Incidental Mutation 'R2318:Plod3'
| ID |
245551 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Plod3
|
| Ensembl Gene |
ENSMUSG00000004846 |
| Gene Name |
procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 |
| Synonyms |
lysyl hydroxylase 3, LH3 |
| Accession Numbers |
|
| Is this an essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R2318 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
5 |
| Chromosomal Location |
136987019-136996648 bp(+) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to C
at 136988146 bp (GRCm38)
|
| 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]
[ENSMUST00000137272]
[ENSMUST00000156963]
|
| 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: 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 |
noncoding transcript
Transcript: ENSMUST00000137419
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144784
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151642
|
| 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 |
0.1039 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.0%
|
| 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: 24 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 0610010F05Rik |
A |
G |
11: 23,588,701 |
Y66H |
probably damaging |
Het |
| Arhgef10 |
G |
A |
8: 14,928,855 |
A41T |
probably damaging |
Het |
| Car15 |
T |
C |
16: 17,836,599 |
M158V |
probably benign |
Het |
| Cinp |
C |
A |
12: 110,874,009 |
W113L |
probably damaging |
Het |
| Col4a3 |
T |
A |
1: 82,648,569 |
|
probably null |
Het |
| Csnk2b |
T |
C |
17: 35,118,061 |
Y101C |
possibly damaging |
Het |
| Ddb1 |
C |
T |
19: 10,626,628 |
R900C |
probably damaging |
Het |
| Eif4g2 |
A |
G |
7: 111,073,858 |
F876L |
possibly damaging |
Het |
| F11 |
A |
G |
8: 45,248,638 |
S353P |
probably damaging |
Het |
| Gm5868 |
T |
C |
5: 72,586,295 |
T27A |
probably benign |
Het |
| Hist1h4d |
A |
G |
13: 23,581,756 |
Y52C |
probably damaging |
Het |
| Mast1 |
T |
C |
8: 84,921,125 |
D540G |
probably damaging |
Het |
| Mis18bp1 |
C |
T |
12: 65,140,843 |
V829M |
possibly damaging |
Het |
| Mtus2 |
C |
T |
5: 148,107,082 |
R827* |
probably null |
Het |
| Nlrp9a |
G |
A |
7: 26,573,852 |
V860M |
probably damaging |
Het |
| Prr14l |
T |
C |
5: 32,830,078 |
E691G |
probably benign |
Het |
| Rad1 |
A |
G |
15: 10,490,409 |
N154S |
probably benign |
Het |
| Smc2 |
T |
C |
4: 52,446,030 |
S133P |
probably damaging |
Het |
| Sstr1 |
T |
A |
12: 58,212,776 |
S62T |
possibly damaging |
Het |
| Thsd7a |
T |
C |
6: 12,405,147 |
Y766C |
probably damaging |
Het |
| Timm44 |
A |
G |
8: 4,268,307 |
V129A |
probably benign |
Het |
| Tinag |
T |
C |
9: 77,045,411 |
Y97C |
probably damaging |
Het |
| Tns2 |
C |
T |
15: 102,108,934 |
R281C |
probably damaging |
Het |
| Ubap2 |
A |
G |
4: 41,251,542 |
V30A |
probably damaging |
Het |
|
| Other mutations in Plod3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00507:Plod3
|
APN |
5 |
136996176 |
missense |
possibly damaging |
0.78 |
|
IGL01090:Plod3
|
APN |
5 |
136990236 |
missense |
probably benign |
0.37 |
|
IGL01443:Plod3
|
APN |
5 |
136990221 |
missense |
probably benign |
0.17 |
|
IGL01583:Plod3
|
APN |
5 |
136996148 |
missense |
probably benign |
0.02 |
|
R0544:Plod3
|
UTSW |
5 |
136991611 |
missense |
probably benign |
0.09 |
|
R0747:Plod3
|
UTSW |
5 |
136988195 |
missense |
probably benign |
0.34 |
|
R0764:Plod3
|
UTSW |
5 |
136989583 |
unclassified |
probably benign |
|
|
R1520:Plod3
|
UTSW |
5 |
136991311 |
missense |
probably damaging |
0.99 |
|
R1631:Plod3
|
UTSW |
5 |
136988993 |
missense |
probably damaging |
1.00 |
|
R1751:Plod3
|
UTSW |
5 |
136990176 |
missense |
possibly damaging |
0.89 |
|
R1767:Plod3
|
UTSW |
5 |
136990176 |
missense |
possibly damaging |
0.89 |
|
R1984:Plod3
|
UTSW |
5 |
136990853 |
splice site |
probably null |
|
|
R1985:Plod3
|
UTSW |
5 |
136990853 |
splice site |
probably null |
|
|
R2137:Plod3
|
UTSW |
5 |
136988717 |
missense |
probably damaging |
1.00 |
|
R2148:Plod3
|
UTSW |
5 |
136987773 |
nonsense |
probably null |
|
|
R2179:Plod3
|
UTSW |
5 |
136991008 |
missense |
possibly damaging |
0.77 |
|
R2319:Plod3
|
UTSW |
5 |
136988146 |
missense |
probably benign |
0.38 |
|
R2512:Plod3
|
UTSW |
5 |
136988146 |
missense |
probably benign |
0.38 |
|
R2513:Plod3
|
UTSW |
5 |
136988146 |
missense |
probably benign |
0.38 |
|
R2696:Plod3
|
UTSW |
5 |
136988146 |
missense |
probably benign |
0.38 |
|
R2891:Plod3
|
UTSW |
5 |
136988146 |
missense |
probably benign |
0.38 |
|
R2893:Plod3
|
UTSW |
5 |
136988146 |
missense |
probably benign |
0.38 |
|
R3030:Plod3
|
UTSW |
5 |
136988146 |
missense |
probably benign |
0.38 |
|
R3439:Plod3
|
UTSW |
5 |
136988146 |
missense |
probably benign |
0.38 |
|
R3957:Plod3
|
UTSW |
5 |
136994192 |
missense |
probably damaging |
1.00 |
|
R4080:Plod3
|
UTSW |
5 |
136988146 |
missense |
probably benign |
0.38 |
|
R4081:Plod3
|
UTSW |
5 |
136988146 |
missense |
probably benign |
0.38 |
|
R4342:Plod3
|
UTSW |
5 |
136988146 |
missense |
probably benign |
0.38 |
|
R4344:Plod3
|
UTSW |
5 |
136988146 |
missense |
probably benign |
0.38 |
|
R4345:Plod3
|
UTSW |
5 |
136988146 |
missense |
probably benign |
0.38 |
|
R4546:Plod3
|
UTSW |
5 |
136988947 |
missense |
possibly damaging |
0.94 |
|
R4799:Plod3
|
UTSW |
5 |
136990800 |
missense |
probably benign |
0.00 |
|
R4843:Plod3
|
UTSW |
5 |
136991000 |
nonsense |
probably null |
|
|
R4956:Plod3
|
UTSW |
5 |
136989918 |
missense |
probably damaging |
1.00 |
|
R5159:Plod3
|
UTSW |
5 |
136995078 |
intron |
probably benign |
|
|
R5162:Plod3
|
UTSW |
5 |
136991307 |
missense |
probably damaging |
1.00 |
|
R5328:Plod3
|
UTSW |
5 |
136989683 |
missense |
probably damaging |
1.00 |
|
R5427:Plod3
|
UTSW |
5 |
136991788 |
missense |
probably damaging |
1.00 |
|
R6627:Plod3
|
UTSW |
5 |
136988456 |
missense |
probably damaging |
0.99 |
|
R7003:Plod3
|
UTSW |
5 |
136989644 |
missense |
probably damaging |
1.00 |
|
R7132:Plod3
|
UTSW |
5 |
136995117 |
missense |
|
|
|
R7376:Plod3
|
UTSW |
5 |
136990481 |
missense |
probably benign |
0.00 |
|
R7404:Plod3
|
UTSW |
5 |
136995047 |
missense |
probably benign |
|
|
R7827:Plod3
|
UTSW |
5 |
136989981 |
missense |
probably benign |
|
|
R8062:Plod3
|
UTSW |
5 |
136990269 |
missense |
possibly damaging |
0.87 |
|
R8506:Plod3
|
UTSW |
5 |
136988976 |
missense |
probably damaging |
1.00 |
|
R8772:Plod3
|
UTSW |
5 |
136988919 |
missense |
probably damaging |
0.99 |
|
R9108:Plod3
|
UTSW |
5 |
136989163 |
missense |
probably damaging |
0.99 |
|
R9439:Plod3
|
UTSW |
5 |
136994182 |
missense |
probably benign |
0.03 |
|
| Predicted Primers |
PCR Primer
(F):5'- CTTCTGGAGATCAAATGTGCTG -3'
(R):5'- AACTGTTCGAGCCACATCAC -3'
Sequencing Primer
(F):5'- TGTGCTGAAAGAACTTTAGTGAAG -3'
(R):5'- CCCAGGGTCTGCAGGAAAGATC -3'
|
| Posted On |
2014-10-30 |
