Incidental Mutation 'R5427:Plod3'
| ID |
426949 |
| 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 |
042993-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5427 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
137015873-137025500 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 137020642 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Phenylalanine
at position 547
(Y547F)
|
| 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 damaging
Transcript: ENSMUST00000004968
AA Change: Y547F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
AA Change: Y547F
| 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 |
unknown
Transcript: ENSMUST00000127100
AA Change: Y17F
|
| SMART Domains |
Protein: ENSMUSP00000123550
Gene: ENSMUSG00000004846
AA Change: Y17F
| 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: ENSMUST00000137419
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144784
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151642
|
| 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 |
0.7600 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.3%
|
| Validation Efficiency |
97% (58/60) |
| 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: 56 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aaas |
A |
G |
15: 102,248,385 (GRCm39) |
V277A |
possibly damaging |
Het |
| Adcy7 |
G |
A |
8: 89,052,829 (GRCm39) |
|
probably null |
Het |
| Adgrg5 |
A |
T |
8: 95,661,730 (GRCm39) |
D157V |
probably benign |
Het |
| Akap13 |
A |
G |
7: 75,378,617 (GRCm39) |
N2090S |
possibly damaging |
Het |
| Alpi |
T |
C |
1: 87,029,076 (GRCm39) |
N33D |
probably benign |
Het |
| Anapc15 |
C |
T |
7: 101,547,810 (GRCm39) |
P68L |
probably damaging |
Het |
| Ankrd34a |
G |
A |
3: 96,504,837 (GRCm39) |
G14R |
probably damaging |
Het |
| Anp32a |
A |
G |
9: 62,284,598 (GRCm39) |
|
probably benign |
Het |
| Atg4b |
G |
C |
1: 93,702,928 (GRCm39) |
K86N |
probably damaging |
Het |
| Bbx |
T |
C |
16: 50,100,860 (GRCm39) |
T12A |
probably benign |
Het |
| Catsperg2 |
T |
C |
7: 29,414,275 (GRCm39) |
T377A |
possibly damaging |
Het |
| Ccdc158 |
T |
C |
5: 92,796,821 (GRCm39) |
Q505R |
probably damaging |
Het |
| Cep135 |
T |
A |
5: 76,786,049 (GRCm39) |
S1051T |
probably benign |
Het |
| Cryab |
A |
G |
9: 50,667,593 (GRCm39) |
D109G |
probably damaging |
Het |
| Crym |
A |
C |
7: 119,798,445 (GRCm39) |
|
probably benign |
Het |
| Csf2rb2 |
T |
A |
15: 78,173,111 (GRCm39) |
S250C |
probably damaging |
Het |
| Diaph1 |
A |
T |
18: 38,023,648 (GRCm39) |
V730E |
unknown |
Het |
| Eci3 |
G |
T |
13: 35,143,931 (GRCm39) |
L65M |
possibly damaging |
Het |
| Erg28 |
T |
C |
12: 85,866,341 (GRCm39) |
N46D |
probably damaging |
Het |
| Fam89b |
A |
G |
19: 5,778,819 (GRCm39) |
S127P |
probably benign |
Het |
| Fign |
A |
G |
2: 63,809,342 (GRCm39) |
Y643H |
probably damaging |
Het |
| Galk2 |
T |
C |
2: 125,788,741 (GRCm39) |
V265A |
probably benign |
Het |
| Gclm |
T |
C |
3: 122,059,976 (GRCm39) |
V252A |
probably damaging |
Het |
| Git2 |
A |
G |
5: 114,868,389 (GRCm39) |
S584P |
possibly damaging |
Het |
| Iqcf3 |
T |
C |
9: 106,421,059 (GRCm39) |
|
probably null |
Het |
| Kcnk3 |
A |
G |
5: 30,779,639 (GRCm39) |
T230A |
possibly damaging |
Het |
| Mettl25b |
T |
C |
3: 87,831,639 (GRCm39) |
|
probably benign |
Het |
| Myh10 |
T |
C |
11: 68,693,757 (GRCm39) |
L1486P |
probably damaging |
Het |
| Myom2 |
C |
A |
8: 15,163,764 (GRCm39) |
A1006E |
probably benign |
Het |
| Myt1l |
G |
A |
12: 29,882,331 (GRCm39) |
G509R |
unknown |
Het |
| Nampt |
A |
T |
12: 32,884,914 (GRCm39) |
H111L |
probably benign |
Het |
| Nid1 |
A |
G |
13: 13,658,268 (GRCm39) |
Y671C |
probably damaging |
Het |
| Npy5r |
G |
A |
8: 67,133,672 (GRCm39) |
R374C |
probably damaging |
Het |
| Or10ag54 |
A |
T |
2: 87,099,858 (GRCm39) |
K244N |
probably benign |
Het |
| Or5b123 |
A |
T |
19: 13,596,714 (GRCm39) |
S20C |
probably benign |
Het |
| Palld |
C |
T |
8: 62,003,106 (GRCm39) |
C720Y |
probably benign |
Het |
| Pcsk6 |
C |
T |
7: 65,683,647 (GRCm39) |
T606M |
probably benign |
Het |
| Pfas |
T |
C |
11: 68,891,979 (GRCm39) |
I176M |
possibly damaging |
Het |
| Pi4kb |
A |
G |
3: 94,901,518 (GRCm39) |
D395G |
probably benign |
Het |
| Plscr1l1 |
G |
A |
9: 92,234,649 (GRCm39) |
C128Y |
probably benign |
Het |
| Pnpo |
T |
C |
11: 96,834,633 (GRCm39) |
Y21C |
probably benign |
Het |
| Rgs1 |
A |
T |
1: 144,122,018 (GRCm39) |
C118* |
probably null |
Het |
| Slc22a27 |
A |
G |
19: 7,856,753 (GRCm39) |
|
probably null |
Het |
| Sntb1 |
C |
G |
15: 55,506,191 (GRCm39) |
G461R |
probably damaging |
Het |
| Sppl2c |
G |
A |
11: 104,078,693 (GRCm39) |
V498I |
probably benign |
Het |
| Stim2 |
A |
T |
5: 54,268,281 (GRCm39) |
I448F |
possibly damaging |
Het |
| Sulf1 |
A |
T |
1: 12,867,136 (GRCm39) |
T107S |
possibly damaging |
Het |
| Tenm3 |
A |
G |
8: 48,689,599 (GRCm39) |
V1996A |
probably damaging |
Het |
| Timm23 |
G |
A |
14: 31,911,103 (GRCm39) |
T171I |
possibly damaging |
Het |
| Tssk2 |
A |
G |
16: 17,716,729 (GRCm39) |
D44G |
probably damaging |
Het |
| Vmn2r28 |
A |
T |
7: 5,489,376 (GRCm39) |
Y488N |
probably damaging |
Het |
| Zbed6 |
A |
G |
1: 133,585,333 (GRCm39) |
V668A |
possibly damaging |
Het |
| Zbtb48 |
A |
G |
4: 152,105,108 (GRCm39) |
F518S |
probably damaging |
Het |
| Zfp709 |
A |
G |
8: 72,642,976 (GRCm39) |
E135G |
probably benign |
Het |
| Zfp788 |
G |
A |
7: 41,299,076 (GRCm39) |
V571I |
possibly damaging |
Het |
| Zfp963 |
A |
G |
8: 70,196,106 (GRCm39) |
S116P |
probably benign |
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 |
|
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'- TGATGTCCTCCTCACGCATG -3'
(R):5'- TAACACTTAGTGTGGCCGTTAGC -3'
Sequencing Primer
(F):5'- AACCAGCACGAGTTTGGC -3'
(R):5'- CCTTCCTCTCGCCCGAATAGG -3'
|
| Posted On |
2016-09-01 |
Incidental Mutation