Incidental Mutation 'R1767:Plod3'
ID |
194464 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Plod3
|
Ensembl Gene |
ENSMUSG00000004846 |
Gene Name |
procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 |
Synonyms |
LH3, lysyl hydroxylase 3 |
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R1767 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
5 |
Chromosomal Location |
137015873-137025500 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 137019030 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Glutamic Acid
at position 305
(V305E)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000004968
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004968]
[ENSMUST00000034953]
[ENSMUST00000085941]
[ENSMUST00000111090]
[ENSMUST00000111091]
[ENSMUST00000156963]
[ENSMUST00000137272]
|
AlphaFold |
Q9R0E1 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000004968
AA Change: V305E
PolyPhen 2
Score 0.893 (Sensitivity: 0.82; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000004968 Gene: ENSMUSG00000004846 AA Change: V305E
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 |
noncoding transcript
Transcript: ENSMUST00000144784
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129896
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151642
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137419
|
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 |
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 |
|
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 |
|
Coding Region Coverage |
- 1x: 97.5%
- 3x: 96.9%
- 10x: 95.4%
- 20x: 92.8%
|
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: 80 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1110065P20Rik |
T |
C |
4: 124,743,754 (GRCm39) |
N128S |
possibly damaging |
Het |
Adam26b |
T |
A |
8: 43,972,948 (GRCm39) |
I685F |
probably benign |
Het |
Adgrf5 |
A |
T |
17: 43,761,455 (GRCm39) |
Y1050F |
possibly damaging |
Het |
Alcam |
A |
T |
16: 52,091,077 (GRCm39) |
N480K |
probably damaging |
Het |
Alk |
T |
A |
17: 72,207,693 (GRCm39) |
H1014L |
possibly damaging |
Het |
Arhgef2 |
A |
G |
3: 88,551,260 (GRCm39) |
Q778R |
probably damaging |
Het |
Arhgef6 |
T |
C |
X: 56,383,922 (GRCm39) |
M5V |
probably benign |
Het |
Ascc3 |
T |
A |
10: 50,594,472 (GRCm39) |
I1189N |
probably damaging |
Het |
AU040320 |
G |
A |
4: 126,734,517 (GRCm39) |
G713D |
probably damaging |
Het |
Bmpr1a |
A |
G |
14: 34,169,727 (GRCm39) |
|
probably null |
Het |
Bpifa6 |
A |
G |
2: 153,829,147 (GRCm39) |
T225A |
possibly damaging |
Het |
Cacna1g |
T |
C |
11: 94,350,628 (GRCm39) |
S406G |
probably benign |
Het |
Ccdc198 |
G |
A |
14: 49,473,341 (GRCm39) |
T128I |
probably benign |
Het |
Ccdc40 |
T |
A |
11: 119,121,522 (GRCm39) |
|
probably null |
Het |
Cckbr |
A |
T |
7: 105,083,758 (GRCm39) |
I229F |
possibly damaging |
Het |
Cers3 |
A |
G |
7: 66,433,151 (GRCm39) |
K156R |
probably damaging |
Het |
Chd1 |
T |
A |
17: 15,990,565 (GRCm39) |
W1706R |
probably damaging |
Het |
Col11a2 |
T |
A |
17: 34,282,869 (GRCm39) |
|
probably benign |
Het |
Coq10b |
A |
G |
1: 55,100,513 (GRCm39) |
R66G |
probably damaging |
Het |
Cpn2 |
A |
T |
16: 30,078,485 (GRCm39) |
Y405* |
probably null |
Het |
Dis3 |
A |
T |
14: 99,321,578 (GRCm39) |
Y590N |
probably damaging |
Het |
Dpy19l1 |
T |
C |
9: 24,373,880 (GRCm39) |
H270R |
probably benign |
Het |
Dync1h1 |
G |
A |
12: 110,602,943 (GRCm39) |
E2195K |
probably benign |
Het |
Ephx1 |
C |
T |
1: 180,822,242 (GRCm39) |
G101S |
probably damaging |
Het |
Flg |
A |
T |
3: 93,187,220 (GRCm39) |
Y224F |
possibly damaging |
Het |
Focad |
G |
T |
4: 88,275,705 (GRCm39) |
V1105L |
unknown |
Het |
Fzd1 |
A |
G |
5: 4,806,812 (GRCm39) |
Y257H |
probably benign |
Het |
Gm11116 |
T |
C |
5: 88,259,311 (GRCm39) |
|
probably benign |
Het |
Gm11938 |
G |
A |
11: 99,494,071 (GRCm39) |
S8F |
unknown |
Het |
Grin3a |
A |
T |
4: 49,844,423 (GRCm39) |
V220E |
probably damaging |
Het |
Gstt2 |
T |
C |
10: 75,670,098 (GRCm39) |
D8G |
probably damaging |
Het |
Gtf3c3 |
C |
T |
1: 54,456,937 (GRCm39) |
A488T |
probably damaging |
Het |
Hook3 |
A |
G |
8: 26,561,084 (GRCm39) |
|
probably null |
Het |
Itpr2 |
T |
C |
6: 146,251,566 (GRCm39) |
D993G |
possibly damaging |
Het |
Jhy |
T |
C |
9: 40,872,444 (GRCm39) |
R22G |
probably benign |
Het |
Krt13 |
A |
C |
11: 100,011,926 (GRCm39) |
H132Q |
possibly damaging |
Het |
Krtap27-1 |
G |
A |
16: 88,468,199 (GRCm39) |
S115L |
probably damaging |
Het |
L1td1 |
T |
C |
4: 98,625,686 (GRCm39) |
V627A |
probably benign |
Het |
Lrrn4cl |
A |
G |
19: 8,829,135 (GRCm39) |
T38A |
probably benign |
Het |
Ly96 |
A |
G |
1: 16,776,399 (GRCm39) |
T112A |
probably benign |
Het |
Meltf |
G |
T |
16: 31,702,747 (GRCm39) |
C158F |
probably damaging |
Het |
Mycbp2 |
A |
T |
14: 103,485,841 (GRCm39) |
H1040Q |
probably damaging |
Het |
Npas4 |
G |
A |
19: 5,038,211 (GRCm39) |
P199L |
probably benign |
Het |
Or12j3 |
T |
C |
7: 139,953,389 (GRCm39) |
I45V |
possibly damaging |
Het |
Or52r1 |
T |
A |
7: 102,536,833 (GRCm39) |
I176F |
probably damaging |
Het |
Or8k3b |
A |
G |
2: 86,520,728 (GRCm39) |
M197T |
probably benign |
Het |
Pcdh10 |
A |
T |
3: 45,338,612 (GRCm39) |
H923L |
probably damaging |
Het |
Pias3 |
T |
C |
3: 96,608,719 (GRCm39) |
S228P |
probably damaging |
Het |
Pign |
A |
G |
1: 105,580,917 (GRCm39) |
V154A |
probably benign |
Het |
Prkra |
G |
T |
2: 76,477,584 (GRCm39) |
H40Q |
possibly damaging |
Het |
Prss22 |
T |
A |
17: 24,215,331 (GRCm39) |
E148D |
probably benign |
Het |
Psg17 |
A |
G |
7: 18,550,727 (GRCm39) |
V376A |
possibly damaging |
Het |
Retnlg |
A |
T |
16: 48,693,991 (GRCm39) |
D49V |
possibly damaging |
Het |
Rnf26rt |
A |
T |
6: 76,474,588 (GRCm39) |
N9K |
unknown |
Het |
Rtp1 |
A |
G |
16: 23,250,124 (GRCm39) |
E163G |
probably damaging |
Het |
Slc6a20a |
T |
A |
9: 123,466,165 (GRCm39) |
I522F |
probably damaging |
Het |
Slco5a1 |
T |
C |
1: 13,059,839 (GRCm39) |
D294G |
probably damaging |
Het |
Slco6d1 |
A |
G |
1: 98,418,274 (GRCm39) |
T487A |
possibly damaging |
Het |
Smarcc2 |
A |
T |
10: 128,304,951 (GRCm39) |
D262V |
possibly damaging |
Het |
Sned1 |
G |
A |
1: 93,209,376 (GRCm39) |
V830M |
possibly damaging |
Het |
Ssbp3 |
G |
T |
4: 106,904,612 (GRCm39) |
D336Y |
probably damaging |
Het |
Sun2 |
A |
G |
15: 79,609,758 (GRCm39) |
S694P |
probably benign |
Het |
Tdp1 |
G |
A |
12: 99,857,602 (GRCm39) |
|
probably null |
Het |
Tfap2a |
A |
T |
13: 40,878,613 (GRCm39) |
I204N |
probably damaging |
Het |
Tfip11 |
T |
A |
5: 112,482,298 (GRCm39) |
W519R |
probably damaging |
Het |
Tie1 |
T |
C |
4: 118,333,373 (GRCm39) |
E831G |
possibly damaging |
Het |
Tjp1 |
A |
G |
7: 64,962,301 (GRCm39) |
|
probably null |
Het |
Tln2 |
C |
T |
9: 67,193,796 (GRCm39) |
A1773T |
probably benign |
Het |
Tmem39b |
A |
C |
4: 129,586,976 (GRCm39) |
I78M |
possibly damaging |
Het |
Trank1 |
T |
C |
9: 111,220,547 (GRCm39) |
V2428A |
probably benign |
Het |
Trim35 |
A |
G |
14: 66,541,617 (GRCm39) |
E247G |
probably damaging |
Het |
Tsc22d1 |
T |
C |
14: 76,655,542 (GRCm39) |
S674P |
probably damaging |
Het |
Tsn |
A |
T |
1: 118,228,618 (GRCm39) |
D201E |
probably damaging |
Het |
Usp42 |
A |
T |
5: 143,700,621 (GRCm39) |
V1134E |
possibly damaging |
Het |
Uvrag |
A |
G |
7: 98,748,601 (GRCm39) |
I117T |
probably damaging |
Het |
Vmn1r192 |
A |
G |
13: 22,371,441 (GRCm39) |
S260P |
probably benign |
Het |
Vmn2r110 |
C |
T |
17: 20,800,840 (GRCm39) |
A531T |
possibly damaging |
Het |
Wdsub1 |
A |
T |
2: 59,689,058 (GRCm39) |
I388N |
probably damaging |
Het |
Wnt10b |
A |
T |
15: 98,670,556 (GRCm39) |
L228Q |
probably damaging |
Het |
Zbtb34 |
A |
C |
2: 33,301,348 (GRCm39) |
S398A |
possibly 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 |
R1631:Plod3
|
UTSW |
5 |
137,017,847 (GRCm39) |
missense |
probably damaging |
1.00 |
R1751: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'- ATTCTGCAACCAGACCCTGAGGAC -3'
(R):5'- TCGTGGTACACCTCCTGAAGATGG -3'
Sequencing Primer
(F):5'- GACCCTGAGGACACTCCC -3'
(R):5'- GGGATACACTGACGGTCTG -3'
|
Posted On |
2014-05-23 |