Incidental Mutation 'R1631:Plod3'
| ID |
172785 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Plod3
|
| Ensembl Gene |
ENSMUSG00000004846 |
| Gene Name |
procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 |
| Synonyms |
LH3, lysyl hydroxylase 3 |
| MMRRC Submission |
039668-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1631 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
5 |
| Chromosomal Location |
137015873-137025500 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 137017847 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Tryptophan
at position 208
(R208W)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000004968
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004968]
[ENSMUST00000034953]
[ENSMUST00000085941]
[ENSMUST00000111090]
[ENSMUST00000111091]
[ENSMUST00000137272]
[ENSMUST00000156963]
|
| AlphaFold |
Q9R0E1 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000004968
AA Change: R208W
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
AA Change: R208W
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
low complexity region
|
312 |
324 |
N/A |
INTRINSIC |
|
Blast:P4Hc
|
456 |
502 |
2e-8 |
BLAST |
|
P4Hc
|
567 |
740 |
1.43e-23 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000034953
|
| SMART Domains |
Protein: ENSMUSP00000034953
Gene: ENSMUSG00000059518
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
14 |
26 |
N/A |
INTRINSIC |
|
low complexity region
|
58 |
73 |
N/A |
INTRINSIC |
|
Pfam:zf-HIT
|
112 |
141 |
6.3e-13 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000085941
|
| SMART Domains |
Protein: ENSMUSP00000083103
Gene: ENSMUSG00000059518
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
15 |
27 |
N/A |
INTRINSIC |
|
low complexity region
|
59 |
74 |
N/A |
INTRINSIC |
|
Pfam:zf-HIT
|
113 |
142 |
3e-13 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000102285
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111090
|
| SMART Domains |
Protein: ENSMUSP00000106719
Gene: ENSMUSG00000059518
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
14 |
26 |
N/A |
INTRINSIC |
|
low complexity region
|
58 |
73 |
N/A |
INTRINSIC |
|
Pfam:zf-HIT
|
112 |
141 |
2.2e-14 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111091
|
| SMART Domains |
Protein: ENSMUSP00000106720
Gene: ENSMUSG00000059518
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
19 |
31 |
N/A |
INTRINSIC |
|
low complexity region
|
63 |
78 |
N/A |
INTRINSIC |
|
Pfam:zf-HIT
|
117 |
146 |
2.1e-13 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000127100
|
| SMART Domains |
Protein: ENSMUSP00000123550
Gene: ENSMUSG00000004846
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:P4Hc
|
2 |
35 |
2e-11 |
BLAST |
|
P4Hc
|
38 |
200 |
3.04e-4 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129896
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144784
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151642
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137419
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000137272
|
| SMART Domains |
Protein: ENSMUSP00000120331
Gene: ENSMUSG00000059518
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
19 |
31 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000156963
|
| SMART Domains |
Protein: ENSMUSP00000115929
Gene: ENSMUSG00000059518
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
14 |
26 |
N/A |
INTRINSIC |
|
low complexity region
|
58 |
73 |
N/A |
INTRINSIC |
|
Pfam:zf-HIT
|
112 |
141 |
6.7e-13 |
PFAM |
|
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.4%
- 20x: 93.0%
|
| Validation Efficiency |
|
| 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 a membrane-bound homodimeric enzyme that is localized to the cisternae of the rough endoplasmic reticulum. The enzyme (cofactors iron and ascorbate) catalyzes the hydroxylation of lysyl residues in collagen-like peptides. The resultant hydroxylysyl groups are attachment sites for carbohydrates in collagen and thus are critical for the stability of intermolecular crosslinks. Some patients with Ehlers-Danlos syndrome type VIB have deficiencies in lysyl hydroxylase activity. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous null mice display embryonic lethality, reduced embryonic growth, fragility, and fragmented basement membranes. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adamts10 |
T |
A |
17: 33,756,316 (GRCm39) |
S320T |
probably benign |
Het |
| Alkbh2 |
C |
T |
5: 114,262,287 (GRCm39) |
E148K |
probably damaging |
Het |
| Als2 |
T |
C |
1: 59,257,226 (GRCm39) |
E12G |
probably benign |
Het |
| Arhgef10 |
A |
T |
8: 14,997,157 (GRCm39) |
D321V |
probably damaging |
Het |
| Atp8a1 |
T |
G |
5: 67,906,395 (GRCm39) |
|
probably null |
Het |
| Avil |
A |
G |
10: 126,846,494 (GRCm39) |
|
probably null |
Het |
| C2cd3 |
G |
A |
7: 100,021,704 (GRCm39) |
|
probably null |
Het |
| Cdhr18 |
C |
T |
14: 13,829,796 (GRCm38) |
E649K |
probably damaging |
Het |
| Col18a1 |
G |
A |
10: 76,895,131 (GRCm39) |
P1177S |
probably damaging |
Het |
| Copb2 |
T |
A |
9: 98,462,213 (GRCm39) |
F428L |
probably benign |
Het |
| Cpa1 |
A |
G |
6: 30,640,923 (GRCm39) |
E138G |
probably damaging |
Het |
| Ctsm |
T |
C |
13: 61,686,249 (GRCm39) |
I12V |
possibly damaging |
Het |
| Dctn1 |
A |
G |
6: 83,174,578 (GRCm39) |
Q967R |
possibly damaging |
Het |
| Dok2 |
T |
C |
14: 71,014,393 (GRCm39) |
Y194H |
probably damaging |
Het |
| Ezh2 |
C |
T |
6: 47,554,592 (GRCm39) |
M1I |
probably null |
Het |
| Fkbp8 |
T |
A |
8: 70,984,282 (GRCm39) |
L210Q |
probably damaging |
Het |
| Fpr1 |
T |
A |
17: 18,097,263 (GRCm39) |
Q242L |
probably benign |
Het |
| Gal3st2b |
T |
A |
1: 93,868,505 (GRCm39) |
D243E |
probably damaging |
Het |
| Gm5422 |
A |
G |
10: 31,125,802 (GRCm39) |
|
noncoding transcript |
Het |
| Gucy1a2 |
A |
G |
9: 3,533,052 (GRCm39) |
N84D |
probably damaging |
Het |
| Hsd3b5 |
A |
C |
3: 98,529,393 (GRCm39) |
V79G |
probably damaging |
Het |
| Htr6 |
A |
T |
4: 138,788,804 (GRCm39) |
V417E |
probably benign |
Het |
| Ifnar2 |
G |
A |
16: 91,188,755 (GRCm39) |
V79I |
probably benign |
Het |
| Ighv10-1 |
T |
C |
12: 114,443,102 (GRCm39) |
|
probably benign |
Het |
| Itpr2 |
A |
G |
6: 146,081,788 (GRCm39) |
F182L |
probably damaging |
Het |
| Kirrel1 |
C |
T |
3: 86,996,458 (GRCm39) |
M380I |
probably null |
Het |
| Lama3 |
A |
G |
18: 12,540,551 (GRCm39) |
Y285C |
probably damaging |
Het |
| Lamc2 |
C |
A |
1: 153,034,680 (GRCm39) |
V108L |
possibly damaging |
Het |
| Lrrc14b |
A |
G |
13: 74,509,373 (GRCm39) |
|
probably null |
Het |
| Magi3 |
T |
C |
3: 103,958,493 (GRCm39) |
T531A |
probably benign |
Het |
| Mapre2 |
A |
G |
18: 23,966,011 (GRCm39) |
Y32C |
probably damaging |
Het |
| Med1 |
C |
T |
11: 98,046,452 (GRCm39) |
|
probably benign |
Het |
| Mslnl |
G |
A |
17: 25,961,908 (GRCm39) |
V128M |
probably damaging |
Het |
| Nt5el |
C |
A |
13: 105,218,749 (GRCm39) |
Q28K |
probably benign |
Het |
| Or10a3b |
A |
C |
7: 108,445,064 (GRCm39) |
L51R |
probably damaging |
Het |
| Or51h1 |
A |
G |
7: 102,308,408 (GRCm39) |
I127V |
probably damaging |
Het |
| Or5h23 |
G |
A |
16: 58,906,408 (GRCm39) |
T146I |
probably benign |
Het |
| Or7a35 |
A |
T |
10: 78,853,239 (GRCm39) |
I28L |
probably benign |
Het |
| Pde1b |
A |
G |
15: 103,430,099 (GRCm39) |
T143A |
probably damaging |
Het |
| Pkhd1 |
T |
C |
1: 20,593,121 (GRCm39) |
D1664G |
probably benign |
Het |
| Pstk |
G |
A |
7: 130,986,271 (GRCm39) |
A277T |
possibly damaging |
Het |
| Qrich1 |
T |
C |
9: 108,411,684 (GRCm39) |
V403A |
probably damaging |
Het |
| Rad21 |
C |
A |
15: 51,833,436 (GRCm39) |
V348F |
probably damaging |
Het |
| Sacs |
T |
A |
14: 61,448,181 (GRCm39) |
L3409* |
probably null |
Het |
| Setd4 |
T |
A |
16: 93,390,136 (GRCm39) |
K98* |
probably null |
Het |
| Skint5 |
A |
G |
4: 113,341,123 (GRCm39) |
V1385A |
probably benign |
Het |
| Stam |
C |
A |
2: 14,151,059 (GRCm39) |
S472* |
probably null |
Het |
| Stx2 |
A |
G |
5: 129,069,289 (GRCm39) |
F141L |
probably damaging |
Het |
| Tia1 |
A |
G |
6: 86,397,330 (GRCm39) |
D101G |
probably damaging |
Het |
| Ttc21a |
T |
A |
9: 119,783,228 (GRCm39) |
|
probably null |
Het |
| Usp34 |
T |
A |
11: 23,410,651 (GRCm39) |
N2700K |
probably damaging |
Het |
|
| Other mutations in Plod3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00507:Plod3
|
APN |
5 |
137,025,030 (GRCm39) |
missense |
possibly damaging |
0.78 |
|
IGL01090:Plod3
|
APN |
5 |
137,019,090 (GRCm39) |
missense |
probably benign |
0.37 |
|
IGL01443:Plod3
|
APN |
5 |
137,019,075 (GRCm39) |
missense |
probably benign |
0.17 |
|
IGL01583:Plod3
|
APN |
5 |
137,025,002 (GRCm39) |
missense |
probably benign |
0.02 |
|
R0544:Plod3
|
UTSW |
5 |
137,020,465 (GRCm39) |
missense |
probably benign |
0.09 |
|
R0747:Plod3
|
UTSW |
5 |
137,017,049 (GRCm39) |
missense |
probably benign |
0.34 |
|
R0764:Plod3
|
UTSW |
5 |
137,018,437 (GRCm39) |
unclassified |
probably benign |
|
|
R1520:Plod3
|
UTSW |
5 |
137,020,165 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1751:Plod3
|
UTSW |
5 |
137,019,030 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R1767:Plod3
|
UTSW |
5 |
137,019,030 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R1984:Plod3
|
UTSW |
5 |
137,019,707 (GRCm39) |
splice site |
probably null |
|
|
R1985:Plod3
|
UTSW |
5 |
137,019,707 (GRCm39) |
splice site |
probably null |
|
|
R2137:Plod3
|
UTSW |
5 |
137,017,571 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2148:Plod3
|
UTSW |
5 |
137,016,627 (GRCm39) |
nonsense |
probably null |
|
|
R2179:Plod3
|
UTSW |
5 |
137,019,862 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R2318:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R2319:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R2512:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R2513:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R2696:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R2891:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R2893:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R3030:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R3439:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R3957:Plod3
|
UTSW |
5 |
137,023,046 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4080:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R4081:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R4342:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R4344:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R4345:Plod3
|
UTSW |
5 |
137,017,000 (GRCm39) |
missense |
probably benign |
0.38 |
|
R4546:Plod3
|
UTSW |
5 |
137,017,801 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R4799:Plod3
|
UTSW |
5 |
137,019,654 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4843:Plod3
|
UTSW |
5 |
137,019,854 (GRCm39) |
nonsense |
probably null |
|
|
R4956:Plod3
|
UTSW |
5 |
137,018,772 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5159:Plod3
|
UTSW |
5 |
137,023,932 (GRCm39) |
intron |
probably benign |
|
|
R5162:Plod3
|
UTSW |
5 |
137,020,161 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5328:Plod3
|
UTSW |
5 |
137,018,537 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5427:Plod3
|
UTSW |
5 |
137,020,642 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6627:Plod3
|
UTSW |
5 |
137,017,310 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7003:Plod3
|
UTSW |
5 |
137,018,498 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7132:Plod3
|
UTSW |
5 |
137,023,971 (GRCm39) |
missense |
|
|
|
R7376:Plod3
|
UTSW |
5 |
137,019,335 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7404:Plod3
|
UTSW |
5 |
137,023,901 (GRCm39) |
missense |
probably benign |
|
|
R7827:Plod3
|
UTSW |
5 |
137,018,835 (GRCm39) |
missense |
probably benign |
|
|
R8062:Plod3
|
UTSW |
5 |
137,019,123 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R8506:Plod3
|
UTSW |
5 |
137,017,830 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8772:Plod3
|
UTSW |
5 |
137,017,773 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9108:Plod3
|
UTSW |
5 |
137,018,017 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9439:Plod3
|
UTSW |
5 |
137,023,036 (GRCm39) |
missense |
probably benign |
0.03 |
|
R9788:Plod3
|
UTSW |
5 |
137,019,911 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGTTCCCAAGACAGACTTGTCCCC -3'
(R):5'- TGGCAGGAACCCATCCCTCATTAC -3'
Sequencing Primer
(F):5'- AGTGGAGCGGGCATTGC -3'
(R):5'- CCATTGAGGTTCTGAAAGATCCG -3'
|
| Posted On |
2014-04-24 |
Incidental Mutation