Incidental Mutation 'IGL01090:Plod3'
ID |
51081 |
Institutional Source |
Australian Phenomics Network
(link to record)
|
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 # |
IGL01090
|
Quality Score |
|
Status
|
|
Chromosome |
5 |
Chromosomal Location |
137015873-137025500 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 137019090 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Aspartic acid to Glycine
at position 325
(D325G)
|
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 benign
Transcript: ENSMUST00000004968
AA Change: D325G
PolyPhen 2
Score 0.370 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000004968 Gene: ENSMUSG00000004846 AA Change: D325G
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: ENSMUST00000137419
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151642
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144784
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129896
|
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 |
|
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: 49 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4930590J08Rik |
T |
C |
6: 91,896,099 (GRCm39) |
S316P |
possibly damaging |
Het |
Actn1 |
A |
T |
12: 80,245,846 (GRCm39) |
|
probably null |
Het |
Agbl3 |
T |
C |
6: 34,776,822 (GRCm39) |
Y443H |
probably benign |
Het |
Akap13 |
T |
A |
7: 75,316,279 (GRCm39) |
D578E |
probably benign |
Het |
Aldoa |
A |
T |
7: 126,395,207 (GRCm39) |
H292Q |
probably benign |
Het |
Als2 |
T |
C |
1: 59,254,775 (GRCm39) |
K194R |
possibly damaging |
Het |
Bivm |
C |
A |
1: 44,168,451 (GRCm39) |
H244N |
probably damaging |
Het |
Cabp5 |
G |
A |
7: 13,139,412 (GRCm39) |
E146K |
probably damaging |
Het |
Cfap206 |
C |
T |
4: 34,721,562 (GRCm39) |
S162N |
probably damaging |
Het |
Cfap251 |
A |
C |
5: 123,418,052 (GRCm39) |
|
probably benign |
Het |
Clcn4 |
A |
G |
7: 7,297,035 (GRCm39) |
V129A |
probably benign |
Het |
Clec4g |
A |
G |
8: 3,769,482 (GRCm39) |
S54P |
probably damaging |
Het |
Crim1 |
G |
T |
17: 78,654,658 (GRCm39) |
V645L |
probably damaging |
Het |
Csta1 |
T |
C |
16: 35,945,421 (GRCm39) |
T31A |
probably damaging |
Het |
D930048N14Rik |
T |
C |
11: 51,544,610 (GRCm39) |
|
probably benign |
Het |
Dhx34 |
G |
T |
7: 15,950,181 (GRCm39) |
P329Q |
probably damaging |
Het |
Dusp16 |
T |
C |
6: 134,702,912 (GRCm39) |
N193S |
probably benign |
Het |
Fbn1 |
A |
G |
2: 125,236,696 (GRCm39) |
|
probably benign |
Het |
Fbxo46 |
A |
G |
7: 18,870,728 (GRCm39) |
Y449C |
probably damaging |
Het |
Fmo4 |
C |
A |
1: 162,637,354 (GRCm39) |
|
probably null |
Het |
Foxi3 |
C |
A |
6: 70,937,729 (GRCm39) |
N320K |
probably damaging |
Het |
Gm9964 |
A |
G |
11: 79,187,210 (GRCm39) |
L79P |
unknown |
Het |
Gpr161 |
T |
C |
1: 165,134,149 (GRCm39) |
I137T |
probably damaging |
Het |
Herc1 |
C |
T |
9: 66,376,457 (GRCm39) |
Q3426* |
probably null |
Het |
Hps5 |
C |
T |
7: 46,437,751 (GRCm39) |
R108H |
probably benign |
Het |
Itch |
T |
A |
2: 155,048,256 (GRCm39) |
V540E |
probably damaging |
Het |
L3mbtl1 |
C |
A |
2: 162,807,925 (GRCm39) |
P520H |
probably damaging |
Het |
Mvp |
A |
G |
7: 126,588,859 (GRCm39) |
V636A |
probably benign |
Het |
Odf4 |
A |
G |
11: 68,812,778 (GRCm39) |
|
probably benign |
Het |
Or7g18 |
A |
G |
9: 18,787,538 (GRCm39) |
K305R |
probably benign |
Het |
Pld1 |
T |
C |
3: 28,142,816 (GRCm39) |
S675P |
probably benign |
Het |
Prss12 |
T |
C |
3: 123,276,388 (GRCm39) |
V339A |
possibly damaging |
Het |
Ptpn13 |
T |
A |
5: 103,689,180 (GRCm39) |
L991Q |
probably null |
Het |
Ptpn3 |
T |
A |
4: 57,240,833 (GRCm39) |
I261F |
probably damaging |
Het |
Rab3gap1 |
T |
C |
1: 127,858,124 (GRCm39) |
|
probably benign |
Het |
Rasa4 |
A |
G |
5: 136,130,847 (GRCm39) |
R373G |
possibly damaging |
Het |
Rmi1 |
T |
C |
13: 58,557,208 (GRCm39) |
S486P |
probably damaging |
Het |
Slc25a23 |
A |
G |
17: 57,354,233 (GRCm39) |
I139T |
probably benign |
Het |
Sspo |
T |
A |
6: 48,467,059 (GRCm39) |
S4017T |
probably benign |
Het |
Tcaf1 |
C |
A |
6: 42,663,556 (GRCm39) |
C108F |
probably benign |
Het |
Tnc |
T |
C |
4: 63,918,317 (GRCm39) |
Q1198R |
probably damaging |
Het |
Tnni3k |
G |
T |
3: 154,645,320 (GRCm39) |
Q522K |
possibly damaging |
Het |
Trio |
T |
A |
15: 27,773,093 (GRCm39) |
E713V |
probably damaging |
Het |
Ugt2b34 |
C |
A |
5: 87,041,679 (GRCm39) |
V338F |
probably damaging |
Het |
Usp40 |
T |
A |
1: 87,890,187 (GRCm39) |
M892L |
probably benign |
Het |
Usp54 |
A |
T |
14: 20,636,225 (GRCm39) |
|
probably benign |
Het |
Vmn2r53 |
T |
C |
7: 12,334,835 (GRCm39) |
E275G |
possibly damaging |
Het |
Vmn2r87 |
A |
G |
10: 130,333,247 (GRCm39) |
M1T |
probably null |
Het |
Wdr83os |
A |
T |
8: 85,808,476 (GRCm39) |
D76V |
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 |
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 |
|
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 |
|
Posted On |
2013-06-21 |