Incidental Mutation 'R5623:Gpcpd1'
| ID |
441670 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Gpcpd1
|
| Ensembl Gene |
ENSMUSG00000027346 |
| Gene Name |
glycerophosphocholine phosphodiesterase 1 |
| Synonyms |
Prei4, 2310004G06Rik, 2310032D16Rik |
| MMRRC Submission |
043162-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.941)
|
| Stock # |
R5623 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
132371002-132420173 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 132376637 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Glutamic Acid
at position 553
(A553E)
|
| 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: A369E
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000028822
Gene: ENSMUSG00000027346
AA Change: A369E
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GDPD
|
142 |
432 |
1.3e-61 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000060955
AA Change: A553E
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000062221
Gene: ENSMUSG00000027346
AA Change: A553E
| 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: A369E
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000105763
Gene: ENSMUSG00000027346
AA Change: A369E
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:GDPD
|
142 |
431 |
4.1e-59 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000110142
AA Change: A553E
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000105769
Gene: ENSMUSG00000027346
AA Change: A553E
| 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 |
0.9217 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.7%
- 10x: 97.2%
- 20x: 95.0%
|
| Validation Efficiency |
98% (65/66) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Atp8b1 |
T |
G |
18: 64,679,165 (GRCm39) |
Q772P |
possibly damaging |
Het |
| B3gnt2 |
C |
G |
11: 22,787,018 (GRCm39) |
A57P |
probably damaging |
Het |
| Birc6 |
T |
G |
17: 74,835,651 (GRCm39) |
D63E |
probably damaging |
Het |
| Ccdc13 |
T |
C |
9: 121,662,799 (GRCm39) |
E72G |
probably damaging |
Het |
| Cfap221 |
C |
T |
1: 119,881,898 (GRCm39) |
A297T |
probably benign |
Het |
| Chd1 |
T |
A |
17: 15,975,194 (GRCm39) |
N1081K |
probably damaging |
Het |
| Chrm3 |
C |
A |
13: 9,927,423 (GRCm39) |
V538L |
possibly damaging |
Het |
| Clec16a |
T |
A |
16: 10,428,985 (GRCm39) |
N37K |
probably benign |
Het |
| Cnksr3 |
T |
A |
10: 7,070,548 (GRCm39) |
I229F |
probably damaging |
Het |
| Cspg4b |
T |
C |
13: 113,483,168 (GRCm39) |
I1590T |
possibly damaging |
Het |
| Dchs1 |
T |
C |
7: 105,421,976 (GRCm39) |
E148G |
probably damaging |
Het |
| Diaph1 |
A |
T |
18: 38,029,146 (GRCm39) |
|
probably benign |
Het |
| Dis3l |
A |
G |
9: 64,214,885 (GRCm39) |
F895L |
possibly damaging |
Het |
| Dnah1 |
G |
T |
14: 31,007,980 (GRCm39) |
D2142E |
possibly damaging |
Het |
| Dst |
T |
C |
1: 34,229,214 (GRCm39) |
V1944A |
possibly damaging |
Het |
| Eif4a2 |
C |
T |
16: 22,928,969 (GRCm39) |
|
probably benign |
Het |
| Ephb6 |
T |
A |
6: 41,593,415 (GRCm39) |
M487K |
probably benign |
Het |
| Fgf18 |
T |
G |
11: 33,084,272 (GRCm39) |
T61P |
probably damaging |
Het |
| G6pc2 |
A |
G |
2: 69,056,927 (GRCm39) |
E191G |
probably damaging |
Het |
| Gm10717 |
C |
T |
9: 3,026,318 (GRCm39) |
S55L |
probably benign |
Het |
| Gm5414 |
A |
G |
15: 101,534,246 (GRCm39) |
F286S |
probably damaging |
Het |
| Gpr153 |
A |
G |
4: 152,366,398 (GRCm39) |
D321G |
possibly damaging |
Het |
| Hecw2 |
T |
A |
1: 53,871,782 (GRCm39) |
Q1388L |
probably null |
Het |
| Ighv14-3 |
A |
C |
12: 114,023,710 (GRCm39) |
S36A |
probably damaging |
Het |
| Inpp5j |
C |
A |
11: 3,444,766 (GRCm39) |
G969V |
probably damaging |
Het |
| Kat5 |
G |
A |
19: 5,657,590 (GRCm39) |
R307W |
probably damaging |
Het |
| Klk1b21 |
A |
G |
7: 43,754,989 (GRCm39) |
S95G |
probably damaging |
Het |
| Mdm1 |
G |
A |
10: 117,986,694 (GRCm39) |
V171I |
possibly damaging |
Het |
| Nfu1 |
TCGC |
T |
6: 86,993,188 (GRCm39) |
|
probably benign |
Het |
| Or5k8 |
C |
T |
16: 58,644,706 (GRCm39) |
R122H |
probably benign |
Het |
| Or6c206 |
G |
A |
10: 129,096,901 (GRCm39) |
V24M |
probably benign |
Het |
| Phkb |
T |
A |
8: 86,569,677 (GRCm39) |
|
probably benign |
Het |
| Pkd1l3 |
A |
T |
8: 110,350,351 (GRCm39) |
T399S |
possibly damaging |
Het |
| Prr14l |
A |
T |
5: 33,001,852 (GRCm39) |
|
probably benign |
Het |
| Psg21 |
A |
C |
7: 18,388,939 (GRCm39) |
L51R |
probably damaging |
Het |
| Ptprg |
T |
A |
14: 12,153,857 (GRCm38) |
I526N |
probably damaging |
Het |
| Rab1a |
T |
C |
11: 20,151,626 (GRCm39) |
|
probably benign |
Het |
| Rims2 |
A |
T |
15: 39,342,011 (GRCm39) |
Q620L |
probably damaging |
Het |
| Rnf215 |
T |
G |
11: 4,085,453 (GRCm39) |
S58A |
probably benign |
Het |
| Scaper |
A |
C |
9: 55,771,791 (GRCm39) |
V375G |
probably benign |
Het |
| Sgk3 |
A |
T |
1: 9,872,520 (GRCm39) |
|
probably benign |
Het |
| Skic2 |
T |
C |
17: 35,066,408 (GRCm39) |
K192E |
probably benign |
Het |
| Slc34a3 |
T |
A |
2: 25,123,312 (GRCm39) |
|
probably null |
Het |
| Sspn |
T |
A |
6: 145,906,952 (GRCm39) |
C52S |
probably damaging |
Het |
| Strip1 |
T |
C |
3: 107,534,142 (GRCm39) |
E164G |
possibly damaging |
Het |
| Sult5a1 |
A |
C |
8: 123,884,181 (GRCm39) |
S47A |
probably damaging |
Het |
| Svep1 |
T |
C |
4: 58,091,964 (GRCm39) |
D1557G |
possibly damaging |
Het |
| Tdrd6 |
T |
C |
17: 43,940,224 (GRCm39) |
I275V |
probably damaging |
Het |
| Thada |
C |
T |
17: 84,499,411 (GRCm39) |
V1929I |
probably benign |
Het |
| Tmem132b |
G |
A |
5: 125,700,416 (GRCm39) |
R318Q |
probably damaging |
Het |
| Tmem176b |
T |
G |
6: 48,811,004 (GRCm39) |
I259L |
probably benign |
Het |
| Tmppe |
C |
A |
9: 114,234,964 (GRCm39) |
P421Q |
possibly damaging |
Het |
| Tmprss11e |
G |
A |
5: 86,857,315 (GRCm39) |
Q333* |
probably null |
Het |
| Tpcn2 |
T |
A |
7: 144,821,071 (GRCm39) |
R328W |
possibly damaging |
Het |
| Trem1 |
C |
T |
17: 48,544,083 (GRCm39) |
T36I |
probably damaging |
Het |
| Trpm2 |
C |
A |
10: 77,767,973 (GRCm39) |
R842L |
probably damaging |
Het |
| Zfp319 |
A |
G |
8: 96,052,199 (GRCm39) |
|
probably benign |
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 |
|
|
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'- AGCCAGCTGTGTTAATCTGTTC -3'
(R):5'- GCCTTCTAGAGTTTCTCAATCTGTAG -3'
Sequencing Primer
(F):5'- CAGCTGTGTTAATCTGTTCATCATG -3'
(R):5'- GAGCTTACAGTGATCCTCCAG -3'
|
| Posted On |
2016-11-08 |
Incidental Mutation