Incidental Mutation 'R5081:Gpcpd1'
| ID |
387111 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Gpcpd1
|
| Ensembl Gene |
ENSMUSG00000027346 |
| Gene Name |
glycerophosphocholine phosphodiesterase 1 |
| Synonyms |
Prei4, 2310004G06Rik, 2310032D16Rik |
| MMRRC Submission |
042670-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.936)
|
| Stock # |
R5081 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
132371002-132420173 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 132389622 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Glutamine
at position 244
(H244Q)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000105769
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028822]
[ENSMUST00000060955]
[ENSMUST00000110136]
[ENSMUST00000110142]
[ENSMUST00000124107]
[ENSMUST00000145694]
[ENSMUST00000148833]
[ENSMUST00000149854]
|
| AlphaFold |
Q8C0L9 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000028822
AA Change: H60Q
PolyPhen 2
Score 0.170 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000028822
Gene: ENSMUSG00000027346
AA Change: H60Q
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GDPD
|
142 |
432 |
1.3e-61 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000060955
AA Change: H244Q
PolyPhen 2
Score 0.170 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000062221
Gene: ENSMUSG00000027346
AA Change: H244Q
| Domain | Start | End | E-Value | Type |
|---|
|
CBM_2
|
3 |
110 |
3.78e-29 |
SMART |
|
low complexity region
|
142 |
160 |
N/A |
INTRINSIC |
|
low complexity region
|
167 |
175 |
N/A |
INTRINSIC |
|
Pfam:GDPD
|
326 |
615 |
5.3e-61 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000110136
AA Change: H60Q
PolyPhen 2
Score 0.170 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000105763
Gene: ENSMUSG00000027346
AA Change: H60Q
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GDPD
|
142 |
431 |
4.1e-59 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000110142
AA Change: H244Q
PolyPhen 2
Score 0.170 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000105769
Gene: ENSMUSG00000027346
AA Change: H244Q
| Domain | Start | End | E-Value | Type |
|---|
|
CBM_2
|
3 |
110 |
3.78e-29 |
SMART |
|
low complexity region
|
142 |
160 |
N/A |
INTRINSIC |
|
low complexity region
|
167 |
175 |
N/A |
INTRINSIC |
|
Pfam:GDPD
|
326 |
615 |
6.1e-63 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000124107
|
| SMART Domains |
Protein: ENSMUSP00000122751
Gene: ENSMUSG00000027346
| Domain | Start | End | E-Value | Type |
|---|
|
CBM_2
|
3 |
110 |
3.78e-29 |
SMART |
|
low complexity region
|
142 |
160 |
N/A |
INTRINSIC |
|
low complexity region
|
167 |
175 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000145694
|
| SMART Domains |
Protein: ENSMUSP00000116457
Gene: ENSMUSG00000027346
| Domain | Start | End | E-Value | Type |
|---|
|
CBM_2
|
3 |
110 |
3.78e-29 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000148833
|
| SMART Domains |
Protein: ENSMUSP00000116156
Gene: ENSMUSG00000027346
| Domain | Start | End | E-Value | Type |
|---|
|
CBM_2
|
3 |
99 |
1.02e-11 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000149854
|
| SMART Domains |
Protein: ENSMUSP00000116949
Gene: ENSMUSG00000027346
| Domain | Start | End | E-Value | Type |
|---|
|
CBM_2
|
3 |
94 |
5.54e-13 |
SMART |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.4%
- 10x: 96.5%
- 20x: 93.2%
|
| Validation Efficiency |
93% (65/70) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Agbl5 |
G |
A |
5: 31,060,403 (GRCm39) |
R141Q |
probably damaging |
Het |
| AI593442 |
TGAGGAGGAGGAGGAGGA |
TGAGGAGGAGGAGGA |
9: 52,589,114 (GRCm39) |
|
probably benign |
Het |
| Aig1 |
A |
G |
10: 13,677,644 (GRCm39) |
I116T |
probably benign |
Het |
| Alox12 |
A |
T |
11: 70,146,140 (GRCm39) |
|
probably null |
Het |
| Ap3s1 |
T |
A |
18: 46,887,497 (GRCm39) |
D43E |
probably benign |
Het |
| Arhgap35 |
A |
G |
7: 16,299,059 (GRCm39) |
M2T |
possibly damaging |
Het |
| Asah2 |
T |
A |
19: 31,991,708 (GRCm39) |
E451V |
probably benign |
Het |
| Ash1l |
T |
G |
3: 88,892,024 (GRCm39) |
I1301S |
probably damaging |
Het |
| Ass1 |
G |
A |
2: 31,378,665 (GRCm39) |
|
probably null |
Het |
| Ccpg1 |
A |
G |
9: 72,906,360 (GRCm39) |
T39A |
possibly damaging |
Het |
| Cd101 |
T |
A |
3: 100,911,021 (GRCm39) |
Y879F |
possibly damaging |
Het |
| Cdc23 |
C |
A |
18: 34,784,742 (GRCm39) |
V7L |
unknown |
Het |
| Cdh23 |
T |
C |
10: 60,272,586 (GRCm39) |
T530A |
possibly damaging |
Het |
| Cep68 |
G |
T |
11: 20,188,477 (GRCm39) |
Q643K |
probably damaging |
Het |
| Ces1c |
A |
G |
8: 93,854,197 (GRCm39) |
S113P |
probably damaging |
Het |
| Cnga4 |
T |
C |
7: 105,056,232 (GRCm39) |
I278T |
probably benign |
Het |
| Col1a1 |
A |
G |
11: 94,842,402 (GRCm39) |
D1440G |
unknown |
Het |
| Cspp1 |
A |
G |
1: 10,117,691 (GRCm39) |
I48V |
possibly damaging |
Het |
| Ctsj |
T |
A |
13: 61,151,664 (GRCm39) |
S85C |
possibly damaging |
Het |
| Cyp39a1 |
C |
A |
17: 44,057,488 (GRCm39) |
D442E |
probably damaging |
Het |
| Dock3 |
A |
T |
9: 106,868,292 (GRCm39) |
F664Y |
probably damaging |
Het |
| Gtf3a |
T |
A |
5: 146,888,092 (GRCm39) |
V131E |
probably benign |
Het |
| Gtpbp3 |
A |
T |
8: 71,943,026 (GRCm39) |
R147W |
probably damaging |
Het |
| H2-Oa |
A |
T |
17: 34,313,344 (GRCm39) |
I132F |
probably damaging |
Het |
| Hsd17b8 |
G |
A |
17: 34,246,552 (GRCm39) |
|
probably benign |
Het |
| Idi1 |
T |
A |
13: 8,937,963 (GRCm39) |
C91* |
probably null |
Het |
| Itga11 |
A |
G |
9: 62,662,478 (GRCm39) |
I484V |
probably benign |
Het |
| Kpna3 |
C |
T |
14: 61,628,694 (GRCm39) |
S101N |
probably damaging |
Het |
| Larp4 |
G |
A |
15: 99,870,898 (GRCm39) |
|
probably benign |
Het |
| Mink1 |
T |
C |
11: 70,495,970 (GRCm39) |
L390P |
probably damaging |
Het |
| Morc1 |
T |
G |
16: 48,322,715 (GRCm39) |
S337R |
probably benign |
Het |
| Myo10 |
A |
G |
15: 25,786,026 (GRCm39) |
R1236G |
probably damaging |
Het |
| Nkx3-1 |
T |
C |
14: 69,429,396 (GRCm39) |
I138T |
possibly damaging |
Het |
| Nnt |
T |
C |
13: 119,502,936 (GRCm39) |
N489S |
probably damaging |
Het |
| Nrcam |
A |
T |
12: 44,617,136 (GRCm39) |
I711F |
probably benign |
Het |
| Ntrk3 |
A |
G |
7: 78,227,522 (GRCm39) |
S4P |
probably damaging |
Het |
| Obsl1 |
T |
C |
1: 75,464,607 (GRCm39) |
T1605A |
possibly damaging |
Het |
| Or1j17 |
A |
G |
2: 36,578,655 (GRCm39) |
I214V |
possibly damaging |
Het |
| Or7g32 |
A |
G |
9: 19,408,557 (GRCm39) |
E171G |
probably benign |
Het |
| Pank1 |
T |
C |
19: 34,856,316 (GRCm39) |
H54R |
probably benign |
Het |
| Pgm2l1 |
A |
G |
7: 99,917,472 (GRCm39) |
I530V |
probably benign |
Het |
| Psmd2 |
A |
G |
16: 20,480,405 (GRCm39) |
T709A |
probably benign |
Het |
| Qsox1 |
G |
T |
1: 155,688,581 (GRCm39) |
|
probably benign |
Het |
| Rbm14 |
A |
G |
19: 4,852,823 (GRCm39) |
S520P |
probably benign |
Het |
| Rbm15b |
G |
A |
9: 106,762,120 (GRCm39) |
R683C |
probably benign |
Het |
| Rhbdd2 |
T |
A |
5: 135,664,876 (GRCm39) |
V69D |
probably damaging |
Het |
| Sart1 |
T |
C |
19: 5,438,576 (GRCm39) |
E27G |
possibly damaging |
Het |
| Scn4a |
G |
A |
11: 106,239,553 (GRCm39) |
P153L |
probably damaging |
Het |
| Serpinb6d |
A |
T |
13: 33,855,230 (GRCm39) |
R301S |
probably benign |
Het |
| Sf3a2 |
C |
A |
10: 80,640,275 (GRCm39) |
|
probably benign |
Het |
| Syne1 |
T |
C |
10: 4,997,767 (GRCm39) |
D400G |
probably benign |
Het |
| Tenm2 |
T |
C |
11: 35,915,460 (GRCm39) |
S2025G |
possibly damaging |
Het |
| Ttc16 |
A |
T |
2: 32,657,988 (GRCm39) |
D476E |
probably damaging |
Het |
| Ttc9c |
A |
T |
19: 8,793,396 (GRCm39) |
C81* |
probably null |
Het |
| Ulk2 |
G |
A |
11: 61,694,488 (GRCm39) |
P474L |
probably damaging |
Het |
| Vmn1r66 |
A |
G |
7: 10,008,722 (GRCm39) |
C104R |
probably damaging |
Het |
| Vwa2 |
C |
T |
19: 56,897,752 (GRCm39) |
H686Y |
probably damaging |
Het |
|
| Other mutations in Gpcpd1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00542:Gpcpd1
|
APN |
2 |
132,398,903 (GRCm39) |
splice site |
probably null |
|
|
IGL00672:Gpcpd1
|
APN |
2 |
132,372,468 (GRCm39) |
utr 3 prime |
probably benign |
|
|
IGL00676:Gpcpd1
|
APN |
2 |
132,395,931 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL00832:Gpcpd1
|
APN |
2 |
132,388,770 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL00931:Gpcpd1
|
APN |
2 |
132,380,038 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01309:Gpcpd1
|
APN |
2 |
132,392,244 (GRCm39) |
missense |
probably damaging |
0.97 |
|
IGL01960:Gpcpd1
|
APN |
2 |
132,381,818 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL02110:Gpcpd1
|
APN |
2 |
132,372,530 (GRCm39) |
nonsense |
probably null |
|
|
IGL02267:Gpcpd1
|
APN |
2 |
132,410,630 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02570:Gpcpd1
|
APN |
2 |
132,389,605 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL02588:Gpcpd1
|
APN |
2 |
132,376,673 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03306:Gpcpd1
|
APN |
2 |
132,375,993 (GRCm39) |
critical splice donor site |
probably null |
|
|
Baependi
|
UTSW |
2 |
132,386,355 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0413:Gpcpd1
|
UTSW |
2 |
132,406,543 (GRCm39) |
splice site |
probably benign |
|
|
R1876:Gpcpd1
|
UTSW |
2 |
132,376,673 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4276:Gpcpd1
|
UTSW |
2 |
132,382,207 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4571:Gpcpd1
|
UTSW |
2 |
132,392,270 (GRCm39) |
missense |
probably benign |
0.05 |
|
R4849:Gpcpd1
|
UTSW |
2 |
132,376,019 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4930:Gpcpd1
|
UTSW |
2 |
132,388,794 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5060:Gpcpd1
|
UTSW |
2 |
132,386,355 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5148:Gpcpd1
|
UTSW |
2 |
132,376,110 (GRCm39) |
nonsense |
probably null |
|
|
R5189:Gpcpd1
|
UTSW |
2 |
132,395,892 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5344:Gpcpd1
|
UTSW |
2 |
132,400,597 (GRCm39) |
intron |
probably benign |
|
|
R5623:Gpcpd1
|
UTSW |
2 |
132,376,637 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6086:Gpcpd1
|
UTSW |
2 |
132,380,034 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6787:Gpcpd1
|
UTSW |
2 |
132,379,758 (GRCm39) |
intron |
probably benign |
|
|
R6885:Gpcpd1
|
UTSW |
2 |
132,395,994 (GRCm39) |
missense |
possibly damaging |
0.56 |
|
R7223:Gpcpd1
|
UTSW |
2 |
132,375,976 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7261:Gpcpd1
|
UTSW |
2 |
132,410,619 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R7900:Gpcpd1
|
UTSW |
2 |
132,376,659 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8120:Gpcpd1
|
UTSW |
2 |
132,395,943 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8494:Gpcpd1
|
UTSW |
2 |
132,386,355 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R9594:Gpcpd1
|
UTSW |
2 |
132,388,848 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
X0018:Gpcpd1
|
UTSW |
2 |
132,376,689 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0060:Gpcpd1
|
UTSW |
2 |
132,376,701 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0066:Gpcpd1
|
UTSW |
2 |
132,386,315 (GRCm39) |
missense |
probably benign |
0.33 |
|
| Predicted Primers |
PCR Primer
(F):5'- TAAGGGCCTAGCTGCTTCTC -3'
(R):5'- CCAAGTTCACTTTGAAGGTTTTAGG -3'
Sequencing Primer
(F):5'- AGCTGCTTCTCCCCAACTTAC -3'
(R):5'- GTCCTCTGACCTCTACATAC -3'
|
| Posted On |
2016-06-06 |
Incidental Mutation