Incidental Mutation 'R7003:Plod3'
| ID |
544657 |
| 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 |
045108-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R7003 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
5 |
| Chromosomal Location |
137015873-137025500 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 137018498 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Lysine
at position 245
(N245K)
|
| 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: N245K
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
AA Change: N245K
| 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 |
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 |
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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.1%
|
| 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: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Actbl2 |
T |
A |
13: 111,392,490 (GRCm39) |
I275N |
probably damaging |
Het |
| Actr3b |
A |
C |
5: 26,003,461 (GRCm39) |
Y21S |
probably damaging |
Het |
| Adam6b |
C |
T |
12: 113,453,662 (GRCm39) |
Q160* |
probably null |
Het |
| Adgrv1 |
C |
T |
13: 81,670,223 (GRCm39) |
|
probably null |
Het |
| Akr1c6 |
A |
G |
13: 4,504,514 (GRCm39) |
N300D |
probably benign |
Het |
| Alox8 |
T |
C |
11: 69,082,416 (GRCm39) |
D170G |
possibly damaging |
Het |
| Amhr2 |
A |
G |
15: 102,354,768 (GRCm39) |
N40S |
probably benign |
Het |
| Ap2a2 |
A |
G |
7: 141,209,109 (GRCm39) |
N767S |
probably benign |
Het |
| Armc3 |
T |
C |
2: 19,274,839 (GRCm39) |
I358T |
probably damaging |
Het |
| Atg2b |
A |
G |
12: 105,620,508 (GRCm39) |
S732P |
probably benign |
Het |
| Atp12a |
A |
G |
14: 56,610,837 (GRCm39) |
Y327C |
possibly damaging |
Het |
| Bcr |
T |
C |
10: 74,897,393 (GRCm39) |
V179A |
probably benign |
Het |
| Cep104 |
T |
C |
4: 154,078,018 (GRCm39) |
L642P |
probably benign |
Het |
| Clspn |
T |
A |
4: 126,486,513 (GRCm39) |
S1302R |
possibly damaging |
Het |
| Cmip |
T |
C |
8: 118,111,727 (GRCm39) |
F153L |
probably benign |
Het |
| Cplane1 |
T |
G |
15: 8,258,246 (GRCm39) |
L2164R |
probably damaging |
Het |
| D630039A03Rik |
T |
C |
4: 57,910,521 (GRCm39) |
D97G |
probably damaging |
Het |
| Dok7 |
A |
T |
5: 35,236,899 (GRCm39) |
T396S |
probably benign |
Het |
| Dsel |
C |
T |
1: 111,788,025 (GRCm39) |
V837I |
probably benign |
Het |
| Etl4 |
C |
T |
2: 20,810,695 (GRCm39) |
T926I |
probably benign |
Het |
| Gpatch2l |
G |
A |
12: 86,290,958 (GRCm39) |
R47H |
probably damaging |
Het |
| Gpr155 |
A |
G |
2: 73,173,961 (GRCm39) |
I816T |
probably damaging |
Het |
| Hpn |
C |
T |
7: 30,810,367 (GRCm39) |
|
probably benign |
Het |
| Inpp5e |
A |
G |
2: 26,287,877 (GRCm39) |
S640P |
probably benign |
Het |
| Irs3 |
C |
T |
5: 137,643,539 (GRCm39) |
V82I |
probably benign |
Het |
| Kif16b |
A |
C |
2: 142,600,749 (GRCm39) |
D461E |
possibly damaging |
Het |
| Krba1 |
A |
G |
6: 48,390,014 (GRCm39) |
T592A |
possibly damaging |
Het |
| Lgsn |
T |
A |
1: 31,243,024 (GRCm39) |
S369T |
possibly damaging |
Het |
| Lrrc4b |
C |
T |
7: 44,094,580 (GRCm39) |
P83S |
probably damaging |
Het |
| Mplkipl1 |
A |
G |
19: 61,164,319 (GRCm39) |
S39P |
possibly damaging |
Het |
| Neil3 |
T |
C |
8: 54,054,001 (GRCm39) |
T343A |
possibly damaging |
Het |
| Nt5e |
A |
G |
9: 88,246,805 (GRCm39) |
Y347C |
probably damaging |
Het |
| Or1j1 |
A |
G |
2: 36,703,047 (GRCm39) |
I19T |
possibly damaging |
Het |
| Or2d3b |
A |
T |
7: 106,514,319 (GRCm39) |
T305S |
probably benign |
Het |
| Or2f2 |
C |
T |
6: 42,767,399 (GRCm39) |
T142I |
probably benign |
Het |
| Or8g26 |
A |
T |
9: 39,096,239 (GRCm39) |
Y255F |
probably benign |
Het |
| P2rx5 |
T |
C |
11: 73,058,800 (GRCm39) |
|
probably null |
Het |
| Phtf2 |
A |
G |
5: 20,999,399 (GRCm39) |
V248A |
probably benign |
Het |
| Plekhd1 |
T |
C |
12: 80,768,734 (GRCm39) |
C406R |
possibly damaging |
Het |
| Polr3c |
G |
T |
3: 96,630,954 (GRCm39) |
H155Q |
possibly damaging |
Het |
| Psap |
T |
A |
10: 60,135,276 (GRCm39) |
C317S |
probably damaging |
Het |
| Rif1 |
A |
G |
2: 51,967,001 (GRCm39) |
I97V |
probably benign |
Het |
| Rnf123 |
T |
A |
9: 107,940,882 (GRCm39) |
|
probably null |
Het |
| Rnf19a |
G |
A |
15: 36,254,650 (GRCm39) |
R303* |
probably null |
Het |
| Sdk1 |
G |
A |
5: 142,082,489 (GRCm39) |
V1036I |
probably benign |
Het |
| Shc3 |
T |
A |
13: 51,620,588 (GRCm39) |
Y146F |
probably benign |
Het |
| Skint6 |
A |
G |
4: 112,963,109 (GRCm39) |
Y441H |
probably benign |
Het |
| Slc7a12 |
T |
C |
3: 14,570,580 (GRCm39) |
I173T |
probably damaging |
Het |
| Spesp1 |
A |
T |
9: 62,189,302 (GRCm39) |
S15T |
possibly damaging |
Het |
| Tarm1 |
A |
T |
7: 3,545,939 (GRCm39) |
|
probably null |
Het |
| Tenm3 |
T |
C |
8: 48,693,479 (GRCm39) |
Y1817C |
probably damaging |
Het |
| Ttc9c |
A |
T |
19: 8,795,904 (GRCm39) |
L45Q |
probably damaging |
Het |
| Ube3a |
C |
T |
7: 58,926,188 (GRCm39) |
T322I |
probably damaging |
Het |
| Vac14 |
T |
A |
8: 111,439,430 (GRCm39) |
V669E |
probably damaging |
Het |
| Vmn1r225 |
A |
G |
17: 20,723,416 (GRCm39) |
M286V |
probably null |
Het |
| Zfp658 |
A |
G |
7: 43,224,172 (GRCm39) |
K816E |
possibly damaging |
Het |
| Zfp846 |
T |
C |
9: 20,499,188 (GRCm39) |
M1T |
probably null |
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 |
|
|
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 |
|
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'- GTGTTTGGAGCTCGATCTACC -3'
(R):5'- ATGGCAAGGACATTGGGCTC -3'
Sequencing Primer
(F):5'- CGATCTACCGAGCACTTGC -3'
(R):5'- CATTGGGCTCAGGAAAAAGTC -3'
|
| Posted On |
2019-05-13 |
Incidental Mutation