Incidental Mutation 'R2179:Plod3'
| ID |
237044 |
| 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 |
040181-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R2179 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
5 |
| Chromosomal Location |
137015873-137025500 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 137019862 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Phenylalanine to Leucine
at position 431
(F431L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000004968
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004968]
[ENSMUST00000034953]
[ENSMUST00000085941]
[ENSMUST00000111090]
[ENSMUST00000111091]
[ENSMUST00000156963]
[ENSMUST00000137272]
|
| AlphaFold |
Q9R0E1 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000004968
AA Change: F431L
PolyPhen 2
Score 0.771 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
AA Change: F431L
| 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: 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 |
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.5%
|
| 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: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgb |
T |
C |
10: 10,271,018 (GRCm39) |
D849G |
possibly damaging |
Het |
| Amz2 |
A |
G |
11: 109,320,658 (GRCm39) |
H155R |
probably damaging |
Het |
| Cfhr4 |
G |
T |
1: 139,659,279 (GRCm39) |
P679Q |
probably damaging |
Het |
| Chuk |
C |
A |
19: 44,092,160 (GRCm39) |
C46F |
possibly damaging |
Het |
| Cp |
A |
T |
3: 20,042,151 (GRCm39) |
D973V |
probably damaging |
Het |
| Cpm |
T |
A |
10: 117,519,266 (GRCm39) |
D391E |
probably benign |
Het |
| Creb3 |
T |
C |
4: 43,566,306 (GRCm39) |
S271P |
probably damaging |
Het |
| Cubn |
T |
A |
2: 13,323,053 (GRCm39) |
H2838L |
possibly damaging |
Het |
| Dennd2d |
A |
G |
3: 106,399,776 (GRCm39) |
H233R |
probably benign |
Het |
| Dnaaf2 |
C |
A |
12: 69,245,071 (GRCm39) |
|
probably benign |
Het |
| Enpp3 |
T |
A |
10: 24,681,793 (GRCm39) |
Q304H |
probably benign |
Het |
| Fermt3 |
C |
A |
19: 6,991,782 (GRCm39) |
R143L |
probably benign |
Het |
| Fndc8 |
A |
C |
11: 82,789,580 (GRCm39) |
K246T |
probably damaging |
Het |
| Gaa |
A |
G |
11: 119,165,884 (GRCm39) |
|
probably null |
Het |
| Gucy2e |
A |
T |
11: 69,119,404 (GRCm39) |
|
probably null |
Het |
| Igf1r |
A |
G |
7: 67,653,698 (GRCm39) |
T79A |
probably damaging |
Het |
| Ikbkb |
C |
T |
8: 23,171,769 (GRCm39) |
|
probably null |
Het |
| Il16 |
A |
T |
7: 83,337,287 (GRCm39) |
|
probably null |
Het |
| Irs1 |
T |
A |
1: 82,267,940 (GRCm39) |
H92L |
possibly damaging |
Het |
| Itpr2 |
A |
G |
6: 146,277,464 (GRCm39) |
M315T |
probably benign |
Het |
| Lrba |
T |
G |
3: 86,261,588 (GRCm39) |
L1514R |
probably damaging |
Het |
| Mcpt2 |
A |
G |
14: 56,279,573 (GRCm39) |
|
probably benign |
Het |
| Metap1d |
A |
G |
2: 71,283,715 (GRCm39) |
I5V |
probably benign |
Het |
| Mga |
T |
A |
2: 119,790,923 (GRCm39) |
S2479T |
probably damaging |
Het |
| Mllt10 |
T |
C |
2: 18,215,604 (GRCm39) |
V1063A |
probably damaging |
Het |
| Mroh2b |
G |
A |
15: 4,950,928 (GRCm39) |
|
probably null |
Het |
| Mtfr1 |
C |
T |
3: 19,254,308 (GRCm39) |
R15* |
probably null |
Het |
| Npm2 |
A |
G |
14: 70,885,749 (GRCm39) |
V152A |
probably benign |
Het |
| Nrxn3 |
T |
A |
12: 89,221,448 (GRCm39) |
V409D |
probably damaging |
Het |
| Ogdhl |
A |
G |
14: 32,057,302 (GRCm39) |
N303D |
probably damaging |
Het |
| Or10g9 |
T |
C |
9: 39,912,220 (GRCm39) |
Y101C |
probably benign |
Het |
| Or10q1b |
T |
C |
19: 13,682,758 (GRCm39) |
V189A |
probably damaging |
Het |
| Or4d11 |
T |
C |
19: 12,013,452 (GRCm39) |
Y218C |
probably damaging |
Het |
| Or6s1 |
A |
G |
14: 51,308,238 (GRCm39) |
V204A |
probably benign |
Het |
| Pah |
T |
C |
10: 87,403,197 (GRCm39) |
F191L |
probably damaging |
Het |
| Paics |
A |
T |
5: 77,109,291 (GRCm39) |
I209F |
probably damaging |
Het |
| Pcare |
T |
C |
17: 72,059,521 (GRCm39) |
D52G |
probably damaging |
Het |
| Pld6 |
A |
G |
11: 59,678,184 (GRCm39) |
L93P |
probably damaging |
Het |
| Ppm1b |
T |
A |
17: 85,301,862 (GRCm39) |
D247E |
probably damaging |
Het |
| Prx |
A |
G |
7: 27,217,410 (GRCm39) |
D637G |
probably benign |
Het |
| Rsf1 |
GGCGGCGGC |
GGCGGCGGCCGCGGCGGC |
7: 97,229,116 (GRCm39) |
|
probably benign |
Het |
| Ryr2 |
A |
T |
13: 11,720,679 (GRCm39) |
Y2656* |
probably null |
Het |
| Setd2 |
T |
A |
9: 110,423,756 (GRCm39) |
Y492* |
probably null |
Het |
| Shmt1 |
A |
G |
11: 60,697,825 (GRCm39) |
W9R |
possibly damaging |
Het |
| Slc25a17 |
A |
G |
15: 81,222,151 (GRCm39) |
V107A |
probably benign |
Het |
| Sptlc1 |
A |
T |
13: 53,505,675 (GRCm39) |
Y248N |
probably damaging |
Het |
| Stam2 |
T |
C |
2: 52,584,936 (GRCm39) |
T453A |
probably benign |
Het |
| Tango2 |
G |
T |
16: 18,128,762 (GRCm39) |
N77K |
probably damaging |
Het |
| Tas2r121 |
A |
T |
6: 132,677,831 (GRCm39) |
I47N |
probably damaging |
Het |
| Terb1 |
A |
T |
8: 105,179,347 (GRCm39) |
C614S |
probably damaging |
Het |
| Terb1 |
T |
C |
8: 105,199,369 (GRCm39) |
N525S |
probably benign |
Het |
| Ttc6 |
A |
G |
12: 57,719,904 (GRCm39) |
D825G |
possibly damaging |
Het |
| U90926 |
A |
T |
5: 92,357,838 (GRCm39) |
H104Q |
probably benign |
Het |
| Zfand4 |
G |
A |
6: 116,291,742 (GRCm39) |
A559T |
possibly damaging |
Het |
| Zfp462 |
T |
C |
4: 55,009,524 (GRCm39) |
S497P |
possibly 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 |
|
|
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'- GATGCTGATGCCGTCCTTAC -3'
(R):5'- CATATCACCCTTTCCATAGCGG -3'
Sequencing Primer
(F):5'- TTACGAACCCGGAGACCTTG -3'
(R):5'- TTTCCATAGCGGGGGCCTAG -3'
|
| Posted On |
2014-10-02 |
Incidental Mutation