Incidental Mutation 'R0747:Plod3'
ID |
70180 |
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 |
038928-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R0747 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
5 |
Chromosomal Location |
137015873-137025500 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 137017049 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Asparagine to Serine
at position 66
(N66S)
|
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: N66S
PolyPhen 2
Score 0.341 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000004968 Gene: ENSMUSG00000004846 AA Change: N66S
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: ENSMUST00000129896
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137419
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151642
|
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 |
0.2330 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 94.8%
|
Validation Efficiency |
100% (50/50) |
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 |
Adam19 |
A |
T |
11: 46,009,322 (GRCm39) |
|
probably null |
Het |
Anks4b |
C |
T |
7: 119,781,386 (GRCm39) |
A139V |
probably damaging |
Het |
Arf1 |
G |
A |
11: 59,103,461 (GRCm39) |
R149C |
probably benign |
Het |
Axl |
A |
T |
7: 25,463,484 (GRCm39) |
C598S |
possibly damaging |
Het |
B3gnt2 |
T |
C |
11: 22,786,316 (GRCm39) |
I291V |
possibly damaging |
Het |
Ccdc158 |
T |
A |
5: 92,781,156 (GRCm39) |
H883L |
probably benign |
Het |
Cep15 |
T |
A |
14: 12,287,287 (GRCm38) |
M16K |
probably benign |
Het |
Col6a3 |
A |
G |
1: 90,730,375 (GRCm39) |
S1644P |
probably damaging |
Het |
Cspg4 |
T |
C |
9: 56,797,564 (GRCm39) |
S1343P |
probably damaging |
Het |
D430041D05Rik |
G |
T |
2: 104,060,651 (GRCm39) |
H1414Q |
probably damaging |
Het |
Dnah5 |
C |
G |
15: 28,444,332 (GRCm39) |
I4043M |
probably damaging |
Het |
Dnah5 |
T |
A |
15: 28,444,333 (GRCm39) |
C4044S |
possibly damaging |
Het |
Dpep3 |
C |
T |
8: 106,704,018 (GRCm39) |
A267T |
probably benign |
Het |
Dync1h1 |
A |
C |
12: 110,578,845 (GRCm39) |
H106P |
probably benign |
Het |
Dync1h1 |
A |
C |
12: 110,595,718 (GRCm39) |
E1466A |
probably damaging |
Het |
Fggy |
T |
C |
4: 95,700,337 (GRCm39) |
|
probably benign |
Het |
Frmd6 |
A |
G |
12: 70,910,830 (GRCm39) |
T5A |
probably benign |
Het |
Gnb5 |
G |
A |
9: 75,218,752 (GRCm39) |
V26I |
probably benign |
Het |
Hephl1 |
A |
T |
9: 14,965,297 (GRCm39) |
|
probably benign |
Het |
Hmmr |
C |
T |
11: 40,612,572 (GRCm39) |
|
probably benign |
Het |
Hpn |
A |
T |
7: 30,798,971 (GRCm39) |
F356Y |
probably damaging |
Het |
Iqgap3 |
T |
C |
3: 88,014,810 (GRCm39) |
|
probably benign |
Het |
Ism2 |
A |
G |
12: 87,332,172 (GRCm39) |
|
probably benign |
Het |
Kansl1 |
T |
A |
11: 104,233,802 (GRCm39) |
M754L |
probably benign |
Het |
Kcnc4 |
A |
T |
3: 107,355,470 (GRCm39) |
I326N |
probably damaging |
Het |
Lcn6 |
G |
A |
2: 25,567,184 (GRCm39) |
V62M |
probably damaging |
Het |
Lrp1b |
A |
T |
2: 40,760,353 (GRCm39) |
C2858S |
probably damaging |
Het |
Lyn |
G |
A |
4: 3,745,638 (GRCm39) |
|
probably benign |
Het |
Mov10 |
T |
A |
3: 104,709,812 (GRCm39) |
H358L |
probably benign |
Het |
Notch1 |
A |
G |
2: 26,362,152 (GRCm39) |
V60A |
unknown |
Het |
Or2t6 |
C |
T |
14: 14,175,429 (GRCm38) |
A218T |
probably benign |
Het |
Pgap2 |
C |
A |
7: 101,886,343 (GRCm39) |
Y176* |
probably null |
Het |
Pglyrp1 |
A |
G |
7: 18,624,200 (GRCm39) |
Q161R |
possibly damaging |
Het |
Psmc3 |
A |
G |
2: 90,884,645 (GRCm39) |
E18G |
probably benign |
Het |
Psme3 |
T |
G |
11: 101,207,872 (GRCm39) |
M9R |
probably benign |
Het |
Rapgef4 |
A |
G |
2: 72,053,417 (GRCm39) |
N428S |
possibly damaging |
Het |
Rbp3 |
A |
G |
14: 33,678,235 (GRCm39) |
I728V |
possibly damaging |
Het |
Sall4 |
A |
T |
2: 168,596,886 (GRCm39) |
H651Q |
probably damaging |
Het |
Skint3 |
T |
A |
4: 112,111,102 (GRCm39) |
Y76N |
probably damaging |
Het |
Slc13a4 |
T |
C |
6: 35,255,263 (GRCm39) |
T342A |
probably damaging |
Het |
Slc25a1 |
G |
T |
16: 17,744,084 (GRCm39) |
T239K |
probably damaging |
Het |
Slc36a2 |
T |
A |
11: 55,060,685 (GRCm39) |
I242F |
probably benign |
Het |
Tekt2 |
G |
A |
4: 126,217,553 (GRCm39) |
Q171* |
probably null |
Het |
Tet2 |
T |
G |
3: 133,173,231 (GRCm39) |
H1677P |
possibly damaging |
Het |
Trappc9 |
G |
A |
15: 72,897,816 (GRCm39) |
R377W |
probably damaging |
Het |
Trcg1 |
C |
T |
9: 57,149,204 (GRCm39) |
P259S |
probably benign |
Het |
Ttn |
A |
C |
2: 76,540,942 (GRCm39) |
S25688A |
probably damaging |
Het |
Vmn2r117 |
T |
A |
17: 23,694,477 (GRCm39) |
R457* |
probably null |
Het |
Zbbx |
C |
T |
3: 75,062,734 (GRCm39) |
V8I |
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 |
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 |
|
Predicted Primers |
PCR Primer
(F):5'- ATGCTGTCAACCCAGGTGAGAACC -3'
(R):5'- AATCACGTCGTAGCTGGGCAAG -3'
Sequencing Primer
(F):5'- TGAAGTAATATGGAGgtgtgtgtg -3'
(R):5'- AGCCAGGAGGAACCTCAGTC -3'
|
Posted On |
2013-09-30 |