Incidental Mutation 'R5060:Gpcpd1'
| ID |
386546 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Gpcpd1
|
| Ensembl Gene |
ENSMUSG00000027346 |
| Gene Name |
glycerophosphocholine phosphodiesterase 1 |
| Synonyms |
Prei4, 2310004G06Rik, 2310032D16Rik |
| MMRRC Submission |
042650-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.936)
|
| Stock # |
R5060 (G1)
|
| Quality Score |
205 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
132371002-132420173 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 132386355 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Glutamic Acid
at position 341
(V341E)
|
| 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: V157E
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000028822
Gene: ENSMUSG00000027346
AA Change: V157E
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GDPD
|
142 |
432 |
1.3e-61 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000060955
AA Change: V341E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000062221
Gene: ENSMUSG00000027346
AA Change: V341E
| 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: V157E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000105763
Gene: ENSMUSG00000027346
AA Change: V157E
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GDPD
|
142 |
431 |
4.1e-59 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000110142
AA Change: V341E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000105769
Gene: ENSMUSG00000027346
AA Change: V341E
| 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 |
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 |
0.6467 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.5%
- 20x: 92.9%
|
| Validation Efficiency |
98% (52/53) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A530064D06Rik |
A |
T |
17: 48,474,107 (GRCm39) |
L17Q |
probably damaging |
Het |
| Abca6 |
A |
G |
11: 110,110,430 (GRCm39) |
V573A |
possibly damaging |
Het |
| Abcc9 |
A |
G |
6: 142,571,836 (GRCm39) |
|
probably benign |
Het |
| Actg1 |
A |
G |
11: 120,237,839 (GRCm39) |
S234P |
probably benign |
Het |
| Acvr2a |
A |
G |
2: 48,780,311 (GRCm39) |
D177G |
probably damaging |
Het |
| Adamts12 |
T |
C |
15: 11,300,054 (GRCm39) |
C914R |
probably damaging |
Het |
| Adprhl1 |
A |
G |
8: 13,298,621 (GRCm39) |
I103T |
possibly damaging |
Het |
| Als2cl |
C |
T |
9: 110,713,205 (GRCm39) |
L32F |
probably damaging |
Het |
| Ank2 |
T |
C |
3: 126,739,570 (GRCm39) |
|
probably benign |
Het |
| Ankrd52 |
T |
A |
10: 128,225,710 (GRCm39) |
S959R |
possibly damaging |
Het |
| Bnc2 |
C |
A |
4: 84,449,872 (GRCm39) |
A122S |
probably benign |
Het |
| Cert1 |
A |
T |
13: 96,739,663 (GRCm39) |
K226N |
probably benign |
Het |
| Cfap54 |
C |
T |
10: 92,875,013 (GRCm39) |
V443M |
probably damaging |
Het |
| Cilk1 |
C |
T |
9: 78,060,978 (GRCm39) |
T208I |
probably benign |
Het |
| Clca4b |
T |
A |
3: 144,617,267 (GRCm39) |
R794S |
probably damaging |
Het |
| Cyp2c65 |
T |
C |
19: 39,049,514 (GRCm39) |
L14P |
unknown |
Het |
| Ggt5 |
T |
C |
10: 75,440,608 (GRCm39) |
M243T |
probably benign |
Het |
| Gmds |
A |
G |
13: 32,124,482 (GRCm39) |
I292T |
probably benign |
Het |
| Grm3 |
A |
G |
5: 9,620,167 (GRCm39) |
F359S |
probably damaging |
Het |
| Hcn1 |
A |
T |
13: 118,010,441 (GRCm39) |
K340* |
probably null |
Het |
| Heatr9 |
T |
C |
11: 83,403,258 (GRCm39) |
E427G |
probably benign |
Het |
| Kif26b |
G |
A |
1: 178,358,195 (GRCm39) |
G102D |
unknown |
Het |
| Mark3 |
T |
C |
12: 111,584,760 (GRCm39) |
F119L |
probably damaging |
Het |
| Melk |
T |
C |
4: 44,350,959 (GRCm39) |
V500A |
probably benign |
Het |
| Mrpl41 |
A |
G |
2: 24,864,295 (GRCm39) |
F126L |
probably damaging |
Het |
| Or10c1 |
C |
A |
17: 37,522,307 (GRCm39) |
A146S |
probably benign |
Het |
| Or6c3b |
C |
T |
10: 129,527,699 (GRCm39) |
M70I |
probably benign |
Het |
| Pax7 |
A |
T |
4: 139,506,928 (GRCm39) |
S372T |
probably benign |
Het |
| Pax7 |
A |
T |
4: 139,556,906 (GRCm39) |
I118N |
probably damaging |
Het |
| Plcl1 |
G |
T |
1: 55,735,671 (GRCm39) |
M337I |
possibly damaging |
Het |
| Poc1a |
G |
T |
9: 106,227,012 (GRCm39) |
|
probably benign |
Het |
| Rabgef1 |
A |
G |
5: 130,240,844 (GRCm39) |
Y321C |
probably damaging |
Het |
| Rhobtb3 |
A |
C |
13: 76,061,389 (GRCm39) |
L252R |
probably benign |
Het |
| Rlf |
A |
G |
4: 121,004,063 (GRCm39) |
V1639A |
probably benign |
Het |
| Tff1 |
A |
G |
17: 31,381,682 (GRCm39) |
V65A |
probably damaging |
Het |
| Trpm4 |
G |
T |
7: 44,971,258 (GRCm39) |
D222E |
probably damaging |
Het |
| Ttn |
A |
T |
2: 76,643,741 (GRCm39) |
D13162E |
probably damaging |
Het |
| Unc5d |
A |
T |
8: 29,209,723 (GRCm39) |
S466T |
probably benign |
Het |
| Vmn1r73 |
A |
G |
7: 11,490,683 (GRCm39) |
Y167C |
probably damaging |
Het |
| Vwde |
C |
T |
6: 13,208,323 (GRCm39) |
|
probably null |
Het |
| Xpr1 |
T |
C |
1: 155,204,430 (GRCm39) |
|
probably null |
Het |
| Zbtb40 |
A |
G |
4: 136,728,604 (GRCm39) |
V413A |
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 |
|
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 |
|
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'- GCATGCGCAAGAGGTTTAAAGC -3'
(R):5'- GGTGCTTGAAATAAGTGCACATAC -3'
Sequencing Primer
(F):5'- AGTGTACAGGATCTGACACCTTCTG -3'
(R):5'- TACCAGCCAAGAGTGTTCACTATC -3'
|
| Posted On |
2016-06-06 |
Incidental Mutation