Incidental Mutation 'R4843:Plod3'
ID |
371981 |
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 |
042456-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R4843 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
5 |
Chromosomal Location |
137015873-137025500 bp(+) (GRCm39) |
Type of Mutation |
nonsense |
DNA Base Change (assembly) |
G to A
at 137019854 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Tryptophan to Stop codon
at position 428
(W428*)
|
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 null
Transcript: ENSMUST00000004968
AA Change: W428*
|
SMART Domains |
Protein: ENSMUSP00000004968 Gene: ENSMUSG00000004846 AA Change: W428*
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: ENSMUST00000144784
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129896
|
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 |
|
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 |
0.9755 |
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.6%
- 20x: 93.1%
|
Validation Efficiency |
95% (58/61) |
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: 53 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Acp1 |
T |
A |
12: 30,946,144 (GRCm39) |
K124* |
probably null |
Het |
Actl11 |
G |
T |
9: 107,806,691 (GRCm39) |
C338F |
possibly damaging |
Het |
Adam5 |
G |
A |
8: 25,303,552 (GRCm39) |
S125F |
probably damaging |
Het |
Ap2s1 |
C |
A |
7: 16,477,271 (GRCm39) |
A44D |
possibly damaging |
Het |
AW554918 |
T |
C |
18: 25,473,057 (GRCm39) |
V84A |
probably benign |
Het |
Bsn |
G |
A |
9: 107,984,388 (GRCm39) |
T3222M |
unknown |
Het |
Car15 |
A |
G |
16: 17,654,472 (GRCm39) |
Y155H |
possibly damaging |
Het |
Cdca2 |
G |
T |
14: 67,914,425 (GRCm39) |
P945T |
probably damaging |
Het |
Cdh16 |
A |
G |
8: 105,348,172 (GRCm39) |
F182L |
probably damaging |
Het |
Cers6 |
G |
A |
2: 68,899,003 (GRCm39) |
A214T |
probably benign |
Het |
Ces1g |
A |
T |
8: 94,057,893 (GRCm39) |
M136K |
probably damaging |
Het |
Cnppd1 |
A |
G |
1: 75,113,086 (GRCm39) |
V394A |
probably benign |
Het |
Cyp3a59 |
A |
T |
5: 146,033,071 (GRCm39) |
I148F |
possibly damaging |
Het |
Dnah1 |
G |
A |
14: 30,986,920 (GRCm39) |
A3624V |
probably damaging |
Het |
Exoc3l4 |
T |
C |
12: 111,394,487 (GRCm39) |
|
probably benign |
Het |
Fap |
G |
T |
2: 62,374,718 (GRCm39) |
P227Q |
probably damaging |
Het |
Fbxw10 |
G |
A |
11: 62,738,151 (GRCm39) |
R15H |
possibly damaging |
Het |
Gm11011 |
T |
C |
2: 169,429,240 (GRCm39) |
|
probably benign |
Het |
Gm11146 |
A |
C |
16: 77,392,144 (GRCm39) |
|
probably benign |
Het |
Grip1 |
G |
A |
10: 119,765,920 (GRCm39) |
R84Q |
probably damaging |
Het |
Hipk2 |
A |
G |
6: 38,796,192 (GRCm39) |
C19R |
possibly damaging |
Het |
Hmgcll1 |
A |
G |
9: 75,979,916 (GRCm39) |
D102G |
possibly damaging |
Het |
Ighv16-1 |
A |
T |
12: 114,032,504 (GRCm39) |
Y99* |
probably null |
Het |
Kank1 |
T |
G |
19: 25,408,371 (GRCm39) |
S1283R |
probably damaging |
Het |
Kcnip1 |
T |
A |
11: 33,594,504 (GRCm39) |
H95L |
probably benign |
Het |
L3mbtl3 |
A |
T |
10: 26,207,777 (GRCm39) |
L314Q |
unknown |
Het |
Marveld3 |
C |
A |
8: 110,688,702 (GRCm39) |
R13L |
possibly damaging |
Het |
Mtrf1l |
G |
T |
10: 5,773,696 (GRCm39) |
P23Q |
possibly damaging |
Het |
Npdc1 |
G |
A |
2: 25,298,957 (GRCm39) |
D284N |
probably damaging |
Het |
Or5p69 |
G |
A |
7: 107,967,350 (GRCm39) |
A218T |
probably benign |
Het |
Or6c1b |
G |
T |
10: 129,273,316 (GRCm39) |
V212L |
probably benign |
Het |
Paqr7 |
A |
G |
4: 134,234,278 (GRCm39) |
Y45C |
probably damaging |
Het |
Pnisr |
T |
A |
4: 21,857,400 (GRCm39) |
|
probably benign |
Het |
Ppip5k1 |
C |
A |
2: 121,157,368 (GRCm39) |
R1046L |
probably damaging |
Het |
Ppp1r12b |
G |
T |
1: 134,883,471 (GRCm39) |
A17E |
probably benign |
Het |
Prmt5 |
A |
T |
14: 54,753,582 (GRCm39) |
I99N |
probably benign |
Het |
Ripk2 |
T |
C |
4: 16,155,073 (GRCm39) |
T149A |
probably damaging |
Het |
Rpf2 |
C |
A |
10: 40,122,998 (GRCm39) |
|
probably benign |
Het |
Rtf1 |
T |
A |
2: 119,536,017 (GRCm39) |
D190E |
possibly damaging |
Het |
Shank2 |
T |
A |
7: 143,585,146 (GRCm39) |
M49K |
probably benign |
Het |
Snd1 |
T |
G |
6: 28,668,642 (GRCm39) |
V443G |
probably damaging |
Het |
Spag9 |
T |
C |
11: 93,988,644 (GRCm39) |
F555L |
probably damaging |
Het |
Srfbp1 |
A |
G |
18: 52,621,749 (GRCm39) |
K270R |
probably benign |
Het |
Tenm2 |
T |
A |
11: 35,914,847 (GRCm39) |
N2230I |
probably damaging |
Het |
Tmem106a |
T |
C |
11: 101,477,021 (GRCm39) |
|
probably benign |
Het |
Tpsg1 |
A |
T |
17: 25,589,591 (GRCm39) |
|
probably benign |
Het |
Trank1 |
A |
G |
9: 111,195,146 (GRCm39) |
S1057G |
probably benign |
Het |
Unc13d |
G |
A |
11: 115,965,085 (GRCm39) |
T220M |
probably damaging |
Het |
Vmn1r68 |
T |
C |
7: 10,261,904 (GRCm39) |
T65A |
probably benign |
Het |
Vps50 |
T |
C |
6: 3,536,974 (GRCm39) |
|
probably null |
Het |
Washc5 |
A |
G |
15: 59,222,220 (GRCm39) |
I85T |
possibly damaging |
Het |
Zfp677 |
C |
T |
17: 21,612,788 (GRCm39) |
T2I |
probably benign |
Het |
Zxdc |
A |
G |
6: 90,359,254 (GRCm39) |
T629A |
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 |
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'- GATGCTGATGCCGTCCTTAC -3'
(R):5'- ATATCACCCTTTCCATAGCGGGG -3'
Sequencing Primer
(F):5'- TTACGAACCCGGAGACCTTG -3'
(R):5'- TTTCCATAGCGGGGGCCTAG -3'
|
Posted On |
2016-03-01 |