Incidental Mutation 'R6281:Ptcd1'
| ID |
507953 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ptcd1
|
| Ensembl Gene |
ENSMUSG00000029624 |
| Gene Name |
pentatricopeptide repeat domain 1 |
| Synonyms |
1110069M14Rik |
| MMRRC Submission |
044451-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.114)
|
| Stock # |
R6281 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
145084324-145103918 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 145101881 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Arginine
at position 146
(K146R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000031628
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000031628]
[ENSMUST00000070487]
[ENSMUST00000160422]
[ENSMUST00000160574]
[ENSMUST00000160629]
[ENSMUST00000161390]
[ENSMUST00000162244]
|
| AlphaFold |
Q8C2E4 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000031628
AA Change: K146R
PolyPhen 2
Score 0.098 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000031628
Gene: ENSMUSG00000029624
AA Change: K146R
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
48 |
58 |
N/A |
INTRINSIC |
|
low complexity region
|
64 |
74 |
N/A |
INTRINSIC |
|
low complexity region
|
110 |
123 |
N/A |
INTRINSIC |
|
Pfam:PPR_2
|
169 |
218 |
1.2e-16 |
PFAM |
|
Pfam:PPR
|
172 |
202 |
1.1e-9 |
PFAM |
|
Pfam:PPR_3
|
173 |
204 |
2.5e-5 |
PFAM |
|
Pfam:PPR_3
|
245 |
278 |
3.2e-5 |
PFAM |
|
Pfam:PPR
|
246 |
276 |
6.5e-4 |
PFAM |
|
internal_repeat_1
|
437 |
595 |
1.57e-9 |
PROSPERO |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000070487
|
| SMART Domains |
Protein: ENSMUSP00000069243
Gene: ENSMUSG00000029625
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_C3H1
|
35 |
61 |
1.7e-5 |
SMART |
|
ZnF_C3H1
|
62 |
88 |
1.4e-10 |
SMART |
|
ZnF_C3H1
|
90 |
110 |
3.7e-1 |
SMART |
|
ZnF_C3H1
|
111 |
136 |
3.4e-9 |
SMART |
|
low complexity region
|
143 |
157 |
N/A |
INTRINSIC |
|
ZnF_C2HC
|
186 |
202 |
4.5e-6 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160422
|
| SMART Domains |
Protein: ENSMUSP00000125019
Gene: ENSMUSG00000029625
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_C3H1
|
35 |
61 |
4.17e-3 |
SMART |
|
ZnF_C3H1
|
62 |
88 |
3.41e-8 |
SMART |
|
ZnF_C3H1
|
90 |
116 |
6.42e-4 |
SMART |
|
ZnF_C3H1
|
118 |
142 |
2.86e-1 |
SMART |
|
ZnF_C3H1
|
143 |
168 |
8.27e-7 |
SMART |
|
low complexity region
|
175 |
191 |
N/A |
INTRINSIC |
|
ZnF_C2HC
|
244 |
260 |
1.04e-3 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160574
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160629
|
| SMART Domains |
Protein: ENSMUSP00000124899
Gene: ENSMUSG00000029625
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_C3H1
|
35 |
61 |
4.17e-3 |
SMART |
|
ZnF_C3H1
|
62 |
88 |
3.41e-8 |
SMART |
|
ZnF_C3H1
|
90 |
116 |
6.42e-4 |
SMART |
|
ZnF_C3H1
|
118 |
142 |
2.86e-1 |
SMART |
|
ZnF_C3H1
|
143 |
168 |
8.27e-7 |
SMART |
|
low complexity region
|
175 |
189 |
N/A |
INTRINSIC |
|
ZnF_C2HC
|
218 |
234 |
1.04e-3 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160762
|
| SMART Domains |
Protein: ENSMUSP00000125640
Gene: ENSMUSG00000029625
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_C3H1
|
3 |
29 |
4.17e-3 |
SMART |
|
ZnF_C3H1
|
30 |
56 |
3.41e-8 |
SMART |
|
ZnF_C3H1
|
58 |
84 |
6.42e-4 |
SMART |
|
ZnF_C3H1
|
86 |
110 |
2.86e-1 |
SMART |
|
ZnF_C3H1
|
111 |
136 |
8.27e-7 |
SMART |
|
low complexity region
|
143 |
157 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000161390
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000162244
|
| SMART Domains |
Protein: ENSMUSP00000124966
Gene: ENSMUSG00000029625
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_C3H1
|
35 |
61 |
4.17e-3 |
SMART |
|
ZnF_C3H1
|
62 |
88 |
3.41e-8 |
SMART |
|
ZnF_C3H1
|
90 |
116 |
6.42e-4 |
SMART |
|
ZnF_C3H1
|
118 |
142 |
2.86e-1 |
SMART |
|
ZnF_C3H1
|
143 |
168 |
8.27e-7 |
SMART |
|
low complexity region
|
175 |
195 |
N/A |
INTRINSIC |
|
ZnF_C2HC
|
219 |
235 |
1.04e-3 |
SMART |
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.5%
- 20x: 95.9%
|
| Validation Efficiency |
100% (40/40) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This locus represents naturally occurring read-through transcription between the ATP5J2 (ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2) and PTCD1 (pentatricopeptide repeat domain 1) genes on chromosome 7. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]
PHENOTYPE: Knockout affects mitochondrial protein synthesis and RNA metabolism. Homozygous KO is embryonic lethal. Heterozygous KO causes adult onset obesity, liver fibrosis and cardiac hypertrophy. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700018B08Rik |
C |
A |
8: 122,258,620 (GRCm39) |
C166F |
probably damaging |
Het |
| Aida |
C |
T |
1: 183,103,145 (GRCm39) |
A237V |
probably damaging |
Het |
| Ankib1 |
T |
C |
5: 3,751,965 (GRCm39) |
T692A |
possibly damaging |
Het |
| As3mt |
T |
C |
19: 46,713,362 (GRCm39) |
V303A |
possibly damaging |
Het |
| Bhlhe40 |
T |
A |
6: 108,641,423 (GRCm39) |
|
probably null |
Het |
| Bhmt2 |
G |
A |
13: 93,799,668 (GRCm39) |
P256L |
probably damaging |
Het |
| Bpifb1 |
T |
C |
2: 154,048,385 (GRCm39) |
I140T |
probably damaging |
Het |
| Cat |
A |
T |
2: 103,302,114 (GRCm39) |
H194Q |
probably damaging |
Het |
| Cbfa2t3 |
C |
A |
8: 123,360,148 (GRCm39) |
R466L |
probably damaging |
Het |
| Fancm |
T |
C |
12: 65,135,044 (GRCm39) |
V279A |
probably damaging |
Het |
| Gabra2 |
T |
C |
5: 71,192,105 (GRCm39) |
T75A |
probably damaging |
Het |
| Gm11595 |
G |
A |
11: 99,663,381 (GRCm39) |
R100C |
unknown |
Het |
| Gm3512 |
T |
A |
14: 7,159,254 (GRCm38) |
D7V |
possibly damaging |
Het |
| Gpr15 |
A |
G |
16: 58,538,957 (GRCm39) |
F44S |
probably damaging |
Het |
| Ighv1-72 |
C |
A |
12: 115,722,023 (GRCm39) |
C5F |
probably benign |
Het |
| Lilra6 |
A |
G |
7: 3,914,972 (GRCm39) |
L474P |
probably damaging |
Het |
| Mboat2 |
T |
C |
12: 25,007,678 (GRCm39) |
V297A |
probably benign |
Het |
| Muc2 |
C |
G |
7: 141,306,140 (GRCm39) |
C276W |
probably damaging |
Het |
| Ncor1 |
T |
C |
11: 62,264,371 (GRCm39) |
S141G |
possibly damaging |
Het |
| Or4k77 |
T |
C |
2: 111,199,894 (GRCm39) |
*306R |
probably null |
Het |
| Or5p80 |
T |
G |
7: 108,229,609 (GRCm39) |
S137A |
probably benign |
Het |
| Pax5 |
T |
G |
4: 44,691,955 (GRCm39) |
E97A |
probably benign |
Het |
| Pcdhga11 |
A |
T |
18: 37,890,426 (GRCm39) |
D478V |
probably damaging |
Het |
| Peg10 |
GAT |
GATCAT |
6: 4,756,449 (GRCm39) |
|
probably benign |
Het |
| Phf21b |
G |
T |
15: 84,738,946 (GRCm39) |
D38E |
probably benign |
Het |
| Rad23a |
A |
T |
8: 85,564,739 (GRCm39) |
M166K |
probably damaging |
Het |
| Rfc4 |
A |
T |
16: 22,936,816 (GRCm39) |
|
probably null |
Het |
| Slc17a3 |
T |
A |
13: 24,040,782 (GRCm39) |
I336N |
probably benign |
Het |
| Slc2a12 |
T |
A |
10: 22,541,219 (GRCm39) |
M358K |
probably damaging |
Het |
| Stk31 |
T |
G |
6: 49,446,114 (GRCm39) |
M939R |
possibly damaging |
Het |
| Tecrl |
T |
A |
5: 83,442,453 (GRCm39) |
T167S |
probably damaging |
Het |
| Tfap2d |
G |
C |
1: 19,174,702 (GRCm39) |
G52R |
probably benign |
Het |
| Ttn |
C |
T |
2: 76,772,172 (GRCm39) |
V2577M |
probably damaging |
Het |
| Uox |
C |
T |
3: 146,330,332 (GRCm39) |
R163* |
probably null |
Het |
| Vezt |
G |
A |
10: 93,809,808 (GRCm39) |
R578C |
probably benign |
Het |
| Vmn2r111 |
T |
C |
17: 22,778,032 (GRCm39) |
N549S |
possibly damaging |
Het |
| Vwa3b |
T |
A |
1: 37,163,063 (GRCm39) |
L562Q |
probably damaging |
Het |
| Zfyve27 |
T |
A |
19: 42,171,194 (GRCm39) |
N127K |
probably damaging |
Het |
| Znfx1 |
A |
G |
2: 166,897,805 (GRCm39) |
F373S |
probably damaging |
Het |
| Zswim8 |
G |
A |
14: 20,764,708 (GRCm39) |
V693I |
probably benign |
Het |
|
| Other mutations in Ptcd1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00858:Ptcd1
|
APN |
5 |
145,088,092 (GRCm39) |
unclassified |
probably benign |
|
|
IGL00984:Ptcd1
|
APN |
5 |
145,102,239 (GRCm39) |
missense |
probably benign |
|
|
IGL01120:Ptcd1
|
APN |
5 |
145,089,053 (GRCm39) |
unclassified |
probably benign |
|
|
IGL01545:Ptcd1
|
APN |
5 |
145,096,346 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01861:Ptcd1
|
APN |
5 |
145,095,587 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
IGL02543:Ptcd1
|
APN |
5 |
145,091,497 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
IGL02835:Ptcd1
|
UTSW |
5 |
145,091,500 (GRCm39) |
missense |
possibly damaging |
0.78 |
|
PIT4366001:Ptcd1
|
UTSW |
5 |
145,088,145 (GRCm39) |
missense |
probably benign |
0.01 |
|
PIT4494001:Ptcd1
|
UTSW |
5 |
145,092,168 (GRCm39) |
missense |
probably benign |
0.01 |
|
R3001:Ptcd1
|
UTSW |
5 |
145,096,386 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3002:Ptcd1
|
UTSW |
5 |
145,096,386 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4460:Ptcd1
|
UTSW |
5 |
145,096,316 (GRCm39) |
missense |
probably benign |
0.25 |
|
R4587:Ptcd1
|
UTSW |
5 |
145,091,531 (GRCm39) |
missense |
possibly damaging |
0.47 |
|
R4652:Ptcd1
|
UTSW |
5 |
145,091,985 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5059:Ptcd1
|
UTSW |
5 |
145,089,034 (GRCm39) |
missense |
probably benign |
0.07 |
|
R5364:Ptcd1
|
UTSW |
5 |
145,088,241 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5367:Ptcd1
|
UTSW |
5 |
145,084,715 (GRCm39) |
utr 3 prime |
probably benign |
|
|
R5733:Ptcd1
|
UTSW |
5 |
145,091,671 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5800:Ptcd1
|
UTSW |
5 |
145,096,475 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6931:Ptcd1
|
UTSW |
5 |
145,091,885 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7472:Ptcd1
|
UTSW |
5 |
145,091,540 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R7723:Ptcd1
|
UTSW |
5 |
145,091,639 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7731:Ptcd1
|
UTSW |
5 |
145,088,174 (GRCm39) |
missense |
probably benign |
0.07 |
|
R8048:Ptcd1
|
UTSW |
5 |
145,091,887 (GRCm39) |
missense |
probably benign |
|
|
R8090:Ptcd1
|
UTSW |
5 |
145,096,345 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R8774:Ptcd1
|
UTSW |
5 |
145,092,175 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8774-TAIL:Ptcd1
|
UTSW |
5 |
145,092,175 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8952:Ptcd1
|
UTSW |
5 |
145,091,944 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8990:Ptcd1
|
UTSW |
5 |
145,102,047 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9072:Ptcd1
|
UTSW |
5 |
145,091,525 (GRCm39) |
missense |
probably benign |
0.36 |
|
R9073:Ptcd1
|
UTSW |
5 |
145,091,525 (GRCm39) |
missense |
probably benign |
0.36 |
|
R9602:Ptcd1
|
UTSW |
5 |
145,096,448 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9740:Ptcd1
|
UTSW |
5 |
145,096,294 (GRCm39) |
missense |
probably benign |
|
|
Z1177:Ptcd1
|
UTSW |
5 |
145,102,245 (GRCm39) |
missense |
probably benign |
0.04 |
|
| Predicted Primers |
PCR Primer
(F):5'- GCTCCAAGCCATAGCAACTG -3'
(R):5'- TAAGCTCAGCACTGTGGCTC -3'
Sequencing Primer
(F):5'- AACTGTGCTAGCCTATCTGCTCAG -3'
(R):5'- AGCACTGTGGCTCCCCAG -3'
|
| Posted On |
2018-03-15 |
Incidental Mutation