Incidental Mutation 'R6885:Gpcpd1'
| ID |
536767 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Gpcpd1
|
| Ensembl Gene |
ENSMUSG00000027346 |
| Gene Name |
glycerophosphocholine phosphodiesterase 1 |
| Synonyms |
Prei4, 2310004G06Rik, 2310032D16Rik |
| MMRRC Submission |
045031-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.941)
|
| Stock # |
R6885 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
132371002-132420173 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 132395994 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Methionine
at position 94
(L94M)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000116949
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028822]
[ENSMUST00000060955]
[ENSMUST00000110135]
[ENSMUST00000110136]
[ENSMUST00000110142]
[ENSMUST00000124107]
[ENSMUST00000145694]
[ENSMUST00000148833]
[ENSMUST00000149854]
|
| AlphaFold |
Q8C0L9 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000028822
|
| SMART Domains |
Protein: ENSMUSP00000028822
Gene: ENSMUSG00000027346
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GDPD
|
142 |
432 |
1.3e-61 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000060955
AA Change: V119D
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000062221
Gene: ENSMUSG00000027346
AA Change: V119D
| 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: ENSMUST00000110135
AA Change: V119D
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000105762
Gene: ENSMUSG00000027346
AA Change: V119D
| Domain | Start | End | E-Value | Type |
|---|
|
CBM_2
|
3 |
110 |
3.78e-29 |
SMART |
|
low complexity region
|
146 |
155 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000110136
|
| SMART Domains |
Protein: ENSMUSP00000105763
Gene: ENSMUSG00000027346
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GDPD
|
142 |
431 |
4.1e-59 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000110142
AA Change: V119D
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000105769
Gene: ENSMUSG00000027346
AA Change: V119D
| 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
AA Change: V119D
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000122751
Gene: ENSMUSG00000027346
AA Change: V119D
| 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 |
possibly damaging
Transcript: ENSMUST00000149854
AA Change: L94M
PolyPhen 2
Score 0.556 (Sensitivity: 0.88; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000116949
Gene: ENSMUSG00000027346
AA Change: L94M
| Domain | Start | End | E-Value | Type |
|---|
|
CBM_2
|
3 |
94 |
5.54e-13 |
SMART |
|
| Meta Mutation Damage Score |
0.1795 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.5%
- 20x: 98.3%
|
| Validation Efficiency |
98% (58/59) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 62 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca16 |
A |
G |
7: 120,119,332 (GRCm39) |
I1025M |
probably benign |
Het |
| Adamtsl5 |
T |
A |
10: 80,179,465 (GRCm39) |
T164S |
probably benign |
Het |
| Ankar |
C |
T |
1: 72,682,195 (GRCm39) |
A1239T |
unknown |
Het |
| Aox4 |
A |
T |
1: 58,303,537 (GRCm39) |
S1192C |
probably damaging |
Het |
| Atl2 |
T |
C |
17: 80,159,982 (GRCm39) |
D68G |
probably damaging |
Het |
| Btnl4 |
T |
C |
17: 34,691,919 (GRCm39) |
I228V |
probably benign |
Het |
| Catsper4 |
T |
C |
4: 133,942,460 (GRCm39) |
T231A |
probably benign |
Het |
| Ccl12 |
A |
T |
11: 81,993,523 (GRCm39) |
T54S |
probably damaging |
Het |
| Cntn1 |
T |
C |
15: 92,140,980 (GRCm39) |
|
probably null |
Het |
| Cog5 |
T |
A |
12: 31,944,198 (GRCm39) |
D694E |
probably damaging |
Het |
| Crat |
T |
A |
2: 30,305,208 (GRCm39) |
|
probably benign |
Het |
| Crot |
T |
C |
5: 9,023,635 (GRCm39) |
T418A |
probably benign |
Het |
| Cubn |
G |
A |
2: 13,323,089 (GRCm39) |
P2826L |
probably damaging |
Het |
| Dnah17 |
A |
G |
11: 117,981,598 (GRCm39) |
F1698L |
possibly damaging |
Het |
| Dock8 |
T |
A |
19: 25,124,742 (GRCm39) |
D1019E |
possibly damaging |
Het |
| Eps15 |
A |
G |
4: 109,166,361 (GRCm39) |
N85D |
probably damaging |
Het |
| Exoc1 |
T |
C |
5: 76,706,889 (GRCm39) |
S457P |
probably damaging |
Het |
| Ext1 |
G |
A |
15: 52,965,088 (GRCm39) |
T426I |
probably damaging |
Het |
| Fat1 |
T |
C |
8: 45,405,489 (GRCm39) |
S747P |
possibly damaging |
Het |
| Gas7 |
A |
G |
11: 67,574,213 (GRCm39) |
D396G |
probably damaging |
Het |
| Gm5114 |
G |
T |
7: 39,057,580 (GRCm39) |
R680S |
probably benign |
Het |
| Gse1 |
C |
A |
8: 120,956,221 (GRCm39) |
|
probably benign |
Het |
| Hmgb1 |
T |
C |
5: 148,987,471 (GRCm39) |
E26G |
probably benign |
Het |
| Incenp |
C |
T |
19: 9,852,496 (GRCm39) |
R714Q |
unknown |
Het |
| Krt73 |
T |
C |
15: 101,704,833 (GRCm39) |
E351G |
probably damaging |
Het |
| Ksr1 |
A |
G |
11: 78,938,121 (GRCm39) |
|
probably null |
Het |
| Lpin2 |
T |
G |
17: 71,522,145 (GRCm39) |
S60A |
probably damaging |
Het |
| Lrrc71 |
T |
C |
3: 87,649,927 (GRCm39) |
|
probably null |
Het |
| Mafb |
A |
G |
2: 160,207,939 (GRCm39) |
S220P |
possibly damaging |
Het |
| Maml3 |
TCTGCTGCTGCTGCTGCTGCTGCTGTTGCTGCTGCTGCTGCTGTTGCTGCTGCTGC |
TCTGCTGCTGCTGCTGCTGCTGTTGCTGCTGCTGCTGCTGTTGCTGCTGCTGC |
3: 51,605,000 (GRCm39) |
|
|
Het |
| Mcmbp |
T |
C |
7: 128,326,833 (GRCm39) |
|
probably null |
Het |
| Or1e30 |
A |
T |
11: 73,677,926 (GRCm39) |
H54L |
possibly damaging |
Het |
| Or4s2 |
A |
G |
2: 88,473,941 (GRCm39) |
T277A |
probably damaging |
Het |
| Paqr9 |
T |
C |
9: 95,442,096 (GRCm39) |
S29P |
probably benign |
Het |
| Parm1 |
A |
G |
5: 91,742,069 (GRCm39) |
T146A |
possibly damaging |
Het |
| Pgm2 |
T |
A |
5: 64,261,221 (GRCm39) |
F238L |
probably benign |
Het |
| Pigv |
A |
T |
4: 133,392,792 (GRCm39) |
F126Y |
probably damaging |
Het |
| Pitx2 |
T |
C |
3: 129,012,257 (GRCm39) |
M222T |
probably damaging |
Het |
| Plekhg6 |
T |
C |
6: 125,355,693 (GRCm39) |
N37S |
probably benign |
Het |
| Pramel25 |
T |
C |
4: 143,520,103 (GRCm39) |
C116R |
probably damaging |
Het |
| Psme4 |
A |
T |
11: 30,784,307 (GRCm39) |
K961* |
probably null |
Het |
| Rbpj |
T |
C |
5: 53,810,493 (GRCm39) |
W392R |
probably damaging |
Het |
| Reg3a |
T |
A |
6: 78,358,038 (GRCm39) |
|
probably null |
Het |
| Rfc3 |
C |
T |
5: 151,571,749 (GRCm39) |
S85N |
probably benign |
Het |
| Rtn3 |
T |
C |
19: 7,435,696 (GRCm39) |
T80A |
probably benign |
Het |
| Sash1 |
T |
C |
10: 8,659,985 (GRCm39) |
T195A |
probably damaging |
Het |
| Ska1 |
A |
G |
18: 74,339,910 (GRCm39) |
V12A |
probably benign |
Het |
| Slc25a1 |
A |
G |
16: 17,745,294 (GRCm39) |
V80A |
probably benign |
Het |
| Slc26a5 |
A |
T |
5: 22,039,342 (GRCm39) |
V217D |
probably damaging |
Het |
| Slc46a1 |
A |
G |
11: 78,357,805 (GRCm39) |
D286G |
probably benign |
Het |
| Spata2l |
A |
T |
8: 123,962,297 (GRCm39) |
L88Q |
probably damaging |
Het |
| Sptbn1 |
T |
G |
11: 30,088,634 (GRCm39) |
Q876P |
probably benign |
Het |
| Tenm2 |
T |
A |
11: 35,914,407 (GRCm39) |
I2377F |
possibly damaging |
Het |
| Thbs4 |
A |
T |
13: 92,899,377 (GRCm39) |
D539E |
probably damaging |
Het |
| Tmem154 |
T |
A |
3: 84,599,813 (GRCm39) |
C162S |
possibly damaging |
Het |
| Tpcn1 |
T |
C |
5: 120,682,502 (GRCm39) |
E502G |
probably benign |
Het |
| Traf7 |
G |
A |
17: 24,731,266 (GRCm39) |
R257C |
probably benign |
Het |
| Tsc22d2 |
T |
C |
3: 58,323,629 (GRCm39) |
Y174H |
probably damaging |
Het |
| Usp8 |
A |
G |
2: 126,594,230 (GRCm39) |
E802G |
probably damaging |
Het |
| Vmn1r5 |
T |
C |
6: 56,963,042 (GRCm39) |
V239A |
possibly damaging |
Het |
| Vmn2r99 |
T |
A |
17: 19,600,457 (GRCm39) |
S494T |
possibly damaging |
Het |
| Zbtb38 |
A |
G |
9: 96,568,517 (GRCm39) |
F856L |
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 |
|
R5081:Gpcpd1
|
UTSW |
2 |
132,389,622 (GRCm39) |
missense |
probably benign |
0.17 |
|
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 |
|
|
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'- TCCTAGAACCCTATAGATTGAAAGG -3'
(R):5'- CACTTACTTGAGTCATTAAGTAGCTG -3'
Sequencing Primer
(F):5'- ACAATCACATGGTCATACC -3'
(R):5'- GCTTTGTTCTTCTAACTTCAAATGG -3'
|
| Posted On |
2018-10-18 |
Incidental Mutation