Incidental Mutation 'R2406:Ptcd3'
| ID |
248005 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ptcd3
|
| Ensembl Gene |
ENSMUSG00000063884 |
| Gene Name |
pentatricopeptide repeat domain 3 |
| Synonyms |
2610034F17Rik, 2810422B04Rik |
| MMRRC Submission |
040372-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R2406 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
6 |
| Chromosomal Location |
71857622-71885734 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 71865631 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 428
(D428G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000080743
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000082094]
[ENSMUST00000206879]
|
| AlphaFold |
Q14C51 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000082094
AA Change: D428G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000080743
Gene: ENSMUSG00000063884
AA Change: D428G
| 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 |
probably benign
Transcript: ENSMUST00000205556
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000205691
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000205761
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000206631
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000206762
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000206879
|
| Meta Mutation Damage Score |
0.7387 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.9%
- 20x: 93.9%
|
| Validation Efficiency |
95% (42/44) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2300002M23Rik |
T |
A |
17: 35,879,352 (GRCm39) |
V230E |
probably damaging |
Het |
| Adam22 |
A |
T |
5: 8,230,064 (GRCm39) |
|
probably benign |
Het |
| AW554918 |
A |
G |
18: 25,473,344 (GRCm39) |
I180V |
possibly damaging |
Het |
| C9 |
T |
C |
15: 6,512,780 (GRCm39) |
S301P |
possibly damaging |
Het |
| Cdc42bpb |
T |
C |
12: 111,268,558 (GRCm39) |
Q1214R |
probably benign |
Het |
| Chaf1b |
T |
C |
16: 93,697,043 (GRCm39) |
I351T |
probably damaging |
Het |
| Clip1 |
T |
C |
5: 123,741,723 (GRCm39) |
E1177G |
probably damaging |
Het |
| Colgalt1 |
G |
A |
8: 72,070,312 (GRCm39) |
C198Y |
probably damaging |
Het |
| Dennd4b |
C |
T |
3: 90,182,795 (GRCm39) |
R871C |
probably damaging |
Het |
| Efcab3 |
A |
T |
11: 104,611,457 (GRCm39) |
D433V |
probably benign |
Het |
| Eif4ebp1 |
A |
G |
8: 27,763,362 (GRCm39) |
I52V |
probably damaging |
Het |
| Fbxw5 |
T |
C |
2: 25,394,195 (GRCm39) |
I86T |
probably damaging |
Het |
| Gm10650 |
A |
G |
3: 127,833,530 (GRCm39) |
|
noncoding transcript |
Het |
| Helz |
G |
A |
11: 107,577,378 (GRCm39) |
A1910T |
unknown |
Het |
| Hsf2 |
C |
T |
10: 57,373,642 (GRCm39) |
T70I |
probably damaging |
Het |
| Ifih1 |
A |
G |
2: 62,437,447 (GRCm39) |
|
probably benign |
Het |
| Kdm2a |
T |
C |
19: 4,372,546 (GRCm39) |
D933G |
probably damaging |
Het |
| Macc1 |
T |
C |
12: 119,429,346 (GRCm39) |
I832T |
probably damaging |
Het |
| Mapk15 |
T |
C |
15: 75,870,697 (GRCm39) |
S512P |
possibly damaging |
Het |
| Mybpc2 |
A |
T |
7: 44,171,149 (GRCm39) |
I134N |
possibly damaging |
Het |
| Myh4 |
A |
G |
11: 67,150,000 (GRCm39) |
E1853G |
probably damaging |
Het |
| Ncoa3 |
T |
C |
2: 165,897,279 (GRCm39) |
V690A |
probably damaging |
Het |
| Nsf |
C |
T |
11: 103,821,578 (GRCm39) |
E26K |
possibly damaging |
Het |
| Or5b97 |
A |
G |
19: 12,878,991 (GRCm39) |
V51A |
probably benign |
Het |
| Pacsin2 |
A |
T |
15: 83,269,313 (GRCm39) |
|
probably benign |
Het |
| Piezo2 |
A |
T |
18: 63,155,596 (GRCm39) |
L2416Q |
probably damaging |
Het |
| Pip5k1c |
T |
A |
10: 81,144,858 (GRCm39) |
I233N |
probably damaging |
Het |
| Ptprf |
T |
C |
4: 118,126,501 (GRCm39) |
D84G |
possibly damaging |
Het |
| Rasgrf2 |
T |
C |
13: 92,120,359 (GRCm39) |
D798G |
probably benign |
Het |
| Setd7 |
A |
G |
3: 51,450,097 (GRCm39) |
Y110H |
probably damaging |
Het |
| Sgta |
T |
C |
10: 80,887,081 (GRCm39) |
I61M |
possibly damaging |
Het |
| Shank1 |
A |
G |
7: 44,006,376 (GRCm39) |
D2031G |
possibly damaging |
Het |
| Skint5 |
A |
G |
4: 113,799,864 (GRCm39) |
Y88H |
probably damaging |
Het |
| Spata31f1a |
A |
T |
4: 42,851,696 (GRCm39) |
D153E |
probably benign |
Het |
| Stox1 |
T |
C |
10: 62,499,945 (GRCm39) |
I872V |
probably benign |
Het |
| Tmc4 |
A |
G |
7: 3,674,025 (GRCm39) |
F385L |
probably benign |
Het |
| Top3a |
A |
G |
11: 60,646,838 (GRCm39) |
F258L |
probably damaging |
Het |
| Ttn |
T |
C |
2: 76,780,499 (GRCm39) |
Y1084C |
probably damaging |
Het |
| Ubtf |
A |
T |
11: 102,199,528 (GRCm39) |
Y504* |
probably null |
Het |
| Wdfy3 |
T |
C |
5: 102,036,125 (GRCm39) |
T2098A |
probably damaging |
Het |
| Wnk2 |
G |
T |
13: 49,214,964 (GRCm39) |
T1194K |
possibly damaging |
Het |
| Zbtb40 |
T |
A |
4: 136,725,879 (GRCm39) |
E560V |
probably benign |
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 |
|
|
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 |
|
R6783:Ptcd3
|
UTSW |
6 |
71,885,627 (GRCm39) |
missense |
probably benign |
0.00 |
|
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'- CTCCCACTGCTGAATCTAGC -3'
(R):5'- CAGTGCTGGTACTTGAAGCTG -3'
Sequencing Primer
(F):5'- TCCTTGGTCCAAAATCATGAGGG -3'
(R):5'- CATGGTGATTTTGATAGTACAGTGC -3'
|
| Posted On |
2014-11-11 |
Incidental Mutation