Incidental Mutation 'R7408:Pxdn'
| ID |
574864 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pxdn
|
| Ensembl Gene |
ENSMUSG00000020674 |
| Gene Name |
peroxidasin |
| Synonyms |
2310075M15Rik, VPO1 |
| MMRRC Submission |
045489-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.601)
|
| Stock # |
R7408 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
12 |
| Chromosomal Location |
29987607-30067657 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 30040944 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Histidine
at position 407
(Y407H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000113703
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000118321]
[ENSMUST00000122328]
[ENSMUST00000220271]
|
| AlphaFold |
Q3UQ28 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000118321
|
| SMART Domains |
Protein: ENSMUSP00000113477
Gene: ENSMUSG00000020674
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
LRRNT
|
32 |
63 |
2.52e-1 |
SMART |
|
LRR
|
62 |
81 |
4.09e1 |
SMART |
|
LRR_TYP
|
82 |
105 |
3.69e-4 |
SMART |
|
LRR_TYP
|
106 |
129 |
1.45e-2 |
SMART |
|
LRR_TYP
|
130 |
153 |
8.02e-5 |
SMART |
|
LRR_TYP
|
154 |
177 |
1.06e-4 |
SMART |
|
LRRCT
|
189 |
241 |
3.97e-5 |
SMART |
|
IGc2
|
255 |
321 |
1.59e-15 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000122328
AA Change: Y407H
PolyPhen 2
Score 0.288 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000113703
Gene: ENSMUSG00000020674
AA Change: Y407H
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
LRRNT
|
32 |
63 |
2.52e-1 |
SMART |
|
LRR
|
62 |
81 |
4.09e1 |
SMART |
|
LRR_TYP
|
82 |
105 |
3.69e-4 |
SMART |
|
LRR_TYP
|
106 |
129 |
1.45e-2 |
SMART |
|
LRR_TYP
|
130 |
153 |
8.02e-5 |
SMART |
|
LRR_TYP
|
154 |
177 |
1.06e-4 |
SMART |
|
LRRCT
|
189 |
241 |
3.97e-5 |
SMART |
|
IGc2
|
255 |
321 |
1.59e-15 |
SMART |
|
IGc2
|
351 |
416 |
3.96e-16 |
SMART |
|
IGc2
|
442 |
506 |
2.96e-15 |
SMART |
|
IGc2
|
534 |
598 |
1.2e-15 |
SMART |
|
Pfam:An_peroxidase
|
738 |
1286 |
1.1e-196 |
PFAM |
|
VWC
|
1411 |
1466 |
8.8e-15 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000220271
AA Change: Y227H
PolyPhen 2
Score 0.288 (Sensitivity: 0.91; Specificity: 0.88)
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.0%
|
| Validation Efficiency |
100% (71/71) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a heme-containing peroxidase that is secreted into the extracellular matrix. It is involved in extracellular matrix formation, and may function in the physiological and pathological fibrogenic response in fibrotic kidney. Mutations in this gene cause corneal opacification and other ocular anomalies, and also microphthalmia and anterior segment dysgenesis. [provided by RefSeq, Aug 2014]
PHENOTYPE: Mice homozygous for an ENU-induced allele exhibit abnormal eye development with early-onset glaucoma and progressive retinal dysgenesis. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 70 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Agfg1 |
T |
C |
1: 82,860,030 (GRCm39) |
F299S |
probably damaging |
Het |
| Arhgap32 |
A |
T |
9: 32,157,220 (GRCm39) |
E72D |
probably benign |
Het |
| Arid1a |
G |
T |
4: 133,408,391 (GRCm39) |
Q1654K |
unknown |
Het |
| Atp6v1f |
A |
C |
6: 29,470,194 (GRCm39) |
H96P |
probably damaging |
Het |
| Cast |
A |
G |
13: 74,887,960 (GRCm39) |
V161A |
probably damaging |
Het |
| Ccdc186 |
A |
T |
19: 56,796,610 (GRCm39) |
C320S |
probably damaging |
Het |
| Cgn |
T |
A |
3: 94,670,362 (GRCm39) |
K1031* |
probably null |
Het |
| Cnot10 |
T |
C |
9: 114,460,894 (GRCm39) |
N92S |
probably benign |
Het |
| Crat |
C |
T |
2: 30,294,577 (GRCm39) |
R497Q |
probably benign |
Het |
| Cstf2t |
T |
C |
19: 31,060,593 (GRCm39) |
V43A |
possibly damaging |
Het |
| D930020B18Rik |
T |
C |
10: 121,525,739 (GRCm39) |
L547P |
probably damaging |
Het |
| Dennd1a |
G |
A |
2: 37,742,184 (GRCm39) |
|
probably null |
Het |
| Dtnb |
T |
A |
12: 3,694,272 (GRCm39) |
|
probably null |
Het |
| Entpd1 |
A |
G |
19: 40,727,309 (GRCm39) |
N486D |
possibly damaging |
Het |
| Fes |
G |
A |
7: 80,028,410 (GRCm39) |
R736C |
probably damaging |
Het |
| Galr1 |
T |
G |
18: 82,411,990 (GRCm39) |
Y292S |
probably damaging |
Het |
| Gda |
T |
A |
19: 21,405,988 (GRCm39) |
D80V |
probably damaging |
Het |
| Ghr |
A |
G |
15: 3,377,054 (GRCm39) |
C56R |
probably benign |
Het |
| Golgb1 |
A |
G |
16: 36,718,909 (GRCm39) |
T313A |
probably damaging |
Het |
| Gpaa1 |
A |
T |
15: 76,217,193 (GRCm39) |
D236V |
probably damaging |
Het |
| Gsdmc |
A |
G |
15: 63,676,315 (GRCm39) |
S43P |
probably benign |
Het |
| Gsdmd |
A |
G |
15: 75,738,202 (GRCm39) |
E295G |
probably damaging |
Het |
| Htatip2 |
A |
G |
7: 49,409,534 (GRCm39) |
K96R |
probably benign |
Het |
| Insm1 |
T |
A |
2: 146,064,711 (GRCm39) |
F176I |
probably benign |
Het |
| Itih1 |
T |
C |
14: 30,665,117 (GRCm39) |
E36G |
probably benign |
Het |
| Jak1 |
A |
G |
4: 101,032,379 (GRCm39) |
V409A |
probably damaging |
Het |
| Knl1 |
A |
G |
2: 118,901,073 (GRCm39) |
I925V |
possibly damaging |
Het |
| Lcmt2 |
A |
G |
2: 120,969,185 (GRCm39) |
S413P |
probably benign |
Het |
| Lmo7 |
T |
C |
14: 102,118,389 (GRCm39) |
S205P |
probably damaging |
Het |
| Lrch3 |
C |
A |
16: 32,807,113 (GRCm39) |
S462* |
probably null |
Het |
| Lrrtm2 |
T |
C |
18: 35,346,688 (GRCm39) |
I205V |
possibly damaging |
Het |
| Mark3 |
T |
G |
12: 111,600,223 (GRCm39) |
N479K |
probably damaging |
Het |
| Mrpl19 |
C |
T |
6: 81,942,793 (GRCm39) |
G39D |
possibly damaging |
Het |
| Msh4 |
A |
G |
3: 153,582,382 (GRCm39) |
Y497H |
probably benign |
Het |
| Msl2 |
T |
A |
9: 100,979,316 (GRCm39) |
D563E |
probably benign |
Het |
| Mta1 |
G |
A |
12: 113,095,088 (GRCm39) |
|
probably null |
Het |
| Nalcn |
T |
A |
14: 123,529,272 (GRCm39) |
Q1401L |
probably benign |
Het |
| Ncapg |
T |
C |
5: 45,853,135 (GRCm39) |
L867P |
probably benign |
Het |
| Nkapl |
T |
C |
13: 21,652,013 (GRCm39) |
D200G |
unknown |
Het |
| Nos1 |
A |
C |
5: 118,005,583 (GRCm39) |
E101A |
probably damaging |
Het |
| Npat |
T |
C |
9: 53,481,216 (GRCm39) |
S1008P |
probably damaging |
Het |
| Ntng1 |
A |
G |
3: 109,760,398 (GRCm39) |
I358T |
probably benign |
Het |
| Or11h6 |
A |
G |
14: 50,879,852 (GRCm39) |
E32G |
probably benign |
Het |
| Or13p4 |
C |
T |
4: 118,546,859 (GRCm39) |
M263I |
probably damaging |
Het |
| Or2d2b |
A |
G |
7: 106,705,274 (GRCm39) |
S265P |
probably benign |
Het |
| Or4b1 |
T |
A |
2: 89,980,188 (GRCm39) |
H54L |
probably benign |
Het |
| Or6c88 |
A |
G |
10: 129,406,493 (GRCm39) |
|
probably benign |
Het |
| Pex1 |
A |
G |
5: 3,680,222 (GRCm39) |
D948G |
probably damaging |
Het |
| Pkd1l2 |
A |
T |
8: 117,755,218 (GRCm39) |
I1660N |
possibly damaging |
Het |
| Pkp2 |
T |
A |
16: 16,079,537 (GRCm39) |
Y540N |
possibly damaging |
Het |
| Pkp4 |
T |
C |
2: 59,142,110 (GRCm39) |
L471P |
probably damaging |
Het |
| Plekhm3 |
A |
T |
1: 64,977,143 (GRCm39) |
M109K |
probably benign |
Het |
| Plekhn1 |
T |
C |
4: 156,318,418 (GRCm39) |
N68S |
probably benign |
Het |
| Pramel7 |
T |
A |
2: 87,321,189 (GRCm39) |
D282V |
possibly damaging |
Het |
| Rab3ip |
T |
C |
10: 116,773,546 (GRCm39) |
D89G |
possibly damaging |
Het |
| Rad17 |
G |
A |
13: 100,766,019 (GRCm39) |
Q370* |
probably null |
Het |
| Robo4 |
T |
C |
9: 37,322,277 (GRCm39) |
C751R |
probably benign |
Het |
| Sez6 |
A |
G |
11: 77,844,356 (GRCm39) |
T60A |
probably damaging |
Het |
| Socs4 |
A |
G |
14: 47,527,296 (GRCm39) |
H77R |
probably benign |
Het |
| Srrm3 |
T |
A |
5: 135,881,060 (GRCm39) |
M120K |
probably benign |
Het |
| Steap4 |
A |
T |
5: 8,028,453 (GRCm39) |
I344F |
probably benign |
Het |
| Stk36 |
T |
A |
1: 74,672,725 (GRCm39) |
F989Y |
probably damaging |
Het |
| Toporsl |
A |
T |
4: 52,612,108 (GRCm39) |
Q667L |
probably benign |
Het |
| Tspan17 |
T |
C |
13: 54,937,466 (GRCm39) |
F20S |
probably benign |
Het |
| Tubgcp3 |
G |
A |
8: 12,711,359 (GRCm39) |
Q65* |
probably null |
Het |
| Ush2a |
A |
T |
1: 188,465,726 (GRCm39) |
I2765F |
probably benign |
Het |
| Vwa8 |
A |
C |
14: 79,219,674 (GRCm39) |
|
probably null |
Het |
| Wdfy4 |
A |
G |
14: 32,800,264 (GRCm39) |
V1954A |
|
Het |
| Xrn2 |
T |
A |
2: 146,884,017 (GRCm39) |
|
probably null |
Het |
| Zfp687 |
C |
T |
3: 94,914,841 (GRCm39) |
R1220H |
probably damaging |
Het |
|
| Other mutations in Pxdn |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01024:Pxdn
|
APN |
12 |
30,037,098 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01152:Pxdn
|
APN |
12 |
30,051,936 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL01286:Pxdn
|
APN |
12 |
30,032,753 (GRCm39) |
missense |
probably benign |
0.04 |
|
IGL01323:Pxdn
|
APN |
12 |
30,037,136 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01338:Pxdn
|
APN |
12 |
30,052,796 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01341:Pxdn
|
APN |
12 |
30,052,486 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01401:Pxdn
|
APN |
12 |
30,051,983 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01580:Pxdn
|
APN |
12 |
30,034,492 (GRCm39) |
missense |
probably benign |
0.18 |
|
IGL01650:Pxdn
|
APN |
12 |
30,052,400 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL01679:Pxdn
|
APN |
12 |
30,049,901 (GRCm39) |
missense |
probably damaging |
0.97 |
|
IGL01866:Pxdn
|
APN |
12 |
30,034,570 (GRCm39) |
missense |
probably benign |
0.02 |
|
IGL02354:Pxdn
|
APN |
12 |
30,049,188 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02361:Pxdn
|
APN |
12 |
30,049,188 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02427:Pxdn
|
APN |
12 |
30,034,531 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02955:Pxdn
|
APN |
12 |
30,053,156 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03079:Pxdn
|
APN |
12 |
30,052,997 (GRCm39) |
missense |
probably damaging |
0.97 |
|
IGL03111:Pxdn
|
APN |
12 |
30,032,755 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02988:Pxdn
|
UTSW |
12 |
30,053,113 (GRCm39) |
nonsense |
probably null |
|
|
PIT4280001:Pxdn
|
UTSW |
12 |
30,045,327 (GRCm39) |
missense |
probably damaging |
0.99 |
|
PIT4469001:Pxdn
|
UTSW |
12 |
30,055,828 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0070:Pxdn
|
UTSW |
12 |
30,032,726 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0070:Pxdn
|
UTSW |
12 |
30,032,726 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0086:Pxdn
|
UTSW |
12 |
30,052,418 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R0140:Pxdn
|
UTSW |
12 |
30,032,753 (GRCm39) |
missense |
probably benign |
0.04 |
|
R0201:Pxdn
|
UTSW |
12 |
30,052,430 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
R0282:Pxdn
|
UTSW |
12 |
30,034,439 (GRCm39) |
nonsense |
probably null |
|
|
R0310:Pxdn
|
UTSW |
12 |
30,065,528 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0426:Pxdn
|
UTSW |
12 |
30,037,065 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R0468:Pxdn
|
UTSW |
12 |
30,044,485 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0825:Pxdn
|
UTSW |
12 |
30,034,995 (GRCm39) |
splice site |
probably benign |
|
|
R0885:Pxdn
|
UTSW |
12 |
30,053,401 (GRCm39) |
missense |
probably benign |
0.30 |
|
R1420:Pxdn
|
UTSW |
12 |
30,052,067 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1588:Pxdn
|
UTSW |
12 |
30,052,558 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2269:Pxdn
|
UTSW |
12 |
30,055,774 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R2280:Pxdn
|
UTSW |
12 |
30,034,905 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2504:Pxdn
|
UTSW |
12 |
30,053,405 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2679:Pxdn
|
UTSW |
12 |
30,025,568 (GRCm39) |
splice site |
probably benign |
|
|
R3116:Pxdn
|
UTSW |
12 |
30,052,306 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R3607:Pxdn
|
UTSW |
12 |
30,040,917 (GRCm39) |
missense |
probably benign |
0.04 |
|
R4033:Pxdn
|
UTSW |
12 |
30,053,224 (GRCm39) |
missense |
probably benign |
0.19 |
|
R4576:Pxdn
|
UTSW |
12 |
30,061,922 (GRCm39) |
missense |
probably benign |
|
|
R4659:Pxdn
|
UTSW |
12 |
30,044,552 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4681:Pxdn
|
UTSW |
12 |
30,062,325 (GRCm39) |
missense |
probably benign |
0.45 |
|
R4968:Pxdn
|
UTSW |
12 |
30,050,011 (GRCm39) |
missense |
probably benign |
0.25 |
|
R5032:Pxdn
|
UTSW |
12 |
30,053,140 (GRCm39) |
missense |
probably benign |
0.08 |
|
R5232:Pxdn
|
UTSW |
12 |
30,040,987 (GRCm39) |
missense |
probably benign |
0.08 |
|
R5366:Pxdn
|
UTSW |
12 |
30,052,899 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5504:Pxdn
|
UTSW |
12 |
30,052,800 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5586:Pxdn
|
UTSW |
12 |
30,053,141 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5739:Pxdn
|
UTSW |
12 |
30,032,333 (GRCm39) |
missense |
probably benign |
0.03 |
|
R5877:Pxdn
|
UTSW |
12 |
30,053,045 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6167:Pxdn
|
UTSW |
12 |
30,024,000 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6191:Pxdn
|
UTSW |
12 |
30,032,716 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R6200:Pxdn
|
UTSW |
12 |
30,053,111 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6609:Pxdn
|
UTSW |
12 |
30,052,940 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6628:Pxdn
|
UTSW |
12 |
30,049,917 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6865:Pxdn
|
UTSW |
12 |
30,064,582 (GRCm39) |
splice site |
probably null |
|
|
R6921:Pxdn
|
UTSW |
12 |
30,065,504 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6995:Pxdn
|
UTSW |
12 |
30,045,370 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R7211:Pxdn
|
UTSW |
12 |
30,034,903 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R7220:Pxdn
|
UTSW |
12 |
30,044,479 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7347:Pxdn
|
UTSW |
12 |
30,062,260 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7402:Pxdn
|
UTSW |
12 |
30,052,438 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7413:Pxdn
|
UTSW |
12 |
30,052,927 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7447:Pxdn
|
UTSW |
12 |
30,034,926 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7572:Pxdn
|
UTSW |
12 |
30,056,704 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7708:Pxdn
|
UTSW |
12 |
30,056,601 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7815:Pxdn
|
UTSW |
12 |
30,055,824 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R7972:Pxdn
|
UTSW |
12 |
30,056,601 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8097:Pxdn
|
UTSW |
12 |
30,056,601 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8098:Pxdn
|
UTSW |
12 |
30,056,601 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8205:Pxdn
|
UTSW |
12 |
30,056,566 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8262:Pxdn
|
UTSW |
12 |
30,049,195 (GRCm39) |
nonsense |
probably null |
|
|
R8335:Pxdn
|
UTSW |
12 |
30,052,096 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8356:Pxdn
|
UTSW |
12 |
30,061,889 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8437:Pxdn
|
UTSW |
12 |
30,052,043 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8456:Pxdn
|
UTSW |
12 |
30,061,889 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8709:Pxdn
|
UTSW |
12 |
30,056,601 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8772:Pxdn
|
UTSW |
12 |
30,065,463 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8903:Pxdn
|
UTSW |
12 |
30,040,992 (GRCm39) |
missense |
probably benign |
|
|
R9310:Pxdn
|
UTSW |
12 |
30,052,051 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9487:Pxdn
|
UTSW |
12 |
30,044,552 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
Z1177:Pxdn
|
UTSW |
12 |
30,040,851 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTGTAATCCAGCCGCAGAAC -3'
(R):5'- GGACAGCTCCTGAAATTGTTCTC -3'
Sequencing Primer
(F):5'- GCCGCAGAACACAGAGGTAC -3'
(R):5'- CATGGACATGTTCTCAGAAGCATGC -3'
|
| Posted On |
2019-10-07 |
Incidental Mutation