Incidental Mutation 'R5972:Pdss2'
ID |
471475 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pdss2
|
Ensembl Gene |
ENSMUSG00000038240 |
Gene Name |
prenyl (solanesyl) diphosphate synthase, subunit 2 |
Synonyms |
5430420P03Rik, kd, PLMP, mDLP1 |
MMRRC Submission |
044155-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R5972 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
10 |
Chromosomal Location |
43097482-43340878 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 43174922 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Tyrosine to Asparagine
at position 143
(Y143N)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000124046
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000095725]
[ENSMUST00000159139]
[ENSMUST00000160823]
|
AlphaFold |
Q33DR3 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000095725
AA Change: Y143N
PolyPhen 2
Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000093393 Gene: ENSMUSG00000038240 AA Change: Y143N
Domain | Start | End | E-Value | Type |
low complexity region
|
2 |
18 |
N/A |
INTRINSIC |
low complexity region
|
32 |
46 |
N/A |
INTRINSIC |
Pfam:polyprenyl_synt
|
106 |
324 |
9e-20 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000159139
AA Change: Y143N
PolyPhen 2
Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000124864 Gene: ENSMUSG00000038240 AA Change: Y143N
Domain | Start | End | E-Value | Type |
low complexity region
|
2 |
18 |
N/A |
INTRINSIC |
low complexity region
|
32 |
46 |
N/A |
INTRINSIC |
Pfam:polyprenyl_synt
|
103 |
323 |
7.9e-15 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160108
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000160823
AA Change: Y143N
PolyPhen 2
Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
|
SMART Domains |
Protein: ENSMUSP00000124046 Gene: ENSMUSG00000038240 AA Change: Y143N
Domain | Start | End | E-Value | Type |
low complexity region
|
2 |
18 |
N/A |
INTRINSIC |
low complexity region
|
32 |
46 |
N/A |
INTRINSIC |
Pfam:polyprenyl_synt
|
103 |
319 |
7.4e-15 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162758
|
Meta Mutation Damage Score |
0.3004 |
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.0%
- 20x: 93.9%
|
Validation Efficiency |
100% (51/51) |
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is an enzyme that synthesizes the prenyl side-chain of coenzyme Q, or ubiquinone, one of the key elements in the respiratory chain. The gene product catalyzes the formation of all trans-polyprenyl pyrophosphates from isopentyl diphosphate in the assembly of polyisoprenoid side chains, the first step in coenzyme Q biosynthesis. Defects in this gene are a cause of coenzyme Q10 deficiency.[provided by RefSeq, Oct 2009] PHENOTYPE: Mutations in this gene result in renal abnormalities leading to early death. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 45 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abcg2 |
T |
A |
6: 58,649,070 (GRCm39) |
M305K |
probably benign |
Het |
Accs |
G |
T |
2: 93,669,572 (GRCm39) |
H283N |
probably damaging |
Het |
Actl6b |
A |
T |
5: 137,564,818 (GRCm39) |
H283L |
possibly damaging |
Het |
Adgra1 |
T |
C |
7: 139,425,583 (GRCm39) |
L32P |
probably damaging |
Het |
Afg3l2 |
G |
T |
18: 67,554,329 (GRCm39) |
L458M |
probably damaging |
Het |
Arfgef2 |
T |
C |
2: 166,733,756 (GRCm39) |
I1672T |
probably damaging |
Het |
Bambi |
T |
A |
18: 3,512,354 (GRCm39) |
V246E |
probably damaging |
Het |
BC048679 |
A |
G |
7: 81,145,479 (GRCm39) |
L29P |
probably damaging |
Het |
Bmal2 |
A |
G |
6: 146,711,187 (GRCm39) |
M64V |
probably damaging |
Het |
Camk4 |
T |
C |
18: 33,240,979 (GRCm39) |
L92P |
probably damaging |
Het |
Ddx11 |
C |
A |
17: 66,455,085 (GRCm39) |
Q655K |
probably benign |
Het |
Ddx52 |
A |
G |
11: 83,844,051 (GRCm39) |
|
probably null |
Het |
Entrep3 |
T |
A |
3: 89,093,115 (GRCm39) |
V213D |
probably damaging |
Het |
Eps8l3 |
T |
C |
3: 107,791,763 (GRCm39) |
|
probably null |
Het |
Erap1 |
T |
A |
13: 74,810,423 (GRCm39) |
|
probably null |
Het |
Flg |
T |
A |
3: 93,186,849 (GRCm39) |
N100K |
probably benign |
Het |
Grip2 |
A |
T |
6: 91,784,262 (GRCm39) |
V13E |
probably benign |
Het |
Iars1 |
T |
C |
13: 49,863,108 (GRCm39) |
V520A |
possibly damaging |
Het |
Impa1 |
A |
G |
3: 10,394,064 (GRCm39) |
M1T |
probably null |
Het |
Ip6k3 |
T |
C |
17: 27,368,934 (GRCm39) |
T179A |
possibly damaging |
Het |
Krt87 |
T |
A |
15: 101,385,467 (GRCm39) |
M302L |
probably benign |
Het |
Lrp8 |
T |
C |
4: 107,726,267 (GRCm39) |
Y899H |
probably damaging |
Het |
Lrpprc |
A |
T |
17: 85,020,250 (GRCm39) |
I1145N |
possibly damaging |
Het |
Mapk11 |
A |
T |
15: 89,028,387 (GRCm39) |
D324E |
probably benign |
Het |
Melk |
C |
T |
4: 44,351,007 (GRCm39) |
T516I |
probably benign |
Het |
Mia2 |
C |
T |
12: 59,193,723 (GRCm39) |
H130Y |
probably damaging |
Het |
Mroh5 |
C |
T |
15: 73,662,568 (GRCm39) |
|
probably null |
Het |
Ncam1 |
T |
C |
9: 49,418,829 (GRCm39) |
T824A |
possibly damaging |
Het |
Neurog1 |
T |
C |
13: 56,399,211 (GRCm39) |
S179G |
probably damaging |
Het |
Ntrk2 |
T |
A |
13: 58,985,633 (GRCm39) |
L79Q |
probably damaging |
Het |
Patj |
T |
A |
4: 98,457,290 (GRCm39) |
M46K |
probably damaging |
Het |
Pdcd6ip |
T |
C |
9: 113,491,366 (GRCm39) |
K626E |
probably benign |
Het |
Pkhd1l1 |
G |
A |
15: 44,408,812 (GRCm39) |
S2433N |
probably damaging |
Het |
Plekha5 |
A |
G |
6: 140,518,639 (GRCm39) |
T309A |
possibly damaging |
Het |
Prdm4 |
C |
T |
10: 85,743,365 (GRCm39) |
V297M |
probably damaging |
Het |
Rab15 |
T |
C |
12: 76,847,377 (GRCm39) |
Y148C |
probably damaging |
Het |
Ryr3 |
A |
T |
2: 112,664,409 (GRCm39) |
N1627K |
probably damaging |
Het |
Scn1a |
G |
T |
2: 66,181,454 (GRCm39) |
A23E |
possibly damaging |
Het |
Smtn |
A |
T |
11: 3,483,486 (GRCm39) |
I30N |
probably damaging |
Het |
Sympk |
A |
G |
7: 18,780,749 (GRCm39) |
K751E |
probably benign |
Het |
Usp24 |
C |
T |
4: 106,225,264 (GRCm39) |
P632L |
probably damaging |
Het |
Vmn2r106 |
A |
G |
17: 20,498,738 (GRCm39) |
I391T |
probably benign |
Het |
Vmn2r54 |
G |
A |
7: 12,349,279 (GRCm39) |
P768S |
probably damaging |
Het |
Vmn2r54 |
C |
T |
7: 12,369,874 (GRCm39) |
C63Y |
probably damaging |
Het |
Zfhx3 |
T |
G |
8: 109,677,483 (GRCm39) |
C2844W |
possibly damaging |
Het |
|
Other mutations in Pdss2 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL02346:Pdss2
|
APN |
10 |
43,221,639 (GRCm39) |
missense |
possibly damaging |
0.80 |
IGL03337:Pdss2
|
APN |
10 |
43,221,589 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL03340:Pdss2
|
APN |
10 |
43,269,997 (GRCm39) |
missense |
probably benign |
0.00 |
whup
|
UTSW |
10 |
43,269,945 (GRCm39) |
missense |
possibly damaging |
0.75 |
R0277:Pdss2
|
UTSW |
10 |
43,248,172 (GRCm39) |
missense |
probably benign |
|
R0323:Pdss2
|
UTSW |
10 |
43,248,172 (GRCm39) |
missense |
probably benign |
|
R0324:Pdss2
|
UTSW |
10 |
43,269,924 (GRCm39) |
missense |
probably damaging |
1.00 |
R0508:Pdss2
|
UTSW |
10 |
43,097,927 (GRCm39) |
small deletion |
probably benign |
|
R0654:Pdss2
|
UTSW |
10 |
43,097,927 (GRCm39) |
small deletion |
probably benign |
|
R1472:Pdss2
|
UTSW |
10 |
43,289,533 (GRCm39) |
missense |
probably benign |
0.00 |
R1801:Pdss2
|
UTSW |
10 |
43,221,601 (GRCm39) |
missense |
probably benign |
0.29 |
R2024:Pdss2
|
UTSW |
10 |
43,269,871 (GRCm39) |
missense |
possibly damaging |
0.81 |
R2025:Pdss2
|
UTSW |
10 |
43,269,871 (GRCm39) |
missense |
possibly damaging |
0.81 |
R2026:Pdss2
|
UTSW |
10 |
43,269,871 (GRCm39) |
missense |
possibly damaging |
0.81 |
R4077:Pdss2
|
UTSW |
10 |
43,278,518 (GRCm39) |
missense |
probably benign |
|
R4079:Pdss2
|
UTSW |
10 |
43,278,518 (GRCm39) |
missense |
probably benign |
|
R4292:Pdss2
|
UTSW |
10 |
43,097,834 (GRCm39) |
missense |
probably benign |
|
R4518:Pdss2
|
UTSW |
10 |
43,248,146 (GRCm39) |
missense |
probably damaging |
0.99 |
R4603:Pdss2
|
UTSW |
10 |
43,248,197 (GRCm39) |
missense |
probably damaging |
0.99 |
R4962:Pdss2
|
UTSW |
10 |
43,174,908 (GRCm39) |
missense |
possibly damaging |
0.47 |
R5016:Pdss2
|
UTSW |
10 |
43,098,001 (GRCm39) |
missense |
probably damaging |
1.00 |
R5610:Pdss2
|
UTSW |
10 |
43,315,828 (GRCm39) |
missense |
probably benign |
0.00 |
R5888:Pdss2
|
UTSW |
10 |
43,097,793 (GRCm39) |
synonymous |
silent |
|
R7246:Pdss2
|
UTSW |
10 |
43,248,172 (GRCm39) |
missense |
probably benign |
|
R7697:Pdss2
|
UTSW |
10 |
43,221,544 (GRCm39) |
missense |
probably damaging |
1.00 |
R7765:Pdss2
|
UTSW |
10 |
43,340,628 (GRCm39) |
missense |
probably benign |
0.33 |
R8227:Pdss2
|
UTSW |
10 |
43,221,577 (GRCm39) |
missense |
probably damaging |
1.00 |
R8497:Pdss2
|
UTSW |
10 |
43,289,521 (GRCm39) |
missense |
possibly damaging |
0.89 |
R8897:Pdss2
|
UTSW |
10 |
43,221,663 (GRCm39) |
missense |
probably damaging |
1.00 |
R9101:Pdss2
|
UTSW |
10 |
43,269,945 (GRCm39) |
missense |
possibly damaging |
0.75 |
R9529:Pdss2
|
UTSW |
10 |
43,269,990 (GRCm39) |
missense |
probably benign |
0.01 |
|
Predicted Primers |
PCR Primer
(F):5'- CAGCCTTGGGAAAGTGTGTC -3'
(R):5'- GATCCCTGTATATCCCTTCTACTGAAG -3'
Sequencing Primer
(F):5'- CCTTGGGAAAGTGTGTCACCTC -3'
(R):5'- GGAAATTTTACTGCTGAGCCACC -3'
|
Posted On |
2017-03-31 |