
C |
A |
14: 30,613,359 (GRCm39) |
H261N |
probably damaging |
Het |
| Jpt1 |
T |
C |
11: 115,405,119 (GRCm39) |
|
probably benign |
Het |
| Kif14 |
G |
T |
1: 136,401,126 (GRCm39) |
M492I |
possibly damaging |
Het |
| Klhl32 |
A |
C |
4: 24,800,822 (GRCm39) |
S3A |
possibly damaging |
Het |
| Kmt2d |
C |
T |
15: 98,737,970 (GRCm39) |
|
probably benign |
Het |
| Lamtor5 |
T |
C |
3: 107,186,354 (GRCm39) |
V41A |
probably benign |
Het |
| Lmtk3 |
G |
A |
7: 45,443,486 (GRCm39) |
C723Y |
possibly damaging |
Het |
| Lrfn1 |
G |
T |
7: 28,159,367 (GRCm39) |
V429L |
probably benign |
Het |
| Mapkbp1 |
T |
A |
2: 119,843,508 (GRCm39) |
I252N |
probably damaging |
Het |
| Nelfa |
A |
G |
5: 34,056,373 (GRCm39) |
F464S |
probably damaging |
Het |
| Nipbl |
G |
A |
15: 8,361,916 (GRCm39) |
L1454F |
probably damaging |
Het |
| Nr4a3 |
C |
T |
4: 48,083,125 (GRCm39) |
P553S |
possibly damaging |
Het |
| Nrg3 |
G |
A |
14: 39,194,198 (GRCm39) |
T187I |
possibly damaging |
Het |
| Or5m5 |
T |
A |
2: 85,814,624 (GRCm39) |
C147S |
possibly damaging |
Het |
| Or8g36 |
A |
G |
9: 39,422,899 (GRCm39) |
V39A |
probably benign |
Het |
| Pcdha8 |
A |
G |
18: 37,125,950 (GRCm39) |
E144G |
probably damaging |
Het |
| Pik3cb |
T |
C |
9: 98,983,229 (GRCm39) |
|
probably null |
Het |
| Pira1 |
C |
T |
7: 3,740,348 (GRCm39) |
G291E |
probably damaging |
Het |
| Pkd1l1 |
C |
T |
11: 8,815,543 (GRCm39) |
R1456K |
possibly damaging |
Het |
| Ppp1r3a |
T |
A |
6: 14,719,780 (GRCm39) |
E378V |
probably damaging |
Het |
| Rnf14 |
T |
A |
18: 38,434,701 (GRCm39) |
|
probably null |
Het |
| Satl1 |
A |
G |
X: 111,316,033 (GRCm39) |
S141P |
probably benign |
Het |
| Setx |
GTGGCT |
GT |
2: 29,044,073 (GRCm39) |
1814 |
probably null |
Het |
| Sh3d19 |
G |
A |
3: 86,033,995 (GRCm39) |
V783I |
probably benign |
Het |
| Snca |
T |
C |
6: 60,710,149 (GRCm39) |
E110G |
possibly damaging |
Het |
| Sumf1 |
A |
C |
6: 108,131,974 (GRCm39) |
V156G |
probably damaging |
Het |
| Trhr |
A |
T |
15: 44,096,856 (GRCm39) |
|
probably null |
Het |
| Tsen2 |
A |
G |
6: 115,524,785 (GRCm39) |
|
probably benign |
Het |
| Tuft1 |
C |
A |
3: 94,522,108 (GRCm39) |
M319I |
probably benign |
Het |
| Vill |
C |
A |
9: 118,889,461 (GRCm39) |
N132K |
probably damaging |
Het |
| Wars2 |
T |
A |
3: 99,123,904 (GRCm39) |
V255E |
probably damaging |
Het |
| Zcchc14 |
CTGATGGTGGTGGTGATGGTGGTGG |
CTGATGGTGGTGG |
8: 122,331,031 (GRCm39) |
|
probably benign |
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 |
|
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 |
|
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 |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GCTACCACCTACAAGCATGG -3'
(R):5'- TTCCTGAGTGAGTCCAGGTAAG -3'
Sequencing Primer
(F):5'- TGCTGACCCGGAAGACTCATG -3'
(R):5'- AGCTGGATGAGACTGAGT -3'
|
| Posted On |
2015-06-12 |
Incidental Mutation