Incidental Mutation 'R1023:Gnpat'
| ID |
94636 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Gnpat
|
| Ensembl Gene |
ENSMUSG00000031985 |
| Gene Name |
glyceronephosphate O-acyltransferase |
| Synonyms |
D1Ertd819e |
| MMRRC Submission |
039125-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.337)
|
| Stock # |
R1023 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
125589772-125616796 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 125597519 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Valine
at position 27
(D27V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000034466
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000034466]
[ENSMUST00000161986]
|
| AlphaFold |
P98192 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000034466
AA Change: D27V
PolyPhen 2
Score 0.276 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000034466
Gene: ENSMUSG00000031985
AA Change: D27V
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
5 |
20 |
N/A |
INTRINSIC |
|
SCOP:d1dbha1
|
27 |
146 |
6e-3 |
SMART |
|
PlsC
|
155 |
284 |
8.3e-21 |
SMART |
|
Blast:PlsC
|
308 |
336 |
1e-6 |
BLAST |
|
low complexity region
|
638 |
652 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000161986
AA Change: D27V
PolyPhen 2
Score 0.160 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000125323
Gene: ENSMUSG00000031985
AA Change: D27V
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
5 |
20 |
N/A |
INTRINSIC |
|
PlsC
|
145 |
274 |
8.3e-21 |
SMART |
|
Blast:PlsC
|
298 |
326 |
2e-6 |
BLAST |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.0%
- 10x: 95.6%
- 20x: 90.7%
|
| Validation Efficiency |
100% (42/42) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an enzyme located in the peroxisomal membrane which is essential to the synthesis of ether phospholipids. Mutations in this gene are associated with rhizomelic chondrodysplasia punctata. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
PHENOTYPE: Homozygous mutant mice lack plasmalogens due to inactivation of ether lipid synthesis. Mutant mice exhibit dwarfism, male infertility, defects in eye development, and optic nerve hypoplasia. While some mice die prematurely, others, particularly females, are long-lived. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1110002E22Rik |
C |
T |
3: 137,772,632 (GRCm39) |
A607V |
probably damaging |
Het |
| 4930523C07Rik |
A |
G |
1: 159,905,057 (GRCm39) |
|
probably benign |
Het |
| Ap3d1 |
A |
T |
10: 80,550,092 (GRCm39) |
L713Q |
probably damaging |
Het |
| Baz2a |
A |
G |
10: 127,957,676 (GRCm39) |
T1010A |
possibly damaging |
Het |
| Cdh15 |
T |
C |
8: 123,591,939 (GRCm39) |
I608T |
probably damaging |
Het |
| Cdkl2 |
A |
T |
5: 92,187,145 (GRCm39) |
D40E |
possibly damaging |
Het |
| Col9a2 |
G |
A |
4: 120,901,207 (GRCm39) |
G118R |
unknown |
Het |
| Cryge |
C |
A |
1: 65,089,945 (GRCm39) |
C79F |
probably damaging |
Het |
| Dapk1 |
T |
C |
13: 60,878,799 (GRCm39) |
L596P |
probably damaging |
Het |
| Dqx1 |
G |
A |
6: 83,038,070 (GRCm39) |
C486Y |
probably damaging |
Het |
| Dync2i1 |
T |
C |
12: 116,196,277 (GRCm39) |
E490G |
probably damaging |
Het |
| Enam |
A |
G |
5: 88,649,826 (GRCm39) |
Q445R |
probably damaging |
Het |
| Gm10608 |
CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA |
CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA |
9: 118,989,784 (GRCm39) |
|
probably benign |
Het |
| Htr5a |
A |
T |
5: 28,047,996 (GRCm39) |
T184S |
possibly damaging |
Het |
| Lap3 |
C |
T |
5: 45,652,553 (GRCm39) |
P50S |
probably benign |
Het |
| Mamdc2 |
A |
T |
19: 23,288,271 (GRCm39) |
M589K |
probably damaging |
Het |
| Mast4 |
A |
G |
13: 102,872,004 (GRCm39) |
S2263P |
probably benign |
Het |
| Mef2b |
C |
T |
8: 70,618,247 (GRCm39) |
P109L |
possibly damaging |
Het |
| Meltf |
T |
A |
16: 31,703,778 (GRCm39) |
F168L |
probably damaging |
Het |
| Mib2 |
C |
T |
4: 155,743,917 (GRCm39) |
G42S |
probably damaging |
Het |
| Nup205 |
T |
A |
6: 35,211,641 (GRCm39) |
F1661I |
probably damaging |
Het |
| Or11h4b |
A |
T |
14: 50,918,473 (GRCm39) |
L206H |
probably damaging |
Het |
| Or5h19 |
A |
T |
16: 58,856,178 (GRCm39) |
N307K |
probably benign |
Het |
| Plac8 |
A |
T |
5: 100,704,447 (GRCm39) |
D83E |
probably benign |
Het |
| Pnpt1 |
T |
C |
11: 29,091,328 (GRCm39) |
|
probably benign |
Het |
| Pold2 |
G |
T |
11: 5,825,140 (GRCm39) |
Q86K |
probably benign |
Het |
| Ptprt |
A |
G |
2: 161,400,863 (GRCm39) |
L1057P |
probably damaging |
Het |
| Rev3l |
A |
G |
10: 39,708,635 (GRCm39) |
H2284R |
probably damaging |
Het |
| Scart1 |
T |
A |
7: 139,804,376 (GRCm39) |
C484S |
possibly damaging |
Het |
| Skint6 |
A |
C |
4: 113,095,300 (GRCm39) |
S120A |
probably benign |
Het |
| Slc1a7 |
G |
A |
4: 107,864,770 (GRCm39) |
V270M |
probably damaging |
Het |
| Spata2 |
A |
G |
2: 167,327,142 (GRCm39) |
M85T |
probably benign |
Het |
| Taf1b |
G |
T |
12: 24,559,558 (GRCm39) |
|
probably benign |
Het |
| Tert |
A |
G |
13: 73,790,178 (GRCm39) |
N844S |
probably benign |
Het |
| Thrap3 |
G |
A |
4: 126,073,882 (GRCm39) |
S288L |
possibly damaging |
Het |
| Ubap2l |
A |
G |
3: 89,955,180 (GRCm39) |
|
probably benign |
Het |
| Ubtf |
T |
C |
11: 102,202,276 (GRCm39) |
E197G |
possibly damaging |
Het |
| Usp20 |
G |
T |
2: 30,897,825 (GRCm39) |
G216W |
probably damaging |
Het |
| Yy1 |
T |
A |
12: 108,759,457 (GRCm39) |
V40E |
unknown |
Het |
| Zfp335 |
G |
A |
2: 164,734,505 (GRCm39) |
H1254Y |
possibly damaging |
Het |
|
| Other mutations in Gnpat |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00089:Gnpat
|
APN |
8 |
125,603,653 (GRCm39) |
splice site |
probably benign |
|
|
IGL00422:Gnpat
|
APN |
8 |
125,611,752 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01327:Gnpat
|
APN |
8 |
125,605,372 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02257:Gnpat
|
APN |
8 |
125,613,587 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02951:Gnpat
|
APN |
8 |
125,597,644 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL03084:Gnpat
|
APN |
8 |
125,605,638 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0114:Gnpat
|
UTSW |
8 |
125,610,096 (GRCm39) |
missense |
probably benign |
0.06 |
|
R0394:Gnpat
|
UTSW |
8 |
125,606,964 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R1052:Gnpat
|
UTSW |
8 |
125,605,255 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1052:Gnpat
|
UTSW |
8 |
125,604,246 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1537:Gnpat
|
UTSW |
8 |
125,597,555 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R1604:Gnpat
|
UTSW |
8 |
125,603,700 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1711:Gnpat
|
UTSW |
8 |
125,613,691 (GRCm39) |
splice site |
probably null |
|
|
R1754:Gnpat
|
UTSW |
8 |
125,603,745 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2118:Gnpat
|
UTSW |
8 |
125,603,680 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2278:Gnpat
|
UTSW |
8 |
125,603,659 (GRCm39) |
missense |
probably benign |
0.35 |
|
R2429:Gnpat
|
UTSW |
8 |
125,603,758 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4579:Gnpat
|
UTSW |
8 |
125,605,241 (GRCm39) |
splice site |
probably null |
|
|
R6176:Gnpat
|
UTSW |
8 |
125,605,593 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7017:Gnpat
|
UTSW |
8 |
125,590,014 (GRCm39) |
missense |
probably benign |
0.33 |
|
R7081:Gnpat
|
UTSW |
8 |
125,590,008 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
R7388:Gnpat
|
UTSW |
8 |
125,614,553 (GRCm39) |
missense |
probably benign |
0.32 |
|
R7716:Gnpat
|
UTSW |
8 |
125,603,673 (GRCm39) |
missense |
probably benign |
0.32 |
|
R7848:Gnpat
|
UTSW |
8 |
125,613,630 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R8169:Gnpat
|
UTSW |
8 |
125,606,869 (GRCm39) |
missense |
probably benign |
0.02 |
|
R8355:Gnpat
|
UTSW |
8 |
125,597,579 (GRCm39) |
missense |
probably benign |
0.11 |
|
R8363:Gnpat
|
UTSW |
8 |
125,590,038 (GRCm39) |
missense |
probably benign |
0.28 |
|
R8851:Gnpat
|
UTSW |
8 |
125,601,004 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9234:Gnpat
|
UTSW |
8 |
125,610,179 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9276:Gnpat
|
UTSW |
8 |
125,614,524 (GRCm39) |
missense |
probably benign |
0.45 |
|
R9701:Gnpat
|
UTSW |
8 |
125,613,678 (GRCm39) |
missense |
probably benign |
0.01 |
|
X0025:Gnpat
|
UTSW |
8 |
125,600,138 (GRCm39) |
missense |
probably null |
0.99 |
|
Z1177:Gnpat
|
UTSW |
8 |
125,590,035 (GRCm39) |
missense |
probably benign |
0.02 |
|
| Predicted Primers |
PCR Primer
(F):5'- GGCAGACAAAATGAGTTTGTAGATGTGG -3'
(R):5'- ACAACTCTGCTCTTACCTGCTTAATGAC -3'
Sequencing Primer
(F):5'- tccaacaaaacaaaaccaccag -3'
(R):5'- CCTGCTTAATGACATAGTTGATCTC -3'
|
| Posted On |
2014-01-05 |
Incidental Mutation