Incidental Mutation 'R6820:Psd'
| ID |
537592 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Psd
|
| Ensembl Gene |
ENSMUSG00000037126 |
| Gene Name |
pleckstrin and Sec7 domain containing |
| Synonyms |
Efa6, Psdl, Efa6a, 1110007H17Rik |
| MMRRC Submission |
044932-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R6820 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
46300526-46315595 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 46309283 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Glutamic Acid
at position 558
(A558E)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000039728
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000041391]
[ENSMUST00000096029]
[ENSMUST00000223903]
[ENSMUST00000223917]
[ENSMUST00000224447]
[ENSMUST00000224556]
[ENSMUST00000225323]
[ENSMUST00000225781]
|
| AlphaFold |
Q5DTT2 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000041391
AA Change: A558E
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000039728
Gene: ENSMUSG00000037126
AA Change: A558E
| 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 damaging
Transcript: ENSMUST00000096029
AA Change: A559E
PolyPhen 2
Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000093729
Gene: ENSMUSG00000037126
AA Change: A559E
| 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: ENSMUST00000223903
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000223917
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000224447
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000224556
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000225323
AA Change: A559E
PolyPhen 2
Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000225781
|
| Meta Mutation Damage Score |
0.5911 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.7%
|
| Validation Efficiency |
98% (46/47) |
| 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: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Accs |
T |
A |
2: 93,673,266 (GRCm39) |
N141Y |
probably null |
Het |
| Chkb |
A |
G |
15: 89,312,379 (GRCm39) |
L46P |
probably damaging |
Het |
| Col9a3 |
G |
A |
2: 180,248,927 (GRCm39) |
V260M |
probably damaging |
Het |
| Dna2 |
T |
C |
10: 62,800,683 (GRCm39) |
I739T |
possibly damaging |
Het |
| Dnah17 |
T |
C |
11: 117,959,826 (GRCm39) |
H2620R |
probably damaging |
Het |
| Dsel |
A |
G |
1: 111,787,547 (GRCm39) |
V996A |
probably damaging |
Het |
| Dst |
T |
C |
1: 34,250,337 (GRCm39) |
L1757S |
probably damaging |
Het |
| Exoc5 |
A |
T |
14: 49,286,387 (GRCm39) |
|
probably null |
Het |
| Fam120a |
A |
T |
13: 49,034,468 (GRCm39) |
V1048E |
possibly damaging |
Het |
| Fam50b |
G |
A |
13: 34,931,084 (GRCm39) |
E187K |
possibly damaging |
Het |
| Fbxw19 |
T |
A |
9: 109,311,079 (GRCm39) |
T377S |
probably benign |
Het |
| Fbxw28 |
A |
T |
9: 109,167,493 (GRCm39) |
F88Y |
probably damaging |
Het |
| Grik5 |
C |
T |
7: 24,745,780 (GRCm39) |
R431Q |
possibly damaging |
Het |
| Gtsf1 |
T |
C |
15: 103,328,954 (GRCm39) |
T92A |
probably benign |
Het |
| Hoxc13 |
A |
G |
15: 102,830,257 (GRCm39) |
Y212C |
probably damaging |
Het |
| Itih2 |
T |
C |
2: 10,102,909 (GRCm39) |
I742V |
probably benign |
Het |
| Kat7 |
T |
C |
11: 95,174,965 (GRCm39) |
T351A |
probably damaging |
Het |
| Mlh3 |
T |
C |
12: 85,294,497 (GRCm39) |
D1233G |
probably damaging |
Het |
| Mroh2b |
A |
G |
15: 4,982,756 (GRCm39) |
D1525G |
probably damaging |
Het |
| Nme5 |
T |
C |
18: 34,704,626 (GRCm39) |
Y73C |
probably damaging |
Het |
| Nr3c2 |
T |
C |
8: 77,969,086 (GRCm39) |
V957A |
probably damaging |
Het |
| Nup153 |
A |
G |
13: 46,863,459 (GRCm39) |
S301P |
probably benign |
Het |
| Obscn |
T |
C |
11: 58,942,019 (GRCm39) |
D5013G |
probably damaging |
Het |
| Or4f54 |
C |
T |
2: 111,123,455 (GRCm39) |
P281S |
probably damaging |
Het |
| Or5p51 |
A |
G |
7: 107,444,298 (GRCm39) |
V214A |
probably benign |
Het |
| Or8g51 |
A |
G |
9: 38,608,771 (GRCm39) |
V297A |
possibly damaging |
Het |
| Pak1 |
A |
G |
7: 97,535,586 (GRCm39) |
N226D |
probably benign |
Het |
| Pak4 |
A |
G |
7: 28,262,461 (GRCm39) |
Y384H |
probably benign |
Het |
| Pkp3 |
T |
C |
7: 140,659,757 (GRCm39) |
|
probably null |
Het |
| Prxl2b |
A |
T |
4: 154,982,623 (GRCm39) |
D50E |
probably damaging |
Het |
| Psmd14 |
C |
A |
2: 61,607,068 (GRCm39) |
H172N |
probably benign |
Het |
| Pygb |
G |
T |
2: 150,658,674 (GRCm39) |
W366L |
possibly damaging |
Het |
| Rbm39 |
A |
T |
2: 156,021,146 (GRCm39) |
M1K |
probably null |
Het |
| Rnf213 |
T |
C |
11: 119,339,664 (GRCm39) |
I3421T |
probably damaging |
Het |
| Rsf1 |
ATGGCG |
ATGGCGACGGTGGCG |
7: 97,229,111 (GRCm39) |
|
probably benign |
Het |
| Smg6 |
T |
C |
11: 74,932,790 (GRCm39) |
V88A |
probably damaging |
Het |
| Tha1 |
T |
C |
11: 117,762,504 (GRCm39) |
E80G |
probably benign |
Het |
| Tie1 |
A |
G |
4: 118,341,583 (GRCm39) |
V243A |
probably damaging |
Het |
| Tmem215 |
T |
C |
4: 40,473,926 (GRCm39) |
M1T |
probably null |
Het |
| Tpm2 |
A |
G |
4: 43,518,443 (GRCm39) |
Y221H |
probably damaging |
Het |
| Ubap1 |
C |
T |
4: 41,379,854 (GRCm39) |
P356L |
probably benign |
Het |
| Wbp2nl |
G |
T |
15: 82,197,996 (GRCm39) |
A178S |
possibly damaging |
Het |
| Wdr54 |
A |
T |
6: 83,131,601 (GRCm39) |
S139T |
probably benign |
Het |
| Wipi2 |
G |
C |
5: 142,615,555 (GRCm39) |
Q14H |
probably benign |
Het |
| Zan |
T |
C |
5: 137,406,106 (GRCm39) |
|
probably benign |
Het |
| Zfp735 |
A |
G |
11: 73,579,783 (GRCm39) |
M1V |
probably null |
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 |
|
|
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 |
|
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'- TCAGTGGCCTAGACAGTCTC -3'
(R):5'- AGCTTCTGGGTGTAGAGCAAG -3'
Sequencing Primer
(F):5'- TAGACAGTCTCTAGGCATGGC -3'
(R):5'- CAAGGGGAGGGTCTAGATGAC -3'
|
| Posted On |
2018-10-18 |
Incidental Mutation