Incidental Mutation 'R6591:Pld3'
| ID |
524574 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pld3
|
| Ensembl Gene |
ENSMUSG00000003363 |
| Gene Name |
phospholipase D family member 3 |
| Synonyms |
Sam-9 |
| MMRRC Submission |
044715-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R6591 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
7 |
| Chromosomal Location |
27231425-27252643 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 27231741 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Lysine
at position 483
(N483K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000112942
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037134]
[ENSMUST00000108353]
[ENSMUST00000117095]
[ENSMUST00000117611]
|
| AlphaFold |
O35405 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000037134
|
| SMART Domains |
Protein: ENSMUSP00000043175
Gene: ENSMUSG00000040424
| Domain | Start | End | E-Value | Type |
|---|
|
SCOP:d1howa_
|
1 |
142 |
8e-12 |
SMART |
|
Blast:S_TKc
|
1 |
143 |
8e-99 |
BLAST |
|
PDB:3ANR|D
|
1 |
155 |
1e-12 |
PDB |
|
low complexity region
|
192 |
206 |
N/A |
INTRINSIC |
|
low complexity region
|
389 |
399 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000108353
|
| SMART Domains |
Protein: ENSMUSP00000103990
Gene: ENSMUSG00000040424
| Domain | Start | End | E-Value | Type |
|---|
|
S_TKc
|
11 |
347 |
9.31e-74 |
SMART |
|
low complexity region
|
396 |
410 |
N/A |
INTRINSIC |
|
low complexity region
|
593 |
603 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000117095
AA Change: N483K
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000113820
Gene: ENSMUSG00000003363
AA Change: N483K
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
25 |
36 |
N/A |
INTRINSIC |
|
transmembrane domain
|
38 |
60 |
N/A |
INTRINSIC |
|
PLDc
|
194 |
221 |
9.25e-10 |
SMART |
|
Pfam:PLDc_3
|
224 |
401 |
1.6e-43 |
PFAM |
|
PLDc
|
409 |
435 |
1.19e-3 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000117611
AA Change: N483K
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000112942
Gene: ENSMUSG00000003363
AA Change: N483K
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
25 |
36 |
N/A |
INTRINSIC |
|
transmembrane domain
|
38 |
60 |
N/A |
INTRINSIC |
|
PLDc
|
194 |
221 |
9.25e-10 |
SMART |
|
low complexity region
|
285 |
297 |
N/A |
INTRINSIC |
|
PLDc
|
409 |
435 |
1.19e-3 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000142981
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155287
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.1%
- 20x: 94.2%
|
| Validation Efficiency |
100% (34/34) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the phospholipase D (PLD) family of enzymes that catalyze the hydrolysis of membrane phospholipids. The encoded protein is a single-pass type II membrane protein and contains two PLD phosphodiesterase domains. This protein influences processing of amyloid-beta precursor protein. Mutations in this gene are associated with Alzheimer disease risk. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Apr 2014]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 32 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2300009A05Rik |
A |
G |
9: 63,306,236 (GRCm39) |
Y90H |
probably damaging |
Het |
| Agk |
A |
G |
6: 40,369,624 (GRCm39) |
D337G |
probably benign |
Het |
| Amn |
A |
G |
12: 111,241,831 (GRCm39) |
H299R |
possibly damaging |
Het |
| Angptl4 |
A |
G |
17: 33,999,755 (GRCm39) |
|
probably null |
Het |
| AU040320 |
G |
A |
4: 126,730,463 (GRCm39) |
M563I |
possibly damaging |
Het |
| Cachd1 |
T |
C |
4: 100,846,683 (GRCm39) |
M1042T |
probably benign |
Het |
| Cd209c |
T |
A |
8: 3,995,680 (GRCm39) |
I41L |
probably benign |
Het |
| Ceacam12 |
T |
A |
7: 17,803,149 (GRCm39) |
V185D |
possibly damaging |
Het |
| Chpt1 |
A |
T |
10: 88,321,762 (GRCm39) |
|
probably benign |
Het |
| Clca3a1 |
G |
C |
3: 144,719,644 (GRCm39) |
A442G |
probably damaging |
Het |
| Cldn8 |
T |
C |
16: 88,359,423 (GRCm39) |
I167M |
possibly damaging |
Het |
| Cln3 |
A |
G |
7: 126,178,606 (GRCm39) |
V143A |
possibly damaging |
Het |
| Dusp11 |
T |
C |
6: 85,938,507 (GRCm39) |
H4R |
possibly damaging |
Het |
| Ephb3 |
T |
A |
16: 21,033,223 (GRCm39) |
F69Y |
probably damaging |
Het |
| Gm11099 |
A |
T |
2: 58,749,485 (GRCm39) |
|
probably benign |
Het |
| Grik2 |
A |
T |
10: 49,149,021 (GRCm39) |
Y521* |
probably null |
Het |
| Igf2r |
A |
G |
17: 12,907,895 (GRCm39) |
L2143P |
probably damaging |
Het |
| Kcnk1 |
T |
C |
8: 126,751,970 (GRCm39) |
V192A |
probably benign |
Het |
| Or4a81 |
A |
T |
2: 89,619,332 (GRCm39) |
Y121* |
probably null |
Het |
| Or8k53 |
A |
C |
2: 86,177,763 (GRCm39) |
S116A |
probably damaging |
Het |
| Parp3 |
A |
G |
9: 106,350,891 (GRCm39) |
S329P |
probably benign |
Het |
| Rbm33 |
A |
T |
5: 28,557,544 (GRCm39) |
E252D |
probably damaging |
Het |
| Ryr2 |
T |
C |
13: 11,609,609 (GRCm39) |
T4406A |
probably benign |
Het |
| Sgsm3 |
A |
G |
15: 80,893,063 (GRCm39) |
D380G |
possibly damaging |
Het |
| Sorl1 |
G |
T |
9: 41,913,863 (GRCm39) |
D1355E |
probably damaging |
Het |
| Sptbn1 |
A |
G |
11: 30,063,984 (GRCm39) |
S1945P |
probably damaging |
Het |
| Ube2m |
A |
T |
7: 12,770,396 (GRCm39) |
F70I |
probably damaging |
Het |
| Ube3b |
A |
G |
5: 114,546,185 (GRCm39) |
I664V |
probably benign |
Het |
| Ugt1a7c |
A |
G |
1: 88,023,378 (GRCm39) |
E179G |
possibly damaging |
Het |
| Vps50 |
T |
C |
6: 3,504,939 (GRCm39) |
|
probably null |
Het |
| Xpo1 |
T |
C |
11: 23,236,875 (GRCm39) |
L718P |
probably damaging |
Het |
| Zfp354c |
A |
G |
11: 50,705,602 (GRCm39) |
I491T |
probably benign |
Het |
|
| Other mutations in Pld3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01474:Pld3
|
APN |
7 |
27,232,044 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0624:Pld3
|
UTSW |
7 |
27,239,000 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R1384:Pld3
|
UTSW |
7 |
27,237,082 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1845:Pld3
|
UTSW |
7 |
27,238,877 (GRCm39) |
missense |
probably benign |
0.01 |
|
R2235:Pld3
|
UTSW |
7 |
27,240,532 (GRCm39) |
missense |
probably benign |
0.00 |
|
R3106:Pld3
|
UTSW |
7 |
27,235,212 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5141:Pld3
|
UTSW |
7 |
27,233,220 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5486:Pld3
|
UTSW |
7 |
27,233,156 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5518:Pld3
|
UTSW |
7 |
27,231,796 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5868:Pld3
|
UTSW |
7 |
27,237,093 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6446:Pld3
|
UTSW |
7 |
27,237,156 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6691:Pld3
|
UTSW |
7 |
27,231,741 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6823:Pld3
|
UTSW |
7 |
27,235,322 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7162:Pld3
|
UTSW |
7 |
27,231,899 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8150:Pld3
|
UTSW |
7 |
27,232,086 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8725:Pld3
|
UTSW |
7 |
27,239,079 (GRCm39) |
nonsense |
probably null |
|
|
R8795:Pld3
|
UTSW |
7 |
27,235,286 (GRCm39) |
missense |
possibly damaging |
0.52 |
|
R9049:Pld3
|
UTSW |
7 |
27,235,293 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R9096:Pld3
|
UTSW |
7 |
27,232,089 (GRCm39) |
missense |
probably benign |
0.08 |
|
R9292:Pld3
|
UTSW |
7 |
27,238,879 (GRCm39) |
missense |
probably benign |
0.02 |
|
| Predicted Primers |
PCR Primer
(F):5'- ACCACTCAGTTAAGCACAGG -3'
(R):5'- ACCTCCAACTGGTCTGGAAG -3'
Sequencing Primer
(F):5'- AATCCCCAGCTCTGCTAGG -3'
(R):5'- AACTGGTCTGGAAGCTACTTCACG -3'
|
| Posted On |
2018-06-22 |
Incidental Mutation