Incidental Mutation 'R6783:Ptcd3'
| ID |
531504 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ptcd3
|
| Ensembl Gene |
ENSMUSG00000063884 |
| Gene Name |
pentatricopeptide repeat domain 3 |
| Synonyms |
2610034F17Rik, 2810422B04Rik |
| MMRRC Submission |
044897-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6783 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
6 |
| Chromosomal Location |
71857622-71885734 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 71885627 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Aspartic acid
at position 33
(V33D)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000080743
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000055296]
[ENSMUST00000082094]
[ENSMUST00000206556]
[ENSMUST00000206879]
|
| AlphaFold |
Q14C51 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000055296
|
| SMART Domains |
Protein: ENSMUSP00000060858
Gene: ENSMUSG00000049553
| Domain | Start | End | E-Value | Type |
|---|
|
RPOLA_N
|
302 |
649 |
8.97e-137 |
SMART |
|
Pfam:RNA_pol_Rpb1_4
|
846 |
958 |
1.3e-26 |
PFAM |
|
Pfam:RNA_pol_Rpb1_5
|
965 |
1669 |
7e-103 |
PFAM |
|
low complexity region
|
1698 |
1708 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000082094
AA Change: V33D
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000080743
Gene: ENSMUSG00000063884
AA Change: V33D
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
8 |
N/A |
INTRINSIC |
|
low complexity region
|
216 |
227 |
N/A |
INTRINSIC |
|
Pfam:PPR_2
|
253 |
300 |
1.4e-10 |
PFAM |
|
Pfam:PPR_3
|
331 |
366 |
2.1e-4 |
PFAM |
|
low complexity region
|
671 |
684 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000206284
AA Change: V25D
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000206556
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000206879
AA Change: V33D
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.4%
- 20x: 95.8%
|
| Validation Efficiency |
95% (42/44) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam12 |
T |
A |
7: 133,576,126 (GRCm39) |
Q228L |
probably damaging |
Het |
| Arhgap45 |
A |
G |
10: 79,853,698 (GRCm39) |
T71A |
possibly damaging |
Het |
| Bag6 |
T |
A |
17: 35,363,211 (GRCm39) |
S684T |
possibly damaging |
Het |
| Bcam |
C |
T |
7: 19,500,806 (GRCm39) |
G123R |
probably damaging |
Het |
| Cdcp3 |
T |
C |
7: 130,828,493 (GRCm39) |
L316P |
probably damaging |
Het |
| Cdr2l |
C |
T |
11: 115,284,495 (GRCm39) |
A277V |
possibly damaging |
Het |
| Clcn4 |
T |
A |
7: 7,302,181 (GRCm39) |
|
probably benign |
Het |
| Csnk1g1 |
T |
A |
9: 65,880,794 (GRCm39) |
I72N |
probably damaging |
Het |
| Cspg4b |
A |
T |
13: 113,456,743 (GRCm39) |
K930* |
probably null |
Het |
| Ddx31 |
G |
A |
2: 28,764,188 (GRCm39) |
V465I |
probably benign |
Het |
| Ddx54 |
C |
T |
5: 120,756,779 (GRCm39) |
Q163* |
probably null |
Het |
| Dnmt3a |
A |
G |
12: 3,947,406 (GRCm39) |
E459G |
probably damaging |
Het |
| Dpp8 |
T |
C |
9: 64,970,844 (GRCm39) |
S568P |
possibly damaging |
Het |
| Drap1 |
G |
T |
19: 5,474,219 (GRCm39) |
T47K |
probably damaging |
Het |
| Epha7 |
G |
T |
4: 28,950,528 (GRCm39) |
R777L |
possibly damaging |
Het |
| Far2 |
T |
G |
6: 148,052,273 (GRCm39) |
|
probably null |
Het |
| Fhdc1 |
T |
C |
3: 84,352,834 (GRCm39) |
K797R |
probably benign |
Het |
| Gm10330 |
A |
T |
12: 23,830,094 (GRCm39) |
M29K |
probably damaging |
Het |
| Grik3 |
A |
T |
4: 125,526,093 (GRCm39) |
I109F |
probably benign |
Het |
| Il31ra |
T |
C |
13: 112,688,522 (GRCm39) |
|
probably null |
Het |
| Itga1 |
T |
G |
13: 115,133,513 (GRCm39) |
I466L |
probably benign |
Het |
| Itpr2 |
A |
T |
6: 146,287,371 (GRCm39) |
|
probably null |
Het |
| Mical3 |
A |
C |
6: 120,935,786 (GRCm39) |
L1580R |
possibly damaging |
Het |
| Or14c43 |
T |
A |
7: 86,114,835 (GRCm39) |
V72D |
probably damaging |
Het |
| Or4n4 |
T |
C |
14: 50,519,644 (GRCm39) |
D22G |
probably benign |
Het |
| Palb2 |
T |
A |
7: 121,726,711 (GRCm39) |
E386D |
probably damaging |
Het |
| Pate8 |
T |
A |
9: 36,492,631 (GRCm39) |
|
probably null |
Het |
| Polm |
C |
A |
11: 5,785,534 (GRCm39) |
R175L |
probably damaging |
Het |
| Prpf40b |
C |
T |
15: 99,212,784 (GRCm39) |
R627W |
probably damaging |
Het |
| Pwwp4c |
C |
T |
X: 73,684,021 (GRCm39) |
R355H |
probably damaging |
Homo |
| Ripk4 |
C |
A |
16: 97,549,237 (GRCm39) |
R273L |
probably damaging |
Het |
| Rpap2 |
A |
G |
5: 107,803,153 (GRCm39) |
T612A |
probably damaging |
Het |
| Serpinb10 |
A |
G |
1: 107,474,597 (GRCm39) |
N253S |
possibly damaging |
Het |
| Sgpp1 |
G |
C |
12: 75,782,243 (GRCm39) |
P32R |
probably benign |
Het |
| Sim1 |
T |
C |
10: 50,784,823 (GRCm39) |
I156T |
possibly damaging |
Het |
| Ski |
A |
T |
4: 155,245,289 (GRCm39) |
|
probably null |
Het |
| Spaca7b |
G |
A |
8: 11,705,661 (GRCm39) |
Q39* |
probably null |
Het |
| Tent2 |
G |
A |
13: 93,291,526 (GRCm39) |
A368V |
probably benign |
Het |
| Tent2 |
C |
G |
13: 93,291,527 (GRCm39) |
A372P |
probably benign |
Het |
| Trdn |
C |
T |
10: 33,314,811 (GRCm39) |
R512C |
probably damaging |
Het |
| Trim33 |
T |
C |
3: 103,259,403 (GRCm39) |
Y1031H |
probably damaging |
Het |
| Use1 |
T |
C |
8: 71,821,880 (GRCm39) |
L188P |
probably damaging |
Het |
| Usp34 |
G |
A |
11: 23,362,318 (GRCm39) |
G1588D |
probably damaging |
Het |
| Vmn2r33 |
C |
A |
7: 7,566,797 (GRCm39) |
R105L |
probably benign |
Het |
| Vmn2r53 |
G |
A |
7: 12,335,360 (GRCm39) |
S100F |
probably damaging |
Het |
|
| Other mutations in Ptcd3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00767:Ptcd3
|
APN |
6 |
71,880,432 (GRCm39) |
missense |
probably damaging |
0.96 |
|
IGL00903:Ptcd3
|
APN |
6 |
71,884,828 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
IGL01545:Ptcd3
|
APN |
6 |
71,865,561 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL01924:Ptcd3
|
APN |
6 |
71,875,411 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02675:Ptcd3
|
APN |
6 |
71,860,426 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0732:Ptcd3
|
UTSW |
6 |
71,858,155 (GRCm39) |
unclassified |
probably benign |
|
|
R1374:Ptcd3
|
UTSW |
6 |
71,885,637 (GRCm39) |
nonsense |
probably null |
|
|
R1393:Ptcd3
|
UTSW |
6 |
71,866,605 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1498:Ptcd3
|
UTSW |
6 |
71,870,479 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1646:Ptcd3
|
UTSW |
6 |
71,875,379 (GRCm39) |
missense |
probably benign |
0.26 |
|
R1712:Ptcd3
|
UTSW |
6 |
71,885,637 (GRCm39) |
nonsense |
probably null |
|
|
R2022:Ptcd3
|
UTSW |
6 |
71,862,537 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2248:Ptcd3
|
UTSW |
6 |
71,871,269 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2406:Ptcd3
|
UTSW |
6 |
71,865,631 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3418:Ptcd3
|
UTSW |
6 |
71,860,470 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R3419:Ptcd3
|
UTSW |
6 |
71,860,470 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R4677:Ptcd3
|
UTSW |
6 |
71,870,498 (GRCm39) |
missense |
probably benign |
0.17 |
|
R4741:Ptcd3
|
UTSW |
6 |
71,879,933 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4752:Ptcd3
|
UTSW |
6 |
71,878,296 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5441:Ptcd3
|
UTSW |
6 |
71,858,505 (GRCm39) |
missense |
possibly damaging |
0.62 |
|
R5583:Ptcd3
|
UTSW |
6 |
71,879,920 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5681:Ptcd3
|
UTSW |
6 |
71,884,643 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6028:Ptcd3
|
UTSW |
6 |
71,875,392 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6324:Ptcd3
|
UTSW |
6 |
71,862,311 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6537:Ptcd3
|
UTSW |
6 |
71,874,094 (GRCm39) |
splice site |
probably null |
|
|
R6600:Ptcd3
|
UTSW |
6 |
71,860,530 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6810:Ptcd3
|
UTSW |
6 |
71,862,516 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6860:Ptcd3
|
UTSW |
6 |
71,874,094 (GRCm39) |
splice site |
probably null |
|
|
R6993:Ptcd3
|
UTSW |
6 |
71,862,299 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7578:Ptcd3
|
UTSW |
6 |
71,885,691 (GRCm39) |
missense |
probably benign |
|
|
R7788:Ptcd3
|
UTSW |
6 |
71,862,541 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7851:Ptcd3
|
UTSW |
6 |
71,879,843 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7888:Ptcd3
|
UTSW |
6 |
71,860,431 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7889:Ptcd3
|
UTSW |
6 |
71,865,592 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7919:Ptcd3
|
UTSW |
6 |
71,880,438 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8162:Ptcd3
|
UTSW |
6 |
71,884,798 (GRCm39) |
missense |
probably benign |
0.02 |
|
R8351:Ptcd3
|
UTSW |
6 |
71,885,625 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8451:Ptcd3
|
UTSW |
6 |
71,885,625 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8701:Ptcd3
|
UTSW |
6 |
71,862,495 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R8826:Ptcd3
|
UTSW |
6 |
71,885,645 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8926:Ptcd3
|
UTSW |
6 |
71,869,464 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8969:Ptcd3
|
UTSW |
6 |
71,880,431 (GRCm39) |
missense |
probably benign |
0.44 |
|
R9031:Ptcd3
|
UTSW |
6 |
71,880,458 (GRCm39) |
nonsense |
probably null |
|
|
R9046:Ptcd3
|
UTSW |
6 |
71,870,364 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9384:Ptcd3
|
UTSW |
6 |
71,874,110 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R9668:Ptcd3
|
UTSW |
6 |
71,871,275 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R9771:Ptcd3
|
UTSW |
6 |
71,872,903 (GRCm39) |
nonsense |
probably null |
|
|
X0024:Ptcd3
|
UTSW |
6 |
71,878,258 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0065:Ptcd3
|
UTSW |
6 |
71,884,790 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGAATTCCCGAACTCGCAGATC -3'
(R):5'- GATGTGTACTGAGCGTTCCG -3'
Sequencing Primer
(F):5'- TTCCCGAACTCGCAGATCTAAAG -3'
(R):5'- TAGTCTAGCCAAACAGGACCTTGTG -3'
|
| Posted On |
2018-08-29 |
Incidental Mutation