Incidental Mutation 'R0764:Plod3'
| ID |
72547 |
| 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 |
038944-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R0764 (G1)
|
| Quality Score |
193 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
137015873-137025500 bp(+) (GRCm39) |
| Type of Mutation |
unclassified |
| DNA Base Change (assembly) |
C to T
at 137018437 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000115929
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004968]
[ENSMUST00000034953]
[ENSMUST00000085941]
[ENSMUST00000111090]
[ENSMUST00000111091]
[ENSMUST00000156963]
[ENSMUST00000137272]
|
| AlphaFold |
Q9R0E1 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000004968
|
| SMART Domains |
Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
| 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: ENSMUST00000129896
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144784
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151642
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137419
|
| 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 |
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.1%
|
| Validation Efficiency |
98% (48/49) |
| 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: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca8a |
A |
T |
11: 109,950,772 (GRCm39) |
Y898N |
probably damaging |
Het |
| Acp4 |
T |
C |
7: 43,901,738 (GRCm39) |
|
probably benign |
Het |
| Adipor2 |
T |
C |
6: 119,334,215 (GRCm39) |
I332V |
probably benign |
Het |
| Ago3 |
T |
A |
4: 126,248,885 (GRCm39) |
K555N |
possibly damaging |
Het |
| Angpt4 |
A |
G |
2: 151,753,204 (GRCm39) |
|
probably benign |
Het |
| Ano5 |
G |
T |
7: 51,187,590 (GRCm39) |
|
probably benign |
Het |
| Ap3b1 |
C |
T |
13: 94,616,387 (GRCm39) |
|
probably benign |
Het |
| Cbl |
A |
T |
9: 44,075,449 (GRCm39) |
C399S |
probably damaging |
Het |
| Cdkl2 |
C |
A |
5: 92,168,136 (GRCm39) |
V353L |
probably benign |
Het |
| Celsr3 |
A |
G |
9: 108,705,017 (GRCm39) |
Y500C |
probably damaging |
Het |
| Cep162 |
A |
G |
9: 87,083,798 (GRCm39) |
S1242P |
probably damaging |
Het |
| Crhr1 |
C |
T |
11: 104,050,152 (GRCm39) |
R66W |
probably damaging |
Het |
| Ddx49 |
T |
C |
8: 70,749,907 (GRCm39) |
E170G |
probably benign |
Het |
| Fam193a |
T |
C |
5: 34,600,685 (GRCm39) |
F305L |
probably damaging |
Het |
| Fam76a |
C |
T |
4: 132,638,010 (GRCm39) |
G198R |
probably damaging |
Het |
| Gm43302 |
T |
A |
5: 105,428,355 (GRCm39) |
I130F |
probably benign |
Het |
| Hectd4 |
T |
A |
5: 121,424,832 (GRCm39) |
I745N |
possibly damaging |
Het |
| Ina |
T |
A |
19: 47,012,087 (GRCm39) |
*502K |
probably null |
Het |
| Kdm1b |
A |
T |
13: 47,222,079 (GRCm39) |
D506V |
possibly damaging |
Het |
| Lrrk2 |
A |
G |
15: 91,659,249 (GRCm39) |
|
probably null |
Het |
| Ly6g2 |
T |
A |
15: 75,092,572 (GRCm39) |
F97Y |
probably benign |
Het |
| Naip5 |
A |
T |
13: 100,353,613 (GRCm39) |
D1215E |
probably benign |
Het |
| Neb |
A |
G |
2: 52,106,879 (GRCm39) |
|
probably benign |
Het |
| Nectin2 |
T |
A |
7: 19,483,096 (GRCm39) |
|
probably null |
Het |
| Nup155 |
A |
T |
15: 8,187,244 (GRCm39) |
H1391L |
probably damaging |
Het |
| Or2aj5 |
G |
T |
16: 19,425,182 (GRCm39) |
P79T |
probably damaging |
Het |
| Or4a71 |
A |
G |
2: 89,358,340 (GRCm39) |
V138A |
probably benign |
Het |
| Osbp |
A |
G |
19: 11,961,520 (GRCm39) |
|
probably benign |
Het |
| Otog |
A |
G |
7: 45,949,918 (GRCm39) |
D2460G |
probably benign |
Het |
| Pcgf1 |
T |
C |
6: 83,056,150 (GRCm39) |
C2R |
probably damaging |
Het |
| Per2 |
C |
T |
1: 91,357,142 (GRCm39) |
V674M |
probably damaging |
Het |
| Pias3 |
C |
T |
3: 96,608,611 (GRCm39) |
P218S |
probably damaging |
Het |
| Purb |
C |
T |
11: 6,425,661 (GRCm39) |
V76M |
probably damaging |
Het |
| Ranbp1 |
C |
A |
16: 18,058,022 (GRCm39) |
E181* |
probably null |
Het |
| Rit2 |
T |
C |
18: 31,286,754 (GRCm39) |
|
probably benign |
Het |
| Rnf103 |
C |
A |
6: 71,486,566 (GRCm39) |
T399K |
probably damaging |
Het |
| Slc22a13 |
T |
C |
9: 119,037,746 (GRCm39) |
|
probably null |
Het |
| Slc35f4 |
T |
A |
14: 49,543,796 (GRCm39) |
|
probably benign |
Het |
| Sucla2 |
C |
T |
14: 73,798,074 (GRCm39) |
|
probably benign |
Het |
| Tnfrsf17 |
C |
T |
16: 11,133,063 (GRCm39) |
T47M |
possibly damaging |
Het |
| Tram1 |
A |
G |
1: 13,649,933 (GRCm39) |
I97T |
probably damaging |
Het |
| Ttc38 |
T |
C |
15: 85,730,604 (GRCm39) |
|
probably benign |
Het |
| Zfp113 |
T |
A |
5: 138,143,506 (GRCm39) |
Q248L |
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 |
|
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'- TCAATGGAGCCTTAGGTGAGGACG -3'
(R):5'- GGCACCCTTTTCTGCTGGAAATGG -3'
Sequencing Primer
(F):5'- gagcacctgcctagaatcc -3'
(R):5'- TTTCTGCTGGAAATGGAGAAAACC -3'
|
| Posted On |
2013-09-30 |
Incidental Mutation