Incidental Mutation 'R0542:Psd'
| ID |
50020 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Psd
|
| Ensembl Gene |
ENSMUSG00000037126 |
| Gene Name |
pleckstrin and Sec7 domain containing |
| Synonyms |
Efa6, Psdl, Efa6a, 1110007H17Rik |
| MMRRC Submission |
038734-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R0542 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
46300526-46315595 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 46302649 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 842
(T842A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000152942
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000041391]
[ENSMUST00000073116]
[ENSMUST00000096029]
[ENSMUST00000111881]
[ENSMUST00000224556]
[ENSMUST00000225323]
|
| AlphaFold |
Q5DTT2 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000041391
AA Change: T841A
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000039728
Gene: ENSMUSG00000037126
AA Change: T841A
| 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: ENSMUST00000073116
|
| SMART Domains |
Protein: ENSMUSP00000072859
Gene: ENSMUSG00000025225
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RHD_DNA_bind
|
40 |
220 |
1.3e-67 |
PFAM |
|
IPT
|
227 |
326 |
3.48e-27 |
SMART |
|
low complexity region
|
351 |
382 |
N/A |
INTRINSIC |
|
low complexity region
|
391 |
409 |
N/A |
INTRINSIC |
|
ANK
|
487 |
522 |
5.58e1 |
SMART |
|
ANK
|
526 |
555 |
9.78e-4 |
SMART |
|
ANK
|
559 |
591 |
3.74e0 |
SMART |
|
ANK
|
599 |
628 |
3.36e-2 |
SMART |
|
ANK
|
633 |
663 |
1.3e1 |
SMART |
|
ANK
|
667 |
696 |
4.26e-4 |
SMART |
|
low complexity region
|
707 |
721 |
N/A |
INTRINSIC |
|
ANK
|
729 |
758 |
2.35e3 |
SMART |
|
DEATH
|
764 |
851 |
5.52e-16 |
SMART |
|
low complexity region
|
879 |
894 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000096029
AA Change: T842A
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000093729
Gene: ENSMUSG00000037126
AA Change: T842A
| 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: ENSMUST00000111881
|
| SMART Domains |
Protein: ENSMUSP00000107512
Gene: ENSMUSG00000025225
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RHD
|
40 |
220 |
1.3e-67 |
PFAM |
|
IPT
|
227 |
326 |
3.48e-27 |
SMART |
|
low complexity region
|
351 |
382 |
N/A |
INTRINSIC |
|
low complexity region
|
391 |
409 |
N/A |
INTRINSIC |
|
ANK
|
487 |
522 |
5.58e1 |
SMART |
|
ANK
|
526 |
555 |
9.78e-4 |
SMART |
|
ANK
|
559 |
591 |
3.74e0 |
SMART |
|
ANK
|
599 |
628 |
3.36e-2 |
SMART |
|
ANK
|
633 |
663 |
1.3e1 |
SMART |
|
ANK
|
667 |
696 |
4.26e-4 |
SMART |
|
low complexity region
|
707 |
721 |
N/A |
INTRINSIC |
|
ANK
|
729 |
758 |
2.35e3 |
SMART |
|
DEATH
|
764 |
851 |
5.52e-16 |
SMART |
|
low complexity region
|
879 |
894 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000224556
AA Change: T210A
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000225323
AA Change: T842A
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000225748
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000226062
|
| Meta Mutation Damage Score |
0.8204 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 95.0%
|
| Validation Efficiency |
99% (70/71) |
| 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: 69 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abhd12b |
C |
A |
12: 70,210,269 (GRCm39) |
N71K |
possibly damaging |
Het |
| Adgrl2 |
A |
G |
3: 148,564,854 (GRCm39) |
I242T |
probably damaging |
Het |
| Adgrv1 |
A |
G |
13: 81,721,437 (GRCm39) |
S714P |
probably damaging |
Het |
| Agap3 |
G |
A |
5: 24,705,184 (GRCm39) |
R704Q |
possibly damaging |
Het |
| Ankrd11 |
T |
C |
8: 123,622,509 (GRCm39) |
R448G |
probably damaging |
Het |
| Anks1b |
T |
C |
10: 89,909,829 (GRCm39) |
|
probably benign |
Het |
| Caml |
A |
T |
13: 55,770,974 (GRCm39) |
Q24L |
possibly damaging |
Het |
| Cdc14b |
G |
A |
13: 64,391,497 (GRCm39) |
T124I |
probably benign |
Het |
| Clca3a2 |
A |
G |
3: 144,781,571 (GRCm39) |
|
probably benign |
Het |
| Col12a1 |
A |
G |
9: 79,512,610 (GRCm39) |
|
probably null |
Het |
| Crispld1 |
T |
C |
1: 17,816,992 (GRCm39) |
V183A |
possibly damaging |
Het |
| Cstdc1 |
A |
G |
2: 148,624,092 (GRCm39) |
N22S |
probably benign |
Het |
| Dhx40 |
C |
T |
11: 86,695,082 (GRCm39) |
|
probably null |
Het |
| Dmxl1 |
T |
A |
18: 50,026,761 (GRCm39) |
D1956E |
probably benign |
Het |
| Dsc2 |
A |
G |
18: 20,184,283 (GRCm39) |
V35A |
probably damaging |
Het |
| Dync2i2 |
A |
G |
2: 29,921,837 (GRCm39) |
V508A |
probably damaging |
Het |
| Elovl2 |
A |
G |
13: 41,345,452 (GRCm39) |
|
probably benign |
Het |
| Gapvd1 |
T |
C |
2: 34,615,048 (GRCm39) |
|
probably benign |
Het |
| Gnaq |
T |
A |
19: 16,196,982 (GRCm39) |
I56N |
probably damaging |
Het |
| Gpr139 |
T |
C |
7: 118,744,306 (GRCm39) |
D93G |
probably benign |
Het |
| Hars1 |
C |
T |
18: 36,904,234 (GRCm39) |
R215H |
probably benign |
Het |
| Helz2 |
C |
A |
2: 180,873,882 (GRCm39) |
W2204L |
probably damaging |
Het |
| Ift70b |
A |
G |
2: 75,767,055 (GRCm39) |
V566A |
probably damaging |
Het |
| Itgb6 |
A |
T |
2: 60,435,480 (GRCm39) |
C757S |
possibly damaging |
Het |
| Kpnb1 |
G |
A |
11: 97,078,398 (GRCm39) |
T5I |
probably benign |
Het |
| Krt82 |
T |
C |
15: 101,454,035 (GRCm39) |
|
probably benign |
Het |
| Lgals9 |
T |
A |
11: 78,860,546 (GRCm39) |
K175N |
possibly damaging |
Het |
| Lrp2 |
A |
G |
2: 69,258,998 (GRCm39) |
I4564T |
probably benign |
Het |
| Mblac1 |
A |
G |
5: 138,192,798 (GRCm39) |
T47A |
possibly damaging |
Het |
| Med12l |
G |
A |
3: 58,949,822 (GRCm39) |
D182N |
probably damaging |
Het |
| Megf9 |
A |
G |
4: 70,353,585 (GRCm39) |
I407T |
probably benign |
Het |
| Mtmr6 |
A |
T |
14: 60,529,578 (GRCm39) |
|
probably null |
Het |
| Mtor |
A |
G |
4: 148,624,907 (GRCm39) |
T2173A |
probably benign |
Het |
| Mzt1 |
A |
T |
14: 99,277,938 (GRCm39) |
|
probably benign |
Het |
| Narf |
T |
C |
11: 121,143,690 (GRCm39) |
L444P |
probably damaging |
Het |
| Nsd1 |
A |
T |
13: 55,408,271 (GRCm39) |
Q1305L |
possibly damaging |
Het |
| Ntsr1 |
A |
G |
2: 180,184,374 (GRCm39) |
Y359C |
probably damaging |
Het |
| Olfm1 |
A |
G |
2: 28,104,640 (GRCm39) |
D159G |
possibly damaging |
Het |
| Or2l13b |
A |
T |
16: 19,348,732 (GRCm39) |
*313R |
probably null |
Het |
| Pcdh1 |
C |
T |
18: 38,322,975 (GRCm39) |
V953I |
probably damaging |
Het |
| Pcdhb11 |
A |
T |
18: 37,556,887 (GRCm39) |
D739V |
probably damaging |
Het |
| Pdgfd |
A |
G |
9: 6,359,769 (GRCm39) |
N280S |
probably damaging |
Het |
| Per2 |
A |
T |
1: 91,366,054 (GRCm39) |
|
probably null |
Het |
| Pfkp |
G |
T |
13: 6,672,028 (GRCm39) |
C122* |
probably null |
Het |
| Plxna4 |
G |
A |
6: 32,169,232 (GRCm39) |
R1322W |
probably damaging |
Het |
| Ppox |
A |
G |
1: 171,106,818 (GRCm39) |
L202P |
probably damaging |
Het |
| Ppp1r3e |
G |
A |
14: 55,114,588 (GRCm39) |
P58L |
probably benign |
Het |
| Prr23a2 |
A |
C |
9: 98,739,086 (GRCm39) |
N148T |
probably benign |
Het |
| Ranbp2 |
C |
T |
10: 58,314,236 (GRCm39) |
A1652V |
probably benign |
Het |
| Rragd |
G |
A |
4: 33,007,103 (GRCm39) |
V144M |
probably damaging |
Het |
| Sema6a |
T |
G |
18: 47,381,643 (GRCm39) |
D968A |
probably damaging |
Het |
| Slc30a5 |
A |
T |
13: 100,945,793 (GRCm39) |
|
probably null |
Het |
| Snx17 |
G |
T |
5: 31,353,895 (GRCm39) |
|
probably null |
Het |
| Styxl2 |
A |
T |
1: 165,928,853 (GRCm39) |
M253K |
possibly damaging |
Het |
| Syt14 |
G |
T |
1: 192,613,111 (GRCm39) |
T563K |
probably damaging |
Het |
| Tada3 |
T |
C |
6: 113,352,175 (GRCm39) |
K85E |
probably damaging |
Het |
| Tspear |
T |
C |
10: 77,716,921 (GRCm39) |
V532A |
probably benign |
Het |
| Ttn |
A |
T |
2: 76,723,453 (GRCm39) |
C6426S |
possibly damaging |
Het |
| Unc79 |
T |
C |
12: 103,060,437 (GRCm39) |
|
probably benign |
Het |
| Usp19 |
A |
G |
9: 108,371,584 (GRCm39) |
|
probably null |
Het |
| Vav3 |
G |
A |
3: 109,434,746 (GRCm39) |
D426N |
probably damaging |
Het |
| Vezt |
T |
C |
10: 93,842,958 (GRCm39) |
|
probably null |
Het |
| Vldlr |
G |
T |
19: 27,213,655 (GRCm39) |
R114L |
probably benign |
Het |
| Wwc2 |
C |
T |
8: 48,321,414 (GRCm39) |
V567I |
unknown |
Het |
| Zfp423 |
T |
C |
8: 88,507,237 (GRCm39) |
T911A |
probably damaging |
Het |
| Zfp719 |
A |
G |
7: 43,238,677 (GRCm39) |
|
probably null |
Het |
| Zkscan16 |
A |
T |
4: 58,956,597 (GRCm39) |
H293L |
possibly damaging |
Het |
| Zkscan6 |
A |
C |
11: 65,719,525 (GRCm39) |
N515T |
possibly damaging |
Het |
| Znfx1 |
A |
G |
2: 166,897,575 (GRCm39) |
S450P |
probably damaging |
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 |
|
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 |
|
|
R3970: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'- ATCCAGGACTGCATTTGCTCCAG -3'
(R):5'- TCCTCAAGGGCATGATCCTCTACC -3'
Sequencing Primer
(F):5'- actcttttgcctccgcc -3'
(R):5'- GCTTGCCAGAGGGGATTAG -3'
|
| Posted On |
2013-06-12 |
Incidental Mutation