Incidental Mutation 'R4276:Gpcpd1'
| ID |
322692 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Gpcpd1
|
| Ensembl Gene |
ENSMUSG00000027346 |
| Gene Name |
glycerophosphocholine phosphodiesterase 1 |
| Synonyms |
Prei4, 2310004G06Rik, 2310032D16Rik |
| MMRRC Submission |
041647-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.936)
|
| Stock # |
R4276 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
132371002-132420173 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 132382207 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Glutamic Acid
at position 412
(K412E)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000105769
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028822]
[ENSMUST00000060955]
[ENSMUST00000110136]
[ENSMUST00000110142]
[ENSMUST00000145694]
[ENSMUST00000148833]
[ENSMUST00000149854]
|
| AlphaFold |
Q8C0L9 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000028822
AA Change: K228E
PolyPhen 2
Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000028822
Gene: ENSMUSG00000027346
AA Change: K228E
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GDPD
|
142 |
432 |
1.3e-61 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000060955
AA Change: K412E
PolyPhen 2
Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000062221
Gene: ENSMUSG00000027346
AA Change: K412E
| 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 damaging
Transcript: ENSMUST00000110136
AA Change: K228E
PolyPhen 2
Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000105763
Gene: ENSMUSG00000027346
AA Change: K228E
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GDPD
|
142 |
431 |
4.1e-59 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000110142
AA Change: K412E
PolyPhen 2
Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000105769
Gene: ENSMUSG00000027346
AA Change: K412E
| 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: ENSMUST00000124632
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000127712
|
| 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 |
0.1913 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.8%
- 10x: 97.6%
- 20x: 95.9%
|
| Validation Efficiency |
98% (46/47) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 41 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acad8 |
C |
A |
9: 26,889,745 (GRCm39) |
Q316H |
probably null |
Het |
| Arl6ip1 |
AAAATAAATAAATAAATAAATAAATA |
AAAATAAATAAATAAATAAATAAATAAATA |
7: 117,721,122 (GRCm39) |
|
probably benign |
Het |
| Brix1 |
T |
C |
15: 10,481,833 (GRCm39) |
D101G |
possibly damaging |
Het |
| Cfap36 |
A |
G |
11: 29,180,584 (GRCm39) |
|
probably null |
Het |
| Chrnb3 |
A |
G |
8: 27,883,779 (GRCm39) |
N172S |
probably damaging |
Het |
| Csnk1e |
T |
C |
15: 79,313,967 (GRCm39) |
N37S |
probably damaging |
Het |
| Ern1 |
T |
C |
11: 106,298,007 (GRCm39) |
I705V |
probably benign |
Het |
| Gimap8 |
T |
C |
6: 48,636,017 (GRCm39) |
M594T |
probably benign |
Het |
| Gm6578 |
G |
A |
6: 12,100,187 (GRCm39) |
|
noncoding transcript |
Het |
| Gpc6 |
A |
G |
14: 117,673,328 (GRCm39) |
D195G |
probably damaging |
Het |
| Insm1 |
C |
A |
2: 146,064,888 (GRCm39) |
H235N |
probably benign |
Het |
| Jmjd8 |
A |
G |
17: 26,048,787 (GRCm39) |
|
probably benign |
Het |
| Kbtbd8 |
T |
C |
6: 95,103,914 (GRCm39) |
V521A |
probably damaging |
Het |
| Kcna5 |
T |
C |
6: 126,510,329 (GRCm39) |
T600A |
probably damaging |
Het |
| Kctd6 |
G |
C |
14: 8,222,806 (GRCm38) |
R216P |
probably damaging |
Het |
| Lbx1 |
C |
A |
19: 45,223,528 (GRCm39) |
V47L |
probably benign |
Het |
| Mefv |
A |
T |
16: 3,533,433 (GRCm39) |
N279K |
probably benign |
Het |
| Mroh1 |
T |
G |
15: 76,278,051 (GRCm39) |
V24G |
probably damaging |
Het |
| Nt5c1b |
A |
G |
12: 10,424,886 (GRCm39) |
E142G |
probably damaging |
Het |
| Or4f4b |
G |
T |
2: 111,313,849 (GRCm39) |
V25L |
probably damaging |
Het |
| Or8u3-ps |
G |
A |
2: 85,952,623 (GRCm39) |
A119T |
probably damaging |
Het |
| Padi2 |
A |
G |
4: 140,663,859 (GRCm39) |
E404G |
possibly damaging |
Het |
| Pitpnb |
A |
G |
5: 111,519,258 (GRCm39) |
|
probably null |
Het |
| Plxna4 |
T |
C |
6: 32,177,883 (GRCm39) |
N1006S |
probably benign |
Het |
| Proc |
A |
G |
18: 32,268,967 (GRCm39) |
V6A |
probably benign |
Het |
| Prrc2c |
T |
A |
1: 162,501,160 (GRCm39) |
K1214N |
probably damaging |
Het |
| Pstpip2 |
A |
G |
18: 77,949,556 (GRCm39) |
I122V |
probably benign |
Het |
| Pus10 |
A |
G |
11: 23,656,895 (GRCm39) |
E207G |
probably damaging |
Het |
| Rabl2 |
G |
A |
15: 89,468,391 (GRCm39) |
|
probably benign |
Het |
| Rbp3 |
G |
A |
14: 33,680,607 (GRCm39) |
V1070I |
probably benign |
Het |
| Rtl6 |
T |
A |
15: 84,441,397 (GRCm39) |
|
probably benign |
Het |
| Scn7a |
T |
G |
2: 66,514,407 (GRCm39) |
K1122N |
probably damaging |
Het |
| Spag16 |
A |
G |
1: 69,912,640 (GRCm39) |
|
probably benign |
Het |
| Spata13 |
C |
T |
14: 60,993,745 (GRCm39) |
R396C |
probably damaging |
Het |
| Stmn4 |
A |
T |
14: 66,593,166 (GRCm39) |
|
probably benign |
Het |
| Syp |
G |
T |
X: 7,504,931 (GRCm39) |
|
probably benign |
Het |
| Tmem260 |
C |
T |
14: 48,715,093 (GRCm39) |
T249M |
probably damaging |
Het |
| Tnrc6b |
A |
G |
15: 80,786,172 (GRCm39) |
I1239V |
probably benign |
Het |
| Ubr3 |
C |
T |
2: 69,768,731 (GRCm39) |
Q510* |
probably null |
Het |
| Vegfa |
A |
G |
17: 46,342,392 (GRCm39) |
V142A |
probably benign |
Het |
| Vmn2r93 |
T |
C |
17: 18,525,092 (GRCm39) |
I250T |
possibly 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 |
|
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 |
|
|
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'- TTAGCAAGCTAGAACAGACAATGTG -3'
(R):5'- AGCTCTCTCATCTTCAGTAAGTTG -3'
Sequencing Primer
(F):5'- GCTAGAACAGACAATGTGAAATTACC -3'
(R):5'- CATCTTCAGTAAGTTGAGAAGGTAGG -3'
|
| Posted On |
2015-06-20 |
Incidental Mutation