Incidental Mutation 'R4984:Pdcd5'
ID |
446641 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pdcd5
|
Ensembl Gene |
ENSMUSG00000030417 |
Gene Name |
programmed cell death 5 |
Synonyms |
2200003D22Rik, Tfar19 |
MMRRC Submission |
042578-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.960)
|
Stock # |
R4984 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
7 |
Chromosomal Location |
35341410-35346907 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to C
at 35342110 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Glycine
at position 166
(V166G)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000113013
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000040844]
[ENSMUST00000118501]
[ENSMUST00000120714]
[ENSMUST00000190503]
|
AlphaFold |
P56812 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000040844
|
SMART Domains |
Protein: ENSMUSP00000041751 Gene: ENSMUSG00000034867
Domain | Start | End | E-Value | Type |
Blast:ANK
|
8 |
37 |
2e-8 |
BLAST |
VPS9
|
264 |
380 |
1.92e-7 |
SMART |
Blast:ANK
|
393 |
418 |
8e-9 |
BLAST |
low complexity region
|
419 |
430 |
N/A |
INTRINSIC |
ANK
|
462 |
491 |
8.65e-5 |
SMART |
ANK
|
495 |
524 |
1.8e-2 |
SMART |
ANK
|
528 |
558 |
2.45e-4 |
SMART |
ANK
|
564 |
593 |
6.46e-4 |
SMART |
low complexity region
|
638 |
658 |
N/A |
INTRINSIC |
ANK
|
742 |
774 |
8.39e-3 |
SMART |
ANK
|
775 |
804 |
5.93e-3 |
SMART |
ANK
|
808 |
837 |
4.46e-7 |
SMART |
ANK
|
841 |
870 |
2.81e-4 |
SMART |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000118501
AA Change: V87G
PolyPhen 2
Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000113761 Gene: ENSMUSG00000030417 AA Change: V87G
Domain | Start | End | E-Value | Type |
Pfam:dsDNA_bind
|
9 |
113 |
9.6e-38 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000120714
AA Change: V166G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000113013 Gene: ENSMUSG00000030417 AA Change: V166G
Domain | Start | End | E-Value | Type |
low complexity region
|
9 |
26 |
N/A |
INTRINSIC |
low complexity region
|
29 |
39 |
N/A |
INTRINSIC |
low complexity region
|
56 |
64 |
N/A |
INTRINSIC |
Pfam:dsDNA_bind
|
91 |
192 |
1.9e-34 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000126734
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000127213
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130306
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130340
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151336
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000190503
|
SMART Domains |
Protein: ENSMUSP00000140259 Gene: ENSMUSG00000034867
Domain | Start | End | E-Value | Type |
Blast:ANK
|
8 |
37 |
2e-8 |
BLAST |
VPS9
|
264 |
380 |
1.92e-7 |
SMART |
Blast:ANK
|
393 |
418 |
7e-9 |
BLAST |
low complexity region
|
419 |
430 |
N/A |
INTRINSIC |
ANK
|
462 |
491 |
8.65e-5 |
SMART |
ANK
|
495 |
524 |
1.8e-2 |
SMART |
ANK
|
528 |
558 |
2.45e-4 |
SMART |
ANK
|
564 |
593 |
6.46e-4 |
SMART |
low complexity region
|
638 |
658 |
N/A |
INTRINSIC |
ANK
|
687 |
719 |
8.39e-3 |
SMART |
ANK
|
720 |
749 |
5.93e-3 |
SMART |
ANK
|
753 |
782 |
4.46e-7 |
SMART |
ANK
|
786 |
815 |
2.81e-4 |
SMART |
|
Meta Mutation Damage Score |
0.8444 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.7%
- 20x: 93.4%
|
Validation Efficiency |
98% (41/42) |
Allele List at MGI |
|
Other mutations in this stock |
Total: 36 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adra2a |
T |
C |
19: 54,035,070 (GRCm39) |
I142T |
probably damaging |
Het |
Cd109 |
T |
C |
9: 78,541,959 (GRCm39) |
|
probably null |
Het |
Cdc42bpg |
T |
A |
19: 6,366,253 (GRCm39) |
I812N |
possibly damaging |
Het |
Cftr |
A |
G |
6: 18,235,198 (GRCm39) |
E479G |
possibly damaging |
Het |
Cimap3 |
T |
A |
3: 105,908,810 (GRCm39) |
|
probably benign |
Het |
Cpb1 |
GTTT |
GTT |
3: 20,324,516 (GRCm39) |
|
probably null |
Het |
Crocc |
T |
C |
4: 140,761,763 (GRCm39) |
E873G |
probably damaging |
Het |
Dnah3 |
C |
T |
7: 119,528,002 (GRCm39) |
V3827I |
probably benign |
Het |
Dync1h1 |
C |
A |
12: 110,624,560 (GRCm39) |
T3700N |
probably damaging |
Het |
E230001N04Rik |
T |
C |
17: 28,742,780 (GRCm39) |
|
noncoding transcript |
Het |
Gpr89 |
T |
A |
3: 96,812,512 (GRCm39) |
M10L |
probably benign |
Het |
Kbtbd7 |
T |
C |
14: 79,664,602 (GRCm39) |
Y145H |
probably damaging |
Het |
Kcnh8 |
T |
A |
17: 53,184,995 (GRCm39) |
Y426N |
probably damaging |
Het |
Mipep |
A |
G |
14: 61,025,631 (GRCm39) |
D129G |
possibly damaging |
Het |
Muc15 |
C |
T |
2: 110,561,918 (GRCm39) |
P118L |
probably damaging |
Het |
Mug1 |
T |
C |
6: 121,815,576 (GRCm39) |
|
probably benign |
Het |
Nubp1 |
T |
A |
16: 10,239,108 (GRCm39) |
D208E |
probably damaging |
Het |
Or4a47 |
A |
T |
2: 89,666,157 (GRCm39) |
V44D |
probably damaging |
Het |
Or4k40 |
A |
T |
2: 111,251,192 (GRCm39) |
Y35N |
probably damaging |
Het |
Or4p4 |
A |
G |
2: 88,242,921 (GRCm39) |
L27P |
probably damaging |
Het |
Or52h9 |
T |
G |
7: 104,202,228 (GRCm39) |
I34S |
probably benign |
Het |
Or8g2 |
A |
G |
9: 39,821,906 (GRCm39) |
D269G |
probably benign |
Het |
Pde4d |
T |
C |
13: 109,876,998 (GRCm39) |
L173P |
probably damaging |
Het |
Phldb2 |
T |
C |
16: 45,645,996 (GRCm39) |
Y195C |
probably damaging |
Het |
Pou4f1 |
T |
C |
14: 104,703,619 (GRCm39) |
E271G |
unknown |
Het |
Ppl |
T |
C |
16: 4,905,505 (GRCm39) |
I1597V |
probably benign |
Het |
Pramel17 |
G |
C |
4: 101,692,796 (GRCm39) |
N401K |
possibly damaging |
Het |
Sorl1 |
C |
A |
9: 41,902,638 (GRCm39) |
D1640Y |
probably damaging |
Het |
Taf4b |
T |
C |
18: 14,968,873 (GRCm39) |
L670P |
probably damaging |
Het |
Tox3 |
TCTGCTGCTGCTGCTGCTG |
TCTGCTGCTGCTGCTG |
8: 90,975,270 (GRCm39) |
|
probably benign |
Het |
Ttc39b |
A |
T |
4: 83,160,446 (GRCm39) |
I377K |
probably benign |
Het |
Ttll3 |
A |
G |
6: 113,389,901 (GRCm39) |
D762G |
probably benign |
Het |
Ubp1 |
T |
A |
9: 113,788,460 (GRCm39) |
I279K |
probably damaging |
Het |
Vmn2r93 |
T |
A |
17: 18,533,389 (GRCm39) |
|
probably null |
Het |
Wdfy3 |
C |
T |
5: 102,090,985 (GRCm39) |
D532N |
probably benign |
Het |
Zfp644 |
A |
T |
5: 106,784,783 (GRCm39) |
L588Q |
possibly damaging |
Het |
|
Other mutations in Pdcd5 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL02447:Pdcd5
|
APN |
7 |
35,342,110 (GRCm39) |
missense |
possibly damaging |
0.95 |
IGL02954:Pdcd5
|
APN |
7 |
35,343,089 (GRCm39) |
missense |
probably damaging |
1.00 |
R0825:Pdcd5
|
UTSW |
7 |
35,346,338 (GRCm39) |
missense |
possibly damaging |
0.75 |
R4426:Pdcd5
|
UTSW |
7 |
35,345,605 (GRCm39) |
missense |
possibly damaging |
0.49 |
R4614:Pdcd5
|
UTSW |
7 |
35,346,472 (GRCm39) |
intron |
probably benign |
|
R4860:Pdcd5
|
UTSW |
7 |
35,343,135 (GRCm39) |
missense |
possibly damaging |
0.50 |
R4860:Pdcd5
|
UTSW |
7 |
35,343,135 (GRCm39) |
missense |
possibly damaging |
0.50 |
R5249:Pdcd5
|
UTSW |
7 |
35,346,421 (GRCm39) |
intron |
probably benign |
|
R5682:Pdcd5
|
UTSW |
7 |
35,346,613 (GRCm39) |
start gained |
probably benign |
|
R6384:Pdcd5
|
UTSW |
7 |
35,346,334 (GRCm39) |
missense |
possibly damaging |
0.60 |
R6787:Pdcd5
|
UTSW |
7 |
35,342,063 (GRCm39) |
missense |
probably damaging |
0.99 |
R8896:Pdcd5
|
UTSW |
7 |
35,346,795 (GRCm39) |
start codon destroyed |
probably null |
0.84 |
R9469:Pdcd5
|
UTSW |
7 |
35,343,827 (GRCm39) |
missense |
probably benign |
0.00 |
|
Predicted Primers |
PCR Primer
(F):5'- CCTCATCGCAGAATTAAGATGTC -3'
(R):5'- CAGAGCTACAAAGAACTGGGTC -3'
Sequencing Primer
(F):5'- GTCTAAAAGCTCACAGGCGCTTG -3'
(R):5'- GCAGAGGTAGCACATCTATGC -3'
|
Posted On |
2016-12-05 |