Incidental Mutation 'R5162:Plod3'
| ID |
397045 |
| 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 |
042744-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5162 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
137015873-137025500 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 137020161 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tryptophan to Arginine
at position 459
(W459R)
|
| 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 damaging
Transcript: ENSMUST00000004968
AA Change: W459R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
AA Change: W459R
| 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: ENSMUST00000129896
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144784
|
| 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 |
0.9525 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.8%
|
| Validation Efficiency |
98% (61/62) |
| 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: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2010315B03Rik |
T |
A |
9: 124,056,301 (GRCm39) |
T229S |
probably benign |
Het |
| Adrb3 |
T |
C |
8: 27,717,348 (GRCm39) |
E367G |
probably benign |
Het |
| Ak9 |
T |
A |
10: 41,233,653 (GRCm39) |
N630K |
probably damaging |
Het |
| Atp8b1 |
T |
C |
18: 64,694,733 (GRCm39) |
I516M |
possibly damaging |
Het |
| Bcor |
C |
T |
X: 11,906,725 (GRCm39) |
R1551Q |
probably damaging |
Het |
| Cry1 |
T |
A |
10: 84,969,150 (GRCm39) |
H558L |
probably benign |
Het |
| Cstdc3 |
A |
T |
16: 36,132,918 (GRCm39) |
H65L |
probably damaging |
Het |
| Cyp3a57 |
T |
A |
5: 145,305,893 (GRCm39) |
W126R |
probably damaging |
Het |
| Dhx36 |
A |
T |
3: 62,401,201 (GRCm39) |
V355E |
probably damaging |
Het |
| Dpp6 |
A |
G |
5: 27,604,013 (GRCm39) |
|
probably benign |
Het |
| Ehmt1 |
G |
T |
2: 24,767,509 (GRCm39) |
P135T |
probably damaging |
Het |
| Enpp2 |
T |
C |
15: 54,710,692 (GRCm39) |
D694G |
probably benign |
Het |
| Esrp2 |
T |
C |
8: 106,859,930 (GRCm39) |
E336G |
probably damaging |
Het |
| Faah |
A |
T |
4: 115,857,938 (GRCm39) |
|
probably benign |
Het |
| Fat1 |
G |
A |
8: 45,478,846 (GRCm39) |
G2608R |
probably benign |
Het |
| Fbxo8 |
A |
T |
8: 57,022,354 (GRCm39) |
Y122F |
probably damaging |
Het |
| Fgd5 |
A |
G |
6: 92,051,215 (GRCm39) |
D1497G |
probably damaging |
Het |
| Fn3krp |
T |
C |
11: 121,320,410 (GRCm39) |
F252L |
probably damaging |
Het |
| Fnip2 |
T |
C |
3: 79,389,084 (GRCm39) |
Y549C |
probably damaging |
Het |
| Gcm2 |
T |
C |
13: 41,257,131 (GRCm39) |
N206S |
probably benign |
Het |
| Grn |
C |
A |
11: 102,321,380 (GRCm39) |
|
probably benign |
Het |
| H2-T10 |
T |
A |
17: 36,429,843 (GRCm39) |
|
probably null |
Het |
| Henmt1 |
T |
C |
3: 108,847,366 (GRCm39) |
|
probably null |
Het |
| Man1b1 |
T |
A |
2: 25,233,365 (GRCm39) |
L246Q |
probably damaging |
Het |
| Mdh2 |
T |
C |
5: 135,812,329 (GRCm39) |
|
probably null |
Het |
| Mocos |
T |
C |
18: 24,787,109 (GRCm39) |
F43L |
probably damaging |
Het |
| Msh2 |
C |
A |
17: 88,030,841 (GRCm39) |
A906E |
probably benign |
Het |
| Naip5 |
T |
A |
13: 100,359,914 (GRCm39) |
I441F |
possibly damaging |
Het |
| Naip6 |
C |
T |
13: 100,437,108 (GRCm39) |
A472T |
probably benign |
Het |
| Nars2 |
T |
C |
7: 96,709,027 (GRCm39) |
|
probably benign |
Het |
| Ncoa2 |
A |
T |
1: 13,245,396 (GRCm39) |
M434K |
possibly damaging |
Het |
| Nlrp4g |
T |
A |
9: 124,350,394 (GRCm38) |
|
noncoding transcript |
Het |
| Or14j8 |
T |
A |
17: 38,263,255 (GRCm39) |
Q220L |
probably benign |
Het |
| Or9a2 |
G |
T |
6: 41,748,706 (GRCm39) |
H176N |
possibly damaging |
Het |
| Pals2 |
T |
A |
6: 50,155,495 (GRCm39) |
W259R |
probably damaging |
Het |
| Pars2 |
A |
G |
4: 106,511,735 (GRCm39) |
T506A |
probably benign |
Het |
| Pkp2 |
T |
C |
16: 16,078,200 (GRCm39) |
S481P |
probably damaging |
Het |
| Pramel13 |
A |
T |
4: 144,121,482 (GRCm39) |
L181M |
probably damaging |
Het |
| Prdm10 |
A |
T |
9: 31,251,714 (GRCm39) |
I361F |
possibly damaging |
Het |
| Ptpro |
T |
A |
6: 137,420,592 (GRCm39) |
V1007D |
probably damaging |
Het |
| Raver2 |
T |
C |
4: 100,959,921 (GRCm39) |
C134R |
probably damaging |
Het |
| Rnf130 |
G |
C |
11: 49,943,722 (GRCm39) |
A123P |
probably damaging |
Het |
| Slc29a4 |
G |
A |
5: 142,707,207 (GRCm39) |
A517T |
possibly damaging |
Het |
| Slc38a6 |
T |
A |
12: 73,376,759 (GRCm39) |
S138T |
possibly damaging |
Het |
| Spred1 |
T |
C |
2: 117,008,102 (GRCm39) |
V336A |
possibly damaging |
Het |
| Sptlc3 |
T |
A |
2: 139,473,263 (GRCm39) |
M504K |
probably benign |
Het |
| Syt11 |
T |
C |
3: 88,655,149 (GRCm39) |
D78G |
probably damaging |
Het |
| Trim23 |
C |
T |
13: 104,317,682 (GRCm39) |
T61I |
probably damaging |
Het |
| Tsg101 |
T |
C |
7: 46,542,174 (GRCm39) |
T260A |
probably damaging |
Het |
| Tyw5 |
T |
C |
1: 57,440,618 (GRCm39) |
Y48C |
probably damaging |
Het |
| Utp25 |
G |
T |
1: 192,796,089 (GRCm39) |
T192K |
probably damaging |
Het |
| Vmn1r17 |
A |
G |
6: 57,337,828 (GRCm39) |
V130A |
probably benign |
Het |
| Vmn2r89 |
C |
A |
14: 51,693,620 (GRCm39) |
H323Q |
possibly damaging |
Het |
| Vps18 |
A |
G |
2: 119,123,423 (GRCm39) |
S117G |
probably benign |
Het |
| Zfp93 |
C |
G |
7: 23,975,757 (GRCm39) |
Q581E |
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 |
|
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 |
|
|
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'- AAGACTACGTGGAACTGGTGC -3'
(R):5'- AACTCGTGCTGGTTGCTGAG -3'
Sequencing Primer
(F):5'- AAGCGAGTGTGAGTCCCAC -3'
(R):5'- ACATCAGGAGGCTGTGGGC -3'
|
| Posted On |
2016-06-21 |
Incidental Mutation