Incidental Mutation 'R4081:Plod3'
| ID |
316875 |
| 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 |
040977-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4081 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
137015873-137025500 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to C
at 137017000 bp (GRCm39)
|
| 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]
[ENSMUST00000156963]
[ENSMUST00000137272]
|
| 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: ENSMUST00000144784
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137419
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151642
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129896
|
| 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 |
0.1039 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 96.0%
|
| Validation Efficiency |
98% (58/59) |
| 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: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aass |
A |
T |
6: 23,109,497 (GRCm39) |
D324E |
possibly damaging |
Het |
| Adad1 |
A |
G |
3: 37,118,512 (GRCm39) |
|
probably null |
Het |
| Aim2 |
T |
C |
1: 173,287,417 (GRCm39) |
|
probably null |
Het |
| Arhgef1 |
G |
T |
7: 24,625,271 (GRCm39) |
D850Y |
probably damaging |
Het |
| Ccnf |
T |
C |
17: 24,442,872 (GRCm39) |
*778W |
probably null |
Het |
| Cd53 |
T |
C |
3: 106,669,461 (GRCm39) |
H179R |
probably benign |
Het |
| Cit |
G |
T |
5: 116,086,109 (GRCm39) |
R891L |
probably damaging |
Het |
| Clec4b1 |
T |
C |
6: 123,046,733 (GRCm39) |
|
probably null |
Het |
| Cntrl |
C |
A |
2: 35,051,938 (GRCm39) |
|
probably benign |
Het |
| Cntrl |
A |
G |
2: 35,065,137 (GRCm39) |
D2148G |
probably damaging |
Het |
| Cpa5 |
T |
C |
6: 30,631,228 (GRCm39) |
S381P |
probably benign |
Het |
| Crybg1 |
A |
T |
10: 43,851,035 (GRCm39) |
V1612D |
probably damaging |
Het |
| Cwc25 |
G |
T |
11: 97,644,744 (GRCm39) |
Q205K |
probably benign |
Het |
| Cyp2d11 |
A |
T |
15: 82,276,002 (GRCm39) |
I193N |
possibly damaging |
Het |
| Gdi2 |
T |
A |
13: 3,598,866 (GRCm39) |
C17S |
probably benign |
Het |
| Gm5436 |
T |
A |
12: 84,305,489 (GRCm39) |
|
noncoding transcript |
Het |
| Ifit1bl1 |
T |
C |
19: 34,572,040 (GRCm39) |
Y139C |
possibly damaging |
Het |
| Insr |
A |
T |
8: 3,261,391 (GRCm39) |
M321K |
probably benign |
Het |
| Ippk |
T |
A |
13: 49,599,852 (GRCm39) |
L237Q |
probably damaging |
Het |
| Itpr1 |
T |
A |
6: 108,368,796 (GRCm39) |
I149N |
probably damaging |
Het |
| Kcnh8 |
GAGACCAACGAGCAGCTGATGCTTCAGA |
GAGA |
17: 53,032,934 (GRCm39) |
74 |
probably benign |
Het |
| Klk14 |
G |
A |
7: 43,341,501 (GRCm39) |
C51Y |
probably damaging |
Het |
| Lrp2 |
T |
A |
2: 69,343,617 (GRCm39) |
H914L |
probably damaging |
Het |
| Myd88 |
G |
T |
9: 119,169,053 (GRCm39) |
|
probably benign |
Het |
| Myh2 |
T |
C |
11: 67,081,256 (GRCm39) |
S1291P |
probably benign |
Het |
| Mylk3 |
G |
A |
8: 86,055,311 (GRCm39) |
L549F |
probably damaging |
Het |
| Otog |
T |
C |
7: 45,937,723 (GRCm39) |
S1811P |
possibly damaging |
Het |
| Phrf1 |
T |
C |
7: 140,838,970 (GRCm39) |
|
probably benign |
Het |
| Prorp |
G |
T |
12: 55,351,398 (GRCm39) |
V236F |
possibly damaging |
Het |
| Ptprh |
T |
A |
7: 4,583,987 (GRCm39) |
T202S |
probably damaging |
Het |
| Ptprr |
A |
T |
10: 116,072,615 (GRCm39) |
K329N |
probably benign |
Het |
| Rgl3 |
T |
A |
9: 21,898,971 (GRCm39) |
H156L |
possibly damaging |
Het |
| Sema6b |
A |
G |
17: 56,435,307 (GRCm39) |
V312A |
probably damaging |
Het |
| Sez6l |
T |
C |
5: 112,609,032 (GRCm39) |
I606V |
probably benign |
Het |
| Slco1a1 |
T |
C |
6: 141,881,688 (GRCm39) |
E148G |
probably damaging |
Het |
| Snph |
T |
C |
2: 151,435,722 (GRCm39) |
D402G |
probably damaging |
Het |
| Sohlh1 |
A |
G |
2: 25,735,734 (GRCm39) |
V135A |
probably benign |
Het |
| Sox14 |
T |
C |
9: 99,757,277 (GRCm39) |
E154G |
possibly damaging |
Het |
| Spta1 |
A |
G |
1: 174,041,632 (GRCm39) |
D1334G |
probably benign |
Het |
| Stard13 |
C |
A |
5: 151,016,294 (GRCm39) |
|
probably null |
Het |
| Szt2 |
A |
G |
4: 118,230,764 (GRCm39) |
|
probably benign |
Het |
| Tab2 |
G |
A |
10: 7,795,595 (GRCm39) |
P296S |
probably damaging |
Het |
| Tbx15 |
A |
G |
3: 99,220,370 (GRCm39) |
D48G |
possibly damaging |
Het |
| Tex10 |
T |
C |
4: 48,468,873 (GRCm39) |
S101G |
probably benign |
Het |
| Tex11 |
C |
A |
X: 99,977,021 (GRCm39) |
A487S |
possibly damaging |
Het |
| Tulp4 |
C |
T |
17: 6,282,055 (GRCm39) |
H695Y |
probably damaging |
Het |
| Vmn1r66 |
A |
G |
7: 10,008,733 (GRCm39) |
I100T |
probably damaging |
Het |
| Vmn2r106 |
A |
T |
17: 20,487,818 (GRCm39) |
Y860* |
probably null |
Het |
| Vwa3b |
C |
T |
1: 37,074,905 (GRCm39) |
T24I |
probably damaging |
Het |
| Zfp541 |
G |
A |
7: 15,806,060 (GRCm39) |
S65N |
probably benign |
Het |
| Zfp992 |
C |
T |
4: 146,551,976 (GRCm39) |
H566Y |
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 |
|
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'- TCTGGAGATCAAATGTGCTGAAAG -3'
(R):5'- ACTGTTCGAGCCACATCACC -3'
Sequencing Primer
(F):5'- TGTGCTGAAAGAACTTTAGTGAAG -3'
(R):5'- CCCAGGGTCTGCAGGAAAGATC -3'
|
| Posted On |
2015-05-15 |
Incidental Mutation