Incidental Mutation 'R0052:Psd3'
| ID |
15315 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Psd3
|
| Ensembl Gene |
ENSMUSG00000030465 |
| Gene Name |
pleckstrin and Sec7 domain containing 3 |
| Synonyms |
EFA6D, 4931420C21Rik |
| MMRRC Submission |
038346-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.093)
|
| Stock # |
R0052 (G1)
|
| Quality Score |
|
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
68141734-68664679 bp(-) (GRCm39) |
| Type of Mutation |
critical splice donor site (2 bp from exon) |
| DNA Base Change (assembly) |
A to G
at 68335631 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000148783
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000038959]
[ENSMUST00000093468]
[ENSMUST00000093469]
[ENSMUST00000098696]
[ENSMUST00000212505]
[ENSMUST00000212505]
[ENSMUST00000212960]
[ENSMUST00000212960]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably null
Transcript: ENSMUST00000038959
|
| SMART Domains |
Protein: ENSMUSP00000041339
Gene: ENSMUSG00000030465
| 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 null
Transcript: ENSMUST00000093468
|
| SMART Domains |
Protein: ENSMUSP00000091178
Gene: ENSMUSG00000030465
| 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 null
Transcript: ENSMUST00000093469
|
| SMART Domains |
Protein: ENSMUSP00000091179
Gene: ENSMUSG00000030465
| 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 null
Transcript: ENSMUST00000098696
|
| SMART Domains |
Protein: ENSMUSP00000096293
Gene: ENSMUSG00000030465
| 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: ENSMUST00000130307
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146480
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150169
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000212505
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000212505
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000212960
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000212960
|
| Meta Mutation Damage Score |
0.9495 |
| Coding Region Coverage |
- 1x: 85.5%
- 3x: 78.2%
- 10x: 46.7%
- 20x: 12.5%
|
| Validation Efficiency |
90% (62/69) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 32 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Apba1 |
T |
C |
19: 23,893,315 (GRCm39) |
S438P |
possibly damaging |
Het |
| Atosa |
A |
G |
9: 74,926,265 (GRCm39) |
|
probably benign |
Het |
| Atp2a1 |
A |
G |
7: 126,057,069 (GRCm39) |
|
probably benign |
Het |
| Bicd2 |
T |
A |
13: 49,528,790 (GRCm39) |
L184Q |
probably damaging |
Het |
| Bub1 |
G |
A |
2: 127,650,959 (GRCm39) |
T618I |
probably benign |
Het |
| Dsp |
A |
G |
13: 38,381,340 (GRCm39) |
D2096G |
possibly damaging |
Het |
| Eno4 |
A |
G |
19: 58,956,985 (GRCm39) |
D357G |
probably damaging |
Het |
| Fcrl2 |
A |
T |
3: 87,164,085 (GRCm39) |
I348N |
possibly damaging |
Het |
| Fgl2 |
A |
T |
5: 21,580,347 (GRCm39) |
S230C |
probably damaging |
Het |
| Ginm1 |
T |
A |
10: 7,655,070 (GRCm39) |
E57D |
possibly damaging |
Het |
| Itga9 |
T |
A |
9: 118,465,617 (GRCm39) |
I157N |
probably damaging |
Het |
| Kif21a |
T |
C |
15: 90,855,060 (GRCm39) |
E700G |
probably damaging |
Het |
| Mmd |
C |
T |
11: 90,150,824 (GRCm39) |
|
probably benign |
Het |
| Morn3 |
T |
C |
5: 123,184,726 (GRCm39) |
Y38C |
probably damaging |
Het |
| Prex2 |
T |
A |
1: 11,230,380 (GRCm39) |
L802Q |
probably damaging |
Het |
| Ralgds |
T |
A |
2: 28,434,400 (GRCm39) |
|
probably null |
Het |
| Rmdn2 |
A |
G |
17: 79,957,760 (GRCm39) |
E16G |
probably damaging |
Het |
| Slc17a3 |
C |
T |
13: 24,039,841 (GRCm39) |
S293F |
probably damaging |
Het |
| Slc4a4 |
A |
C |
5: 89,304,195 (GRCm39) |
H502P |
possibly damaging |
Het |
| Slco3a1 |
A |
T |
7: 74,154,074 (GRCm39) |
I166N |
probably benign |
Het |
| Snx5 |
A |
T |
2: 144,101,112 (GRCm39) |
|
probably null |
Het |
| Srgap1 |
T |
C |
10: 121,636,732 (GRCm39) |
D741G |
possibly damaging |
Het |
| St8sia2 |
G |
T |
7: 73,593,038 (GRCm39) |
Y339* |
probably null |
Het |
| Tdo2 |
T |
A |
3: 81,874,332 (GRCm39) |
N210I |
probably benign |
Het |
| Thada |
A |
T |
17: 84,762,586 (GRCm39) |
N104K |
probably damaging |
Het |
| Timm8b |
A |
T |
9: 50,516,330 (GRCm39) |
D61V |
possibly damaging |
Het |
| Trbv12-1 |
T |
C |
6: 41,090,850 (GRCm39) |
F74S |
possibly damaging |
Het |
| Tshz1 |
G |
A |
18: 84,033,070 (GRCm39) |
T446I |
possibly damaging |
Het |
| Ubap2l |
T |
C |
3: 89,946,235 (GRCm39) |
N123S |
possibly damaging |
Het |
| Usp12 |
A |
G |
5: 146,675,914 (GRCm39) |
V336A |
possibly damaging |
Het |
| Xrn2 |
T |
A |
2: 146,882,885 (GRCm39) |
|
probably benign |
Het |
| Zfp14 |
G |
T |
7: 29,737,753 (GRCm39) |
Q411K |
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 |
|
|
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 |
|
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 |
|
|
| Protein Function and Prediction |
The function of Psd3 (alternatively, EFA6R) is unknown, but the protein has a plekstrin homology domain (this domain indicates that Psd3 could be involved in intracellular signaling or is a constituent of the cytoskeleton) (1). Psd3 also contains a Sec7 domain (Sec7 proteins are ADP-ribosylation factor-specific guanine nucleotide exchange factors) (1). Psd3 expression is decreased in high-grade ovarian tumors (1).
|
| References |
1. Pils, D., Horak, P., Gleiss, A., Sax, C., Fabjani, G., Moebus, V. J., Zielinski, C., Reinthaller, A., Zeillinger, R., and Krainer, M. (2005) Five Genes from Chromosomal Band 8p22 are significantly Down-Regulated in Ovarian Carcinoma: N33 and EFA6R have a Potential Impact on overall Survival. Cancer. 104, 2417-2429. |
| Posted On |
2012-12-17 |
| Science Writer |
Anne Murray |
Incidental Mutation