Incidental Mutation 'R1646:Ptcd3'
| ID |
173874 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ptcd3
|
| Ensembl Gene |
ENSMUSG00000063884 |
| Gene Name |
pentatricopeptide repeat domain 3 |
| Synonyms |
2610034F17Rik, 2810422B04Rik |
| MMRRC Submission |
039682-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1646 (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 71875379 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 201
(D201G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000080743
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000082094]
[ENSMUST00000206879]
|
| AlphaFold |
Q14C51 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000082094
AA Change: D201G
PolyPhen 2
Score 0.260 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000080743
Gene: ENSMUSG00000063884
AA Change: D201G
| 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 |
probably benign
Transcript: ENSMUST00000205556
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000205761
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000206284
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000206631
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000206879
AA Change: D201G
PolyPhen 2
Score 0.047 (Sensitivity: 0.94; Specificity: 0.83)
|
| Meta Mutation Damage Score |
0.1465 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.1%
- 20x: 91.8%
|
| Validation Efficiency |
96% (69/72) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 68 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Akna |
T |
G |
4: 63,302,129 (GRCm39) |
I581L |
probably benign |
Het |
| Cacnb4 |
A |
G |
2: 52,364,912 (GRCm39) |
I117T |
possibly damaging |
Het |
| Capn1 |
A |
T |
19: 6,047,760 (GRCm39) |
F434L |
probably benign |
Het |
| Cbs |
T |
C |
17: 31,832,169 (GRCm39) |
T547A |
probably benign |
Het |
| Col6a5 |
A |
T |
9: 105,739,948 (GRCm39) |
L2557* |
probably null |
Het |
| Dach1 |
A |
G |
14: 98,406,550 (GRCm39) |
S66P |
unknown |
Het |
| Ddx31 |
T |
C |
2: 28,782,532 (GRCm39) |
V625A |
probably benign |
Het |
| Dmxl1 |
T |
G |
18: 50,095,328 (GRCm39) |
V2969G |
probably damaging |
Het |
| Eapp |
T |
A |
12: 54,732,745 (GRCm39) |
K122* |
probably null |
Het |
| Elapor1 |
A |
T |
3: 108,370,306 (GRCm39) |
S751T |
probably damaging |
Het |
| Epb41l5 |
G |
T |
1: 119,477,752 (GRCm39) |
|
probably benign |
Het |
| Fat1 |
T |
C |
8: 45,471,079 (GRCm39) |
S1628P |
probably damaging |
Het |
| Fgfr2 |
T |
A |
7: 129,844,374 (GRCm39) |
E37V |
probably damaging |
Het |
| Fgfr4 |
A |
T |
13: 55,313,777 (GRCm39) |
N529Y |
probably damaging |
Het |
| Fsip2 |
A |
T |
2: 82,808,861 (GRCm39) |
T1727S |
probably benign |
Het |
| Gak |
A |
T |
5: 108,750,720 (GRCm39) |
S397T |
probably damaging |
Het |
| Gm6040 |
T |
A |
8: 21,407,113 (GRCm39) |
I36F |
possibly damaging |
Het |
| Grhl1 |
A |
G |
12: 24,661,860 (GRCm39) |
D513G |
possibly damaging |
Het |
| Gstt1 |
T |
A |
10: 75,619,940 (GRCm39) |
D219V |
possibly damaging |
Het |
| Hcfc2 |
T |
G |
10: 82,536,861 (GRCm39) |
V91G |
probably damaging |
Het |
| Hells |
A |
T |
19: 38,956,227 (GRCm39) |
I808L |
probably benign |
Het |
| Icmt |
T |
A |
4: 152,384,172 (GRCm39) |
V110E |
possibly damaging |
Het |
| Ilrun |
A |
G |
17: 28,012,934 (GRCm39) |
S88P |
probably damaging |
Het |
| Iqca1 |
C |
T |
1: 90,067,760 (GRCm39) |
V164M |
probably damaging |
Het |
| Klri1 |
G |
A |
6: 129,680,299 (GRCm39) |
P119S |
probably benign |
Het |
| Krt71 |
C |
A |
15: 101,647,199 (GRCm39) |
|
probably null |
Het |
| Lpin1 |
A |
G |
12: 16,623,659 (GRCm39) |
|
probably null |
Het |
| Macir |
A |
T |
1: 97,573,531 (GRCm39) |
I178N |
probably damaging |
Het |
| Metap2 |
T |
C |
10: 93,706,059 (GRCm39) |
H241R |
probably damaging |
Het |
| Myh15 |
A |
G |
16: 49,015,931 (GRCm39) |
Y1869C |
probably damaging |
Het |
| Myo1h |
G |
A |
5: 114,455,693 (GRCm39) |
G59E |
possibly damaging |
Het |
| Ncam2 |
T |
G |
16: 81,262,594 (GRCm39) |
|
probably benign |
Het |
| Npat |
T |
C |
9: 53,466,434 (GRCm39) |
V241A |
probably benign |
Het |
| Npbwr1 |
C |
A |
1: 5,987,473 (GRCm39) |
V14L |
probably benign |
Het |
| Nup37 |
T |
A |
10: 88,014,096 (GRCm39) |
V323E |
possibly damaging |
Het |
| Or11g27 |
A |
T |
14: 50,771,040 (GRCm39) |
Q57L |
probably benign |
Het |
| Or5m9b |
A |
G |
2: 85,905,960 (GRCm39) |
N292S |
probably damaging |
Het |
| Or5p59 |
C |
T |
7: 107,702,798 (GRCm39) |
T94I |
probably benign |
Het |
| Or7a35 |
C |
A |
10: 78,853,340 (GRCm39) |
Y61* |
probably null |
Het |
| Pdlim4 |
A |
T |
11: 53,947,080 (GRCm39) |
L132Q |
possibly damaging |
Het |
| Ptk7 |
A |
T |
17: 46,897,223 (GRCm39) |
F370I |
probably benign |
Het |
| Pus7l |
T |
C |
15: 94,431,517 (GRCm39) |
N371D |
probably benign |
Het |
| Pzp |
G |
A |
6: 128,480,518 (GRCm39) |
A589V |
probably benign |
Het |
| Rasef |
T |
A |
4: 73,652,786 (GRCm39) |
R572W |
probably damaging |
Het |
| Reep5 |
T |
C |
18: 34,482,712 (GRCm39) |
T166A |
probably benign |
Het |
| Rhov |
A |
G |
2: 119,101,501 (GRCm39) |
V35A |
probably damaging |
Het |
| Ripk4 |
C |
T |
16: 97,545,097 (GRCm39) |
G517R |
probably damaging |
Het |
| Rnasel |
A |
G |
1: 153,630,800 (GRCm39) |
T439A |
probably damaging |
Het |
| Slamf9 |
A |
G |
1: 172,304,907 (GRCm39) |
T174A |
probably benign |
Het |
| Slc12a9 |
A |
G |
5: 137,321,411 (GRCm39) |
L414P |
probably damaging |
Het |
| Slf1 |
G |
A |
13: 77,214,767 (GRCm39) |
R640* |
probably null |
Het |
| Slfn8 |
G |
T |
11: 82,907,712 (GRCm39) |
P277Q |
probably damaging |
Het |
| Stpg2 |
T |
A |
3: 139,125,463 (GRCm39) |
|
probably benign |
Het |
| Tm9sf3 |
A |
C |
19: 41,211,618 (GRCm39) |
N408K |
possibly damaging |
Het |
| Trio |
A |
G |
15: 27,758,433 (GRCm39) |
V2049A |
possibly damaging |
Het |
| Ttn |
A |
T |
2: 76,645,077 (GRCm39) |
I11180N |
probably damaging |
Het |
| Ush2a |
T |
C |
1: 188,148,018 (GRCm39) |
C982R |
probably damaging |
Het |
| Usp36 |
C |
T |
11: 118,164,392 (GRCm39) |
V207M |
probably damaging |
Het |
| Uvrag |
T |
C |
7: 98,767,431 (GRCm39) |
T67A |
probably damaging |
Het |
| Vasp |
G |
A |
7: 18,994,903 (GRCm39) |
|
probably benign |
Het |
| Vmn2r115 |
T |
C |
17: 23,578,513 (GRCm39) |
F662S |
probably damaging |
Het |
| Vmn2r54 |
A |
T |
7: 12,366,434 (GRCm39) |
C167S |
probably damaging |
Het |
| Vmn2r71 |
C |
A |
7: 85,270,476 (GRCm39) |
N547K |
probably damaging |
Het |
| Wasf2 |
A |
G |
4: 132,903,902 (GRCm39) |
I37V |
probably benign |
Het |
| Wwc2 |
T |
C |
8: 48,295,937 (GRCm39) |
E1111G |
unknown |
Het |
| Zfp317 |
A |
G |
9: 19,558,608 (GRCm39) |
Y274C |
probably damaging |
Het |
| Zhx3 |
T |
C |
2: 160,623,195 (GRCm39) |
Y324C |
probably damaging |
Het |
| Zzef1 |
T |
C |
11: 72,754,862 (GRCm39) |
|
probably null |
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 |
|
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 |
|
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'- CACAGTTTCACAATTCGGTCCTTGC -3'
(R):5'- ACATGGTAGTGGAAATAAGCCACCATC -3'
Sequencing Primer
(F):5'- CTGGAAAACAAGTTCATGTGTCCC -3'
(R):5'- TAGTGGAAATAAGCCACCATCAATAG -3'
|
| Posted On |
2014-04-24 |
Incidental Mutation