Incidental Mutation 'R4741:Ptcd3'
ID |
358074 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Ptcd3
|
Ensembl Gene |
ENSMUSG00000063884 |
Gene Name |
pentatricopeptide repeat domain 3 |
Synonyms |
2610034F17Rik, 2810422B04Rik |
MMRRC Submission |
042026-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R4741 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
6 |
Chromosomal Location |
71857622-71885734 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 71879933 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Leucine to Phenylalanine
at position 108
(L108F)
|
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: L108F
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000080743 Gene: ENSMUSG00000063884 AA Change: L108F
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 |
noncoding transcript
Transcript: ENSMUST00000205293
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000205420
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000205761
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000206284
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000206879
AA Change: L108F
PolyPhen 2
Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
|
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.1%
|
Validation Efficiency |
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 52 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Angptl2 |
T |
C |
2: 33,136,200 (GRCm39) |
Y462H |
probably benign |
Het |
Arhgef12 |
A |
G |
9: 42,883,449 (GRCm39) |
I1360T |
possibly damaging |
Het |
Armc10 |
T |
G |
5: 21,856,834 (GRCm39) |
L111R |
probably damaging |
Het |
Atm |
T |
C |
9: 53,364,907 (GRCm39) |
K2628E |
probably benign |
Het |
Best3 |
A |
T |
10: 116,859,901 (GRCm39) |
N387I |
probably benign |
Het |
Bltp1 |
A |
G |
3: 36,996,524 (GRCm39) |
T1079A |
probably damaging |
Het |
Brpf3 |
T |
C |
17: 29,036,758 (GRCm39) |
F721S |
possibly damaging |
Het |
Cacna1c |
A |
G |
6: 118,590,271 (GRCm39) |
S1411P |
probably damaging |
Het |
Cldn8 |
G |
A |
16: 88,359,296 (GRCm39) |
H210Y |
probably benign |
Het |
Clip2 |
T |
A |
5: 134,545,123 (GRCm39) |
T344S |
probably benign |
Het |
Csmd1 |
A |
C |
8: 15,960,447 (GRCm39) |
W3323G |
probably damaging |
Het |
Doc2a |
A |
T |
7: 126,450,617 (GRCm39) |
T298S |
possibly damaging |
Het |
Dpp9 |
T |
C |
17: 56,512,286 (GRCm39) |
N234S |
probably benign |
Het |
Dtx2 |
C |
T |
5: 136,055,371 (GRCm39) |
R353C |
probably benign |
Het |
Epm2aip1 |
A |
G |
9: 111,101,681 (GRCm39) |
H218R |
probably benign |
Het |
F2rl1 |
G |
A |
13: 95,650,651 (GRCm39) |
T77M |
probably damaging |
Het |
Fsd2 |
A |
G |
7: 81,201,643 (GRCm39) |
|
probably null |
Het |
Grin2a |
T |
C |
16: 9,481,376 (GRCm39) |
Y475C |
probably damaging |
Het |
H2-Ob |
T |
A |
17: 34,461,545 (GRCm39) |
S95T |
possibly damaging |
Het |
Hddc3 |
A |
G |
7: 79,995,464 (GRCm39) |
T160A |
probably benign |
Het |
Hp |
A |
T |
8: 110,302,104 (GRCm39) |
C281* |
probably null |
Het |
Ighg1 |
T |
C |
12: 113,290,178 (GRCm39) |
|
probably benign |
Het |
Ints7 |
A |
G |
1: 191,351,747 (GRCm39) |
I819V |
probably benign |
Het |
Jam2 |
G |
A |
16: 84,609,840 (GRCm39) |
V151M |
probably damaging |
Het |
Jmjd1c |
A |
G |
10: 67,060,718 (GRCm39) |
I737V |
possibly damaging |
Het |
Krt74 |
C |
T |
15: 101,669,876 (GRCm39) |
|
noncoding transcript |
Het |
Lnpep |
T |
C |
17: 17,791,920 (GRCm39) |
Y407C |
probably damaging |
Het |
Lrp4 |
T |
G |
2: 91,341,912 (GRCm39) |
C1842G |
probably damaging |
Het |
Mug2 |
T |
A |
6: 122,056,572 (GRCm39) |
N1172K |
probably benign |
Het |
Npy6r |
A |
T |
18: 44,408,791 (GRCm39) |
T71S |
probably damaging |
Het |
Nsd3 |
A |
T |
8: 26,163,382 (GRCm39) |
I591F |
probably damaging |
Het |
Oog2 |
A |
C |
4: 143,921,715 (GRCm39) |
E208D |
possibly damaging |
Het |
Otogl |
A |
G |
10: 107,615,121 (GRCm39) |
I1928T |
probably benign |
Het |
Papss1 |
T |
C |
3: 131,324,860 (GRCm39) |
L418P |
probably damaging |
Het |
Pcdhb13 |
T |
A |
18: 37,576,571 (GRCm39) |
D316E |
probably benign |
Het |
Pcdhgb2 |
T |
A |
18: 37,824,737 (GRCm39) |
|
probably null |
Het |
Ralgps1 |
T |
C |
2: 33,226,599 (GRCm39) |
S31G |
probably benign |
Het |
Rnf225 |
A |
T |
7: 12,661,857 (GRCm39) |
H12L |
probably benign |
Het |
Ryr3 |
T |
A |
2: 112,633,613 (GRCm39) |
M2047L |
probably damaging |
Het |
Secisbp2l |
C |
T |
2: 125,582,657 (GRCm39) |
G933D |
possibly damaging |
Het |
Serpinb3b |
G |
T |
1: 107,082,200 (GRCm39) |
Q355K |
probably benign |
Het |
Slc8a2 |
T |
A |
7: 15,868,233 (GRCm39) |
F155Y |
probably damaging |
Het |
Taf1c |
A |
G |
8: 120,330,134 (GRCm39) |
|
probably benign |
Het |
Tln2 |
A |
G |
9: 67,293,837 (GRCm39) |
|
probably null |
Het |
Tmpo |
A |
G |
10: 90,998,506 (GRCm39) |
V427A |
probably benign |
Het |
Vmn1r17 |
A |
T |
6: 57,338,337 (GRCm39) |
Y9* |
probably null |
Het |
Vmn2r63 |
C |
T |
7: 42,577,544 (GRCm39) |
M331I |
probably benign |
Het |
Zdhhc1 |
CGGGGG |
CGGGGGG |
8: 106,210,376 (GRCm39) |
|
probably null |
Het |
Zfand5 |
C |
T |
19: 21,253,845 (GRCm39) |
T16I |
probably damaging |
Het |
Zfp352 |
A |
T |
4: 90,113,177 (GRCm39) |
K439M |
possibly damaging |
Het |
Zfp786 |
G |
A |
6: 47,797,625 (GRCm39) |
H438Y |
probably damaging |
Het |
Zfp808 |
T |
A |
13: 62,319,763 (GRCm39) |
C331S |
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 |
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'- AAATGGCTAAATCTGCTGTGGAAG -3'
(R):5'- GCAAACCATGTGTGTCTGTGG -3'
Sequencing Primer
(F):5'- CTGCTGTGGAAGTATGATTTAATTTG -3'
(R):5'- GAAATCAGTACCATACTCAGAAGTG -3'
|
Posted On |
2015-11-11 |