Incidental Mutation 'R3970:Psd'
| ID |
310952 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Psd
|
| Ensembl Gene |
ENSMUSG00000037126 |
| Gene Name |
pleckstrin and Sec7 domain containing |
| Synonyms |
Efa6, Psdl, Efa6a, 1110007H17Rik |
| MMRRC Submission |
040938-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R3970 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
46300526-46315595 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 46312845 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Histidine
at position 175
(R175H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000152942
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000026256]
[ENSMUST00000041391]
[ENSMUST00000096029]
[ENSMUST00000177667]
[ENSMUST00000223903]
[ENSMUST00000223917]
[ENSMUST00000225323]
[ENSMUST00000224447]
[ENSMUST00000225781]
|
| AlphaFold |
Q5DTT2 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000026256
|
| SMART Domains |
Protein: ENSMUSP00000026256
Gene: ENSMUSG00000025226
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:F-box
|
18 |
63 |
1.9e-6 |
PFAM |
|
low complexity region
|
76 |
84 |
N/A |
INTRINSIC |
|
LRR
|
113 |
138 |
1.01e1 |
SMART |
|
LRR
|
139 |
164 |
1.89e-1 |
SMART |
|
LRR
|
165 |
190 |
2.27e-4 |
SMART |
|
LRR
|
192 |
217 |
3.47e0 |
SMART |
|
LRR
|
218 |
243 |
2.57e-3 |
SMART |
|
LRR
|
244 |
269 |
2.05e1 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000041391
AA Change: R175H
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000039728
Gene: ENSMUSG00000037126
AA Change: R175H
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
48 |
63 |
N/A |
INTRINSIC |
|
low complexity region
|
79 |
99 |
N/A |
INTRINSIC |
|
low complexity region
|
329 |
368 |
N/A |
INTRINSIC |
|
low complexity region
|
419 |
431 |
N/A |
INTRINSIC |
|
low complexity region
|
445 |
466 |
N/A |
INTRINSIC |
|
Sec7
|
519 |
708 |
5.08e-75 |
SMART |
|
low complexity region
|
714 |
724 |
N/A |
INTRINSIC |
|
low complexity region
|
736 |
744 |
N/A |
INTRINSIC |
|
PH
|
757 |
871 |
1.87e-13 |
SMART |
|
Blast:Sec7
|
900 |
952 |
1e-6 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000096029
AA Change: R175H
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000093729
Gene: ENSMUSG00000037126
AA Change: R175H
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
48 |
63 |
N/A |
INTRINSIC |
|
low complexity region
|
79 |
99 |
N/A |
INTRINSIC |
|
low complexity region
|
329 |
368 |
N/A |
INTRINSIC |
|
low complexity region
|
419 |
431 |
N/A |
INTRINSIC |
|
low complexity region
|
445 |
466 |
N/A |
INTRINSIC |
|
Sec7
|
520 |
709 |
5.08e-75 |
SMART |
|
low complexity region
|
715 |
725 |
N/A |
INTRINSIC |
|
low complexity region
|
737 |
745 |
N/A |
INTRINSIC |
|
PH
|
758 |
872 |
1.87e-13 |
SMART |
|
Blast:Sec7
|
901 |
953 |
1e-6 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000177667
|
| SMART Domains |
Protein: ENSMUSP00000137489
Gene: ENSMUSG00000025226
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:F-box
|
18 |
63 |
2.1e-6 |
PFAM |
|
low complexity region
|
76 |
84 |
N/A |
INTRINSIC |
|
LRR
|
113 |
138 |
1.01e1 |
SMART |
|
LRR
|
139 |
164 |
1.89e-1 |
SMART |
|
LRR
|
165 |
190 |
2.27e-4 |
SMART |
|
LRR
|
192 |
217 |
3.47e0 |
SMART |
|
LRR
|
218 |
243 |
2.57e-3 |
SMART |
|
LRR
|
244 |
269 |
2.05e1 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000223903
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000223917
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224094
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000225323
AA Change: R175H
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000225072
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224444
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000224447
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000225781
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000225770
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 94.4%
|
| Validation Efficiency |
96% (53/55) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a Plekstrin homology and SEC7 domains-containing protein that functions as a guanine nucleotide exchange factor. The encoded protein regulates signal transduction by activating ADP-ribosylation factor 6. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 54 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2510039O18Rik |
T |
C |
4: 148,029,779 (GRCm39) |
M583T |
probably damaging |
Het |
| Actn4 |
T |
C |
7: 28,661,457 (GRCm39) |
K51R |
probably benign |
Het |
| Adamts15 |
T |
C |
9: 30,821,898 (GRCm39) |
Y513C |
probably benign |
Het |
| Akap13 |
T |
A |
7: 75,219,699 (GRCm39) |
L34* |
probably null |
Het |
| Akap6 |
A |
T |
12: 53,188,236 (GRCm39) |
K1883N |
probably damaging |
Het |
| Ano1 |
T |
C |
7: 144,161,700 (GRCm39) |
N749D |
probably benign |
Het |
| Armcx6 |
G |
T |
X: 133,650,505 (GRCm39) |
H109N |
possibly damaging |
Het |
| Camk4 |
T |
A |
18: 33,312,634 (GRCm39) |
I258N |
possibly damaging |
Het |
| Cdhr2 |
A |
T |
13: 54,874,271 (GRCm39) |
N781I |
probably damaging |
Het |
| Cherp |
T |
C |
8: 73,223,795 (GRCm39) |
H196R |
possibly damaging |
Het |
| Chia1 |
T |
G |
3: 106,028,951 (GRCm39) |
|
probably null |
Het |
| Col11a1 |
A |
T |
3: 113,890,838 (GRCm39) |
T392S |
unknown |
Het |
| Commd9 |
C |
A |
2: 101,727,486 (GRCm39) |
N93K |
probably benign |
Het |
| Csf2rb |
T |
C |
15: 78,225,667 (GRCm39) |
V286A |
probably benign |
Het |
| Dnah17 |
G |
A |
11: 117,931,984 (GRCm39) |
|
probably benign |
Het |
| E2f1 |
C |
G |
2: 154,405,942 (GRCm39) |
G144R |
probably damaging |
Het |
| Fcho2 |
A |
T |
13: 98,871,564 (GRCm39) |
S551T |
probably benign |
Het |
| Flna |
A |
T |
X: 73,279,273 (GRCm39) |
V1253E |
probably damaging |
Het |
| Gm12185 |
A |
T |
11: 48,798,172 (GRCm39) |
C774S |
probably benign |
Het |
| Gm14401 |
T |
C |
2: 176,778,789 (GRCm39) |
Y292H |
possibly damaging |
Het |
| Insyn2b |
A |
T |
11: 34,369,739 (GRCm39) |
Q481L |
probably damaging |
Het |
| Kif5c |
A |
G |
2: 49,578,756 (GRCm39) |
E128G |
probably damaging |
Het |
| Lama3 |
A |
T |
18: 12,713,398 (GRCm39) |
K3230M |
probably damaging |
Het |
| Myof |
C |
T |
19: 37,889,711 (GRCm39) |
V1287M |
probably damaging |
Het |
| Myof |
T |
G |
19: 38,011,058 (GRCm39) |
D60A |
possibly damaging |
Het |
| Myrf |
A |
G |
19: 10,200,601 (GRCm39) |
L332P |
probably damaging |
Het |
| Nampt |
T |
A |
12: 32,883,095 (GRCm39) |
D93E |
probably benign |
Het |
| Narf |
A |
T |
11: 121,129,247 (GRCm39) |
E10D |
possibly damaging |
Het |
| Nlrp6 |
C |
A |
7: 140,501,568 (GRCm39) |
A45E |
probably damaging |
Het |
| Obscn |
G |
A |
11: 58,942,488 (GRCm39) |
P4898L |
probably damaging |
Het |
| Or8c11 |
T |
C |
9: 38,289,222 (GRCm39) |
V15A |
probably damaging |
Het |
| Pabpc5 |
A |
G |
X: 118,838,321 (GRCm39) |
E212G |
probably benign |
Het |
| Pcdh8 |
C |
T |
14: 80,007,706 (GRCm39) |
G286S |
possibly damaging |
Het |
| Pcdha2 |
C |
A |
18: 37,073,750 (GRCm39) |
Y460* |
probably null |
Het |
| Pcdhga4 |
G |
T |
18: 37,820,654 (GRCm39) |
L734F |
possibly damaging |
Het |
| Pecr |
G |
A |
1: 72,315,468 (GRCm39) |
T94I |
probably damaging |
Het |
| Piezo2 |
A |
T |
18: 63,144,767 (GRCm39) |
V2776E |
probably damaging |
Het |
| Pign |
A |
C |
1: 105,583,728 (GRCm39) |
S125A |
probably damaging |
Het |
| Pik3r2 |
G |
A |
8: 71,223,065 (GRCm39) |
R452C |
probably benign |
Het |
| Pkd1l1 |
C |
T |
11: 8,824,218 (GRCm39) |
E1566K |
probably damaging |
Het |
| Plcb2 |
A |
G |
2: 118,546,171 (GRCm39) |
|
probably benign |
Het |
| Ppl |
T |
C |
16: 4,918,196 (GRCm39) |
|
probably null |
Het |
| Pramel4 |
A |
T |
4: 143,795,044 (GRCm39) |
N477I |
possibly damaging |
Het |
| Sema3g |
T |
C |
14: 30,948,478 (GRCm39) |
|
probably null |
Het |
| Sf3b1 |
G |
A |
1: 55,051,341 (GRCm39) |
R196* |
probably null |
Het |
| Slc26a4 |
G |
T |
12: 31,578,686 (GRCm39) |
H656N |
probably damaging |
Het |
| Slc6a7 |
A |
C |
18: 61,136,417 (GRCm39) |
L328R |
possibly damaging |
Het |
| Stab2 |
T |
C |
10: 86,714,750 (GRCm39) |
T139A |
probably damaging |
Het |
| Tiam2 |
T |
A |
17: 3,479,106 (GRCm39) |
I613N |
probably damaging |
Het |
| Tlk1 |
A |
G |
2: 70,546,996 (GRCm39) |
V695A |
probably damaging |
Het |
| Trpc2 |
A |
G |
7: 101,733,531 (GRCm39) |
D160G |
probably damaging |
Het |
| Uhrf2 |
T |
C |
19: 30,057,315 (GRCm39) |
V491A |
probably damaging |
Het |
| Vwa7 |
G |
A |
17: 35,236,684 (GRCm39) |
A84T |
probably damaging |
Het |
| Zfp219 |
T |
A |
14: 52,244,421 (GRCm39) |
Q541L |
probably benign |
Het |
|
| Other mutations in Psd |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01291:Psd
|
APN |
19 |
46,303,186 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
IGL01307:Psd
|
APN |
19 |
46,303,097 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02329:Psd
|
APN |
19 |
46,308,098 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
IGL02423:Psd
|
APN |
19 |
46,302,943 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL02644:Psd
|
APN |
19 |
46,311,834 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02724:Psd
|
APN |
19 |
46,307,984 (GRCm39) |
missense |
probably benign |
0.04 |
|
IGL03117:Psd
|
APN |
19 |
46,311,561 (GRCm39) |
unclassified |
probably benign |
|
|
ANU05:Psd
|
UTSW |
19 |
46,303,186 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
G1Funyon:Psd
|
UTSW |
19 |
46,309,541 (GRCm39) |
intron |
probably benign |
|
|
P0035:Psd
|
UTSW |
19 |
46,309,400 (GRCm39) |
missense |
possibly damaging |
0.56 |
|
R0054:Psd
|
UTSW |
19 |
46,311,781 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0054:Psd
|
UTSW |
19 |
46,311,781 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0403:Psd
|
UTSW |
19 |
46,309,411 (GRCm39) |
unclassified |
probably benign |
|
|
R0499:Psd
|
UTSW |
19 |
46,310,600 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R0542:Psd
|
UTSW |
19 |
46,302,649 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0543:Psd
|
UTSW |
19 |
46,307,956 (GRCm39) |
missense |
possibly damaging |
0.62 |
|
R0894:Psd
|
UTSW |
19 |
46,301,880 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1449:Psd
|
UTSW |
19 |
46,313,250 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1586:Psd
|
UTSW |
19 |
46,303,237 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2096:Psd
|
UTSW |
19 |
46,313,088 (GRCm39) |
splice site |
probably null |
|
|
R2504:Psd
|
UTSW |
19 |
46,313,352 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R2857:Psd
|
UTSW |
19 |
46,312,859 (GRCm39) |
missense |
probably benign |
0.00 |
|
R2863:Psd
|
UTSW |
19 |
46,303,201 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R3897:Psd
|
UTSW |
19 |
46,313,024 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R3967:Psd
|
UTSW |
19 |
46,312,845 (GRCm39) |
missense |
probably benign |
|
|
R4435:Psd
|
UTSW |
19 |
46,302,933 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4612:Psd
|
UTSW |
19 |
46,301,778 (GRCm39) |
missense |
probably benign |
0.15 |
|
R4940:Psd
|
UTSW |
19 |
46,310,856 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5055:Psd
|
UTSW |
19 |
46,310,907 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5485:Psd
|
UTSW |
19 |
46,304,528 (GRCm39) |
splice site |
probably null |
|
|
R5768:Psd
|
UTSW |
19 |
46,301,178 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R5775:Psd
|
UTSW |
19 |
46,303,211 (GRCm39) |
nonsense |
probably null |
|
|
R6057:Psd
|
UTSW |
19 |
46,311,753 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R6349:Psd
|
UTSW |
19 |
46,301,826 (GRCm39) |
splice site |
probably null |
|
|
R6496:Psd
|
UTSW |
19 |
46,308,753 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6614:Psd
|
UTSW |
19 |
46,301,851 (GRCm39) |
missense |
probably benign |
0.11 |
|
R6820:Psd
|
UTSW |
19 |
46,309,283 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6849:Psd
|
UTSW |
19 |
46,306,185 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R6860:Psd
|
UTSW |
19 |
46,310,858 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7286:Psd
|
UTSW |
19 |
46,303,240 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7326:Psd
|
UTSW |
19 |
46,312,893 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7351:Psd
|
UTSW |
19 |
46,310,869 (GRCm39) |
missense |
probably benign |
0.27 |
|
R7593:Psd
|
UTSW |
19 |
46,301,352 (GRCm39) |
missense |
possibly damaging |
0.47 |
|
R7614:Psd
|
UTSW |
19 |
46,301,877 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7943:Psd
|
UTSW |
19 |
46,313,169 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R8301:Psd
|
UTSW |
19 |
46,309,541 (GRCm39) |
intron |
probably benign |
|
|
R8498:Psd
|
UTSW |
19 |
46,312,788 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8712:Psd
|
UTSW |
19 |
46,301,775 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8952:Psd
|
UTSW |
19 |
46,310,900 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8980:Psd
|
UTSW |
19 |
46,310,657 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R9168:Psd
|
UTSW |
19 |
46,309,233 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9322:Psd
|
UTSW |
19 |
46,301,880 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9512:Psd
|
UTSW |
19 |
46,306,154 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
R9569:Psd
|
UTSW |
19 |
46,308,717 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R9638:Psd
|
UTSW |
19 |
46,301,841 (GRCm39) |
frame shift |
probably null |
|
|
R9645:Psd
|
UTSW |
19 |
46,301,841 (GRCm39) |
frame shift |
probably null |
|
|
R9721:Psd
|
UTSW |
19 |
46,311,628 (GRCm39) |
missense |
probably benign |
0.00 |
|
Z1177:Psd
|
UTSW |
19 |
46,313,100 (GRCm39) |
missense |
probably benign |
0.16 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGTCCCTTAGCTGAGGTACTAG -3'
(R):5'- TCCGTTTTGTGGAGAAGGCC -3'
Sequencing Primer
(F):5'- TTAGCTGAGGTACTAGGGCCC -3'
(R):5'- AATGGCCTACCTGCTTCTGGAG -3'
|
| Posted On |
2015-04-29 |
Incidental Mutation