Incidental Mutation 'R4342:Plod3'
| ID |
324166 |
| 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 |
041100-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4342 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
137015873-137025500 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to C
at 137017000 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Proline
at position 50
(A50P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000004968
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004968]
[ENSMUST00000034953]
[ENSMUST00000085941]
[ENSMUST00000111090]
[ENSMUST00000111091]
[ENSMUST00000156963]
[ENSMUST00000137272]
|
| AlphaFold |
Q9R0E1 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000004968
AA Change: A50P
PolyPhen 2
Score 0.382 (Sensitivity: 0.90; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
AA Change: A50P
| 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: ENSMUST00000137419
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151642
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129896
|
| 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 |
|
| Meta Mutation Damage Score |
0.1039 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.4%
|
| Validation Efficiency |
99% (68/69) |
| 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: 58 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aars2 |
T |
C |
17: 45,827,421 (GRCm39) |
C488R |
probably benign |
Het |
| Adamts19 |
A |
T |
18: 59,075,572 (GRCm39) |
H489L |
probably damaging |
Het |
| Ahnak |
T |
C |
19: 8,989,447 (GRCm39) |
V3577A |
possibly damaging |
Het |
| Ajm1 |
A |
G |
2: 25,469,120 (GRCm39) |
Y264H |
possibly damaging |
Het |
| Arhgap44 |
G |
A |
11: 64,902,887 (GRCm39) |
R401* |
probably null |
Het |
| Cbx3-ps2 |
T |
C |
13: 65,707,502 (GRCm39) |
|
noncoding transcript |
Het |
| Ccdc174 |
T |
A |
6: 91,862,337 (GRCm39) |
L86* |
probably null |
Het |
| Cd38 |
A |
C |
5: 44,026,431 (GRCm39) |
I72L |
probably benign |
Het |
| Cers4 |
T |
C |
8: 4,571,223 (GRCm39) |
L264P |
probably damaging |
Het |
| Cldn23 |
A |
G |
8: 36,292,652 (GRCm39) |
S279P |
probably benign |
Het |
| Cth |
T |
A |
3: 157,630,613 (GRCm39) |
T19S |
probably damaging |
Het |
| Dnajc22 |
T |
A |
15: 99,002,345 (GRCm39) |
L330* |
probably null |
Het |
| Epas1 |
G |
A |
17: 87,131,228 (GRCm39) |
C336Y |
probably damaging |
Het |
| Evi5l |
A |
C |
8: 4,233,492 (GRCm39) |
|
probably benign |
Het |
| Fbxl2 |
A |
T |
9: 113,814,374 (GRCm39) |
H272Q |
probably benign |
Het |
| Fgd3 |
C |
T |
13: 49,427,185 (GRCm39) |
|
probably null |
Het |
| Fhdc1 |
C |
A |
3: 84,352,133 (GRCm39) |
V1031F |
probably benign |
Het |
| Fscn1 |
T |
C |
5: 142,957,776 (GRCm39) |
Y308H |
probably damaging |
Het |
| Garin3 |
A |
G |
11: 46,298,043 (GRCm39) |
D449G |
possibly damaging |
Het |
| Gm5878 |
G |
A |
6: 85,102,633 (GRCm39) |
R31* |
probably null |
Het |
| Gpatch2l |
T |
C |
12: 86,307,453 (GRCm39) |
V277A |
probably benign |
Het |
| Greb1l |
T |
A |
18: 10,544,561 (GRCm39) |
M1385K |
probably benign |
Het |
| Grin2a |
A |
G |
16: 9,471,453 (GRCm39) |
I605T |
possibly damaging |
Het |
| Hoxc11 |
C |
T |
15: 102,863,106 (GRCm39) |
S49F |
probably damaging |
Het |
| Igf2r |
C |
T |
17: 12,928,398 (GRCm39) |
E982K |
possibly damaging |
Het |
| Ighv10-3 |
A |
T |
12: 114,487,124 (GRCm39) |
M99K |
possibly damaging |
Het |
| Itgb4 |
A |
T |
11: 115,879,555 (GRCm39) |
T614S |
probably benign |
Het |
| Kcnv1 |
G |
A |
15: 44,977,840 (GRCm39) |
T66M |
probably damaging |
Het |
| Mast4 |
A |
G |
13: 102,910,756 (GRCm39) |
V461A |
probably damaging |
Het |
| Mcts2 |
G |
A |
2: 152,529,584 (GRCm39) |
V132M |
probably damaging |
Het |
| Mical3 |
C |
A |
6: 120,911,799 (GRCm39) |
E1083* |
probably null |
Het |
| Nbeal2 |
A |
G |
9: 110,460,861 (GRCm39) |
|
probably benign |
Het |
| Nek4 |
T |
C |
14: 30,675,863 (GRCm39) |
V66A |
probably damaging |
Het |
| Nfasc |
A |
G |
1: 132,559,443 (GRCm39) |
F229S |
probably damaging |
Het |
| Nhsl1 |
T |
C |
10: 18,402,437 (GRCm39) |
F1221S |
probably damaging |
Het |
| Nr1d1 |
T |
G |
11: 98,662,640 (GRCm39) |
K118Q |
probably damaging |
Het |
| Ntaq1 |
T |
C |
15: 58,016,110 (GRCm39) |
S120P |
probably benign |
Het |
| Ntm |
T |
C |
9: 29,020,727 (GRCm39) |
E164G |
probably damaging |
Het |
| Or51a7 |
A |
G |
7: 102,615,231 (GRCm39) |
N308S |
probably benign |
Het |
| Parp1 |
G |
T |
1: 180,414,894 (GRCm39) |
A411S |
probably benign |
Het |
| Pds5b |
A |
G |
5: 150,724,319 (GRCm39) |
T1301A |
probably benign |
Het |
| Pkhd1 |
A |
G |
1: 20,128,841 (GRCm39) |
V3954A |
probably benign |
Het |
| Pkp4 |
A |
T |
2: 59,180,952 (GRCm39) |
K739I |
probably damaging |
Het |
| Pla2g4e |
T |
C |
2: 120,016,927 (GRCm39) |
|
probably benign |
Het |
| Ralgds |
T |
C |
2: 28,442,107 (GRCm39) |
L96P |
probably damaging |
Het |
| Rbm6 |
A |
T |
9: 107,724,446 (GRCm39) |
|
probably benign |
Het |
| Scp2d1 |
T |
C |
2: 144,666,087 (GRCm39) |
L142P |
probably damaging |
Het |
| Setd5 |
AT |
ATT |
6: 113,088,281 (GRCm39) |
|
probably benign |
Het |
| Sgf29 |
G |
A |
7: 126,270,949 (GRCm39) |
C143Y |
probably damaging |
Het |
| Slc22a12 |
A |
G |
19: 6,591,129 (GRCm39) |
I156T |
probably benign |
Het |
| Stambpl1 |
A |
G |
19: 34,211,446 (GRCm39) |
Q169R |
probably benign |
Het |
| Tex2 |
T |
C |
11: 106,457,832 (GRCm39) |
|
probably benign |
Het |
| Trip11 |
A |
T |
12: 101,850,575 (GRCm39) |
I878N |
probably damaging |
Het |
| Ttf1 |
C |
T |
2: 28,955,488 (GRCm39) |
S284L |
probably benign |
Het |
| Ttn |
A |
T |
2: 76,641,587 (GRCm39) |
L5176Q |
possibly damaging |
Het |
| Ugt2b5 |
A |
T |
5: 87,287,582 (GRCm39) |
V195E |
probably damaging |
Het |
| Vmn1r14 |
T |
A |
6: 57,210,808 (GRCm39) |
Y85N |
probably benign |
Het |
| Zfp131 |
C |
T |
13: 120,237,554 (GRCm39) |
R268H |
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 |
|
|
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 |
|
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'- TTCTGGAGATCAAATGTGCTGAAAG -3'
(R):5'- CCAACTGTTCGAGCCACATC -3'
Sequencing Primer
(F):5'- TGTGCTGAAAGAACTTTAGTGAAG -3'
(R):5'- CCCAGGGTCTGCAGGAAAGATC -3'
|
| Posted On |
2015-06-24 |
Incidental Mutation