Incidental Mutation 'R1985:Plod3'
| ID |
220439 |
| 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 |
039997-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1985 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
137015873-137025500 bp(+) (GRCm39) |
| Type of Mutation |
splice site (4 bp from exon) |
| DNA Base Change (assembly) |
A to G
at 137019707 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| 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 null
Transcript: ENSMUST00000004968
|
| SMART Domains |
Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
| 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: ENSMUST00000144784
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151642
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129896
|
| 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 |
|
| Meta Mutation Damage Score |
0.9755 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.2%
|
| Validation Efficiency |
94% (76/81) |
| 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 |
|---|
| Abhd8 |
C |
A |
8: 71,916,157 (GRCm39) |
|
probably benign |
Het |
| Adam5 |
A |
T |
8: 25,236,755 (GRCm39) |
D648E |
probably benign |
Het |
| Akr1d1 |
A |
G |
6: 37,535,336 (GRCm39) |
D240G |
probably damaging |
Het |
| Ankmy2 |
A |
G |
12: 36,207,363 (GRCm39) |
H3R |
possibly damaging |
Het |
| Anpep |
A |
C |
7: 79,490,605 (GRCm39) |
|
probably null |
Het |
| Apobr |
A |
G |
7: 126,186,903 (GRCm39) |
T20A |
possibly damaging |
Het |
| Atp2a2 |
A |
T |
5: 122,604,899 (GRCm39) |
Y427N |
probably benign |
Het |
| Camkk2 |
A |
C |
5: 122,902,190 (GRCm39) |
S40A |
possibly damaging |
Het |
| Camp |
T |
C |
9: 109,677,497 (GRCm39) |
N112S |
probably benign |
Het |
| Cbx7 |
A |
G |
15: 79,802,591 (GRCm39) |
S229P |
probably damaging |
Het |
| Cnot2 |
T |
C |
10: 116,363,781 (GRCm39) |
N41S |
probably damaging |
Het |
| Dchs1 |
A |
G |
7: 105,421,605 (GRCm39) |
F272L |
possibly damaging |
Het |
| Dct |
T |
C |
14: 118,273,954 (GRCm39) |
K318E |
probably benign |
Het |
| Dhrs11 |
A |
C |
11: 84,719,633 (GRCm39) |
L31V |
probably damaging |
Het |
| Dnah7a |
T |
C |
1: 53,543,093 (GRCm39) |
D2359G |
probably benign |
Het |
| Dnajc7 |
A |
G |
11: 100,481,718 (GRCm39) |
S305P |
probably benign |
Het |
| Dscc1 |
CTGAATGAAT |
CTGAAT |
15: 54,943,572 (GRCm39) |
|
probably benign |
Het |
| Flnc |
A |
G |
6: 29,444,415 (GRCm39) |
|
probably benign |
Het |
| Garin3 |
T |
C |
11: 46,298,693 (GRCm39) |
*666Q |
probably null |
Het |
| Gm7535 |
A |
G |
17: 18,131,800 (GRCm39) |
|
probably benign |
Het |
| Grtp1 |
A |
G |
8: 13,229,376 (GRCm39) |
F313L |
probably damaging |
Het |
| Haus6 |
T |
C |
4: 86,511,846 (GRCm39) |
Y425C |
possibly damaging |
Het |
| Hdac1 |
T |
A |
4: 129,422,753 (GRCm39) |
N83Y |
possibly damaging |
Het |
| Hdlbp |
A |
G |
1: 93,358,840 (GRCm39) |
I237T |
probably damaging |
Het |
| Hfm1 |
A |
T |
5: 107,046,442 (GRCm39) |
D481E |
probably damaging |
Het |
| Hipk3 |
T |
C |
2: 104,264,780 (GRCm39) |
I737V |
probably benign |
Het |
| Il23r |
T |
A |
6: 67,467,652 (GRCm39) |
|
probably null |
Het |
| Il24 |
G |
A |
1: 130,810,268 (GRCm39) |
T196I |
probably benign |
Het |
| Ints3 |
C |
T |
3: 90,307,610 (GRCm39) |
|
probably null |
Het |
| Kcna6 |
T |
C |
6: 126,715,473 (GRCm39) |
E472G |
probably benign |
Het |
| Kcnj16 |
C |
T |
11: 110,916,409 (GRCm39) |
T357M |
probably benign |
Het |
| Kdm4b |
T |
A |
17: 56,708,302 (GRCm39) |
V957E |
probably damaging |
Het |
| Kif21b |
G |
A |
1: 136,075,284 (GRCm39) |
D166N |
probably damaging |
Het |
| Klhl11 |
G |
T |
11: 100,354,070 (GRCm39) |
Q584K |
probably benign |
Het |
| Krt9 |
A |
T |
11: 100,080,817 (GRCm39) |
M345K |
probably benign |
Het |
| Lgr5 |
T |
C |
10: 115,331,150 (GRCm39) |
|
probably benign |
Het |
| Lilrb4b |
A |
T |
10: 51,357,831 (GRCm39) |
Q80L |
possibly damaging |
Het |
| Lrrc69 |
T |
C |
4: 14,708,669 (GRCm39) |
E225G |
possibly damaging |
Het |
| Ly9 |
A |
G |
1: 171,427,341 (GRCm39) |
S405P |
probably damaging |
Het |
| Myh2 |
A |
G |
11: 67,071,740 (GRCm39) |
D519G |
possibly damaging |
Het |
| Nav3 |
G |
A |
10: 109,606,045 (GRCm39) |
|
probably benign |
Het |
| Nfkb1 |
G |
A |
3: 135,321,110 (GRCm39) |
T215I |
possibly damaging |
Het |
| Ninj2 |
A |
T |
6: 120,175,600 (GRCm39) |
|
probably benign |
Het |
| Obsl1 |
A |
G |
1: 75,482,244 (GRCm39) |
C209R |
probably damaging |
Het |
| Or13a25 |
G |
A |
7: 140,247,734 (GRCm39) |
C171Y |
probably damaging |
Het |
| Or2d4 |
A |
G |
7: 106,544,133 (GRCm39) |
I25T |
probably benign |
Het |
| Or2j6 |
A |
T |
7: 139,980,713 (GRCm39) |
M82K |
possibly damaging |
Het |
| Or2t44 |
A |
C |
11: 58,677,210 (GRCm39) |
D50A |
probably damaging |
Het |
| Or2y1g |
T |
C |
11: 49,171,110 (GRCm39) |
I45T |
probably damaging |
Het |
| Or52z14 |
A |
T |
7: 103,252,879 (GRCm39) |
Y6F |
probably benign |
Het |
| Otud4 |
G |
C |
8: 80,366,641 (GRCm39) |
R36P |
probably damaging |
Het |
| Pcnt |
C |
T |
10: 76,216,171 (GRCm39) |
R2239H |
possibly damaging |
Het |
| Pgbd5 |
T |
A |
8: 125,097,331 (GRCm39) |
M491L |
probably benign |
Het |
| Pitrm1 |
A |
T |
13: 6,608,220 (GRCm39) |
D316V |
probably damaging |
Het |
| Plppr3 |
A |
T |
10: 79,703,294 (GRCm39) |
Y63* |
probably null |
Het |
| Pramel52-ps |
A |
T |
5: 94,531,931 (GRCm39) |
I272L |
probably benign |
Het |
| Prickle2 |
T |
C |
6: 92,388,433 (GRCm39) |
D323G |
probably damaging |
Het |
| Psmd11 |
A |
T |
11: 80,336,089 (GRCm39) |
I114F |
probably damaging |
Het |
| Ptch1 |
T |
G |
13: 63,672,773 (GRCm39) |
E944A |
probably benign |
Het |
| Rbp3 |
C |
T |
14: 33,677,975 (GRCm39) |
T641M |
probably damaging |
Het |
| Rbp3 |
T |
G |
14: 33,678,418 (GRCm39) |
S789A |
probably benign |
Het |
| Rfxap |
C |
A |
3: 54,714,747 (GRCm39) |
R117L |
probably damaging |
Het |
| Rims2 |
T |
A |
15: 39,208,710 (GRCm39) |
M171K |
probably damaging |
Het |
| Scin |
A |
G |
12: 40,183,907 (GRCm39) |
|
probably null |
Het |
| Scn11a |
A |
G |
9: 119,583,744 (GRCm39) |
S1624P |
probably benign |
Het |
| Slc41a3 |
G |
A |
6: 90,619,210 (GRCm39) |
V330M |
probably damaging |
Het |
| Slc9c1 |
A |
G |
16: 45,370,469 (GRCm39) |
I237V |
probably benign |
Het |
| Spag6 |
A |
G |
2: 18,736,930 (GRCm39) |
I218V |
probably benign |
Het |
| Stam2 |
T |
C |
2: 52,599,638 (GRCm39) |
T257A |
possibly damaging |
Het |
| Tbc1d24 |
G |
A |
17: 24,426,938 (GRCm39) |
R318* |
probably null |
Het |
| Tedc2 |
T |
A |
17: 24,435,291 (GRCm39) |
E366V |
probably damaging |
Het |
| Tedc2 |
C |
A |
17: 24,435,292 (GRCm39) |
E366* |
probably null |
Het |
| Trpm3 |
T |
A |
19: 22,903,446 (GRCm39) |
Y1069N |
possibly damaging |
Het |
| Tuba8 |
A |
G |
6: 121,197,479 (GRCm39) |
D47G |
probably benign |
Het |
| Tulp3 |
A |
T |
6: 128,303,769 (GRCm39) |
S277T |
probably benign |
Het |
| Uqcc6 |
T |
A |
10: 82,456,051 (GRCm39) |
T37S |
possibly damaging |
Het |
| Wdr7 |
GTT |
GT |
18: 63,893,654 (GRCm39) |
|
probably null |
Het |
| Ybx2 |
A |
G |
11: 69,827,294 (GRCm39) |
|
probably null |
Het |
| Zfp407 |
C |
T |
18: 84,577,898 (GRCm39) |
A1072T |
probably benign |
Het |
| Zfp788 |
T |
A |
7: 41,299,905 (GRCm39) |
I795N |
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 |
|
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 |
|
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 |
|
|
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'- TCATGTCAGAACCAGGAGAGC -3'
(R):5'- CGTAGTACTCATTGGGGCTC -3'
Sequencing Primer
(F):5'- AACCAGGAGAGCCCCGC -3'
(R):5'- TACTCATTGGGGCTCAGGGC -3'
|
| Posted On |
2014-08-25 |
Incidental Mutation