Incidental Mutation 'R1216:Plod1'
| ID |
99633 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Plod1
|
| Ensembl Gene |
ENSMUSG00000019055 |
| Gene Name |
procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 |
| Synonyms |
2410042F05Rik, LH1, lysyl hydroxylase 1 |
| MMRRC Submission |
039285-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R1216 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
147994210-148021224 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 148005584 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Aspartic acid
at position 404
(V404D)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000019199
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000019199]
|
| AlphaFold |
Q9R0E2 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000019199
AA Change: V404D
PolyPhen 2
Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000019199
Gene: ENSMUSG00000019055
AA Change: V404D
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
|
low complexity region
|
301 |
313 |
N/A |
INTRINSIC |
|
Blast:P4Hc
|
444 |
492 |
1e-8 |
BLAST |
|
P4Hc
|
554 |
727 |
4.87e-26 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000124041
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000124292
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000149129
|
| SMART Domains |
Protein: ENSMUSP00000118857
Gene: ENSMUSG00000019055
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:P4Hc
|
31 |
136 |
5e-33 |
BLAST |
|
Blast:P4Hc
|
141 |
269 |
4e-47 |
BLAST |
|
| Meta Mutation Damage Score |
0.6520 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.2%
- 10x: 96.1%
- 20x: 92.3%
|
| Validation Efficiency |
98% (45/46) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Lysyl hydroxylase is a membrane-bound homodimeric protein localized to the cisternae of the 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 VI have deficiencies in lysyl hydroxylase activity. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
PHENOTYPE: Mice homozygous for a null allele exhibit hypotonia, reduced voluntary movement, abnormal aorta and skin collagen fibers, irregular vascular smooth muscle and premature death associated with thoracic cavity hemorrhage and aortic dissection. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A830018L16Rik |
A |
T |
1: 11,868,716 (GRCm39) |
D332V |
probably damaging |
Het |
| Akr1c12 |
T |
C |
13: 4,326,322 (GRCm39) |
Y53C |
probably benign |
Het |
| Arhgap23 |
T |
C |
11: 97,383,498 (GRCm39) |
|
probably benign |
Het |
| AU040320 |
T |
C |
4: 126,710,276 (GRCm39) |
|
probably benign |
Het |
| B4galnt2 |
A |
G |
11: 95,782,767 (GRCm39) |
L15P |
probably benign |
Het |
| Cadps2 |
A |
G |
6: 23,583,472 (GRCm39) |
|
probably benign |
Het |
| Cul9 |
C |
G |
17: 46,833,101 (GRCm39) |
A1326P |
probably damaging |
Het |
| Dppa4 |
T |
C |
16: 48,113,343 (GRCm39) |
F244S |
possibly damaging |
Het |
| Exoc1 |
A |
G |
5: 76,702,035 (GRCm39) |
K445R |
probably benign |
Het |
| Fam47e |
A |
G |
5: 92,710,343 (GRCm39) |
E114G |
probably damaging |
Het |
| Fgf12 |
A |
T |
16: 27,981,202 (GRCm39) |
N171K |
possibly damaging |
Het |
| Fyb2 |
G |
A |
4: 104,852,903 (GRCm39) |
V528M |
possibly damaging |
Het |
| Ghr |
A |
G |
15: 3,349,337 (GRCm39) |
S614P |
probably damaging |
Het |
| Gm10985 |
A |
C |
3: 53,752,674 (GRCm39) |
Y19S |
probably damaging |
Het |
| Gpr152 |
T |
A |
19: 4,193,554 (GRCm39) |
V365D |
possibly damaging |
Het |
| Guca1a |
A |
G |
17: 47,706,637 (GRCm39) |
|
probably benign |
Het |
| Hivep1 |
G |
A |
13: 42,310,997 (GRCm39) |
G1079D |
probably benign |
Het |
| Hnrnpm |
T |
C |
17: 33,868,687 (GRCm39) |
D580G |
probably damaging |
Het |
| Ints6 |
A |
T |
14: 62,945,147 (GRCm39) |
D394E |
probably damaging |
Het |
| Kat6b |
T |
A |
14: 21,672,108 (GRCm39) |
Y339* |
probably null |
Het |
| Kcnj11 |
C |
A |
7: 45,749,285 (GRCm39) |
V13L |
probably benign |
Het |
| Lama3 |
C |
T |
18: 12,554,191 (GRCm39) |
|
probably benign |
Het |
| Mtrex |
A |
G |
13: 113,050,876 (GRCm39) |
|
probably benign |
Het |
| Myo18a |
A |
G |
11: 77,709,473 (GRCm39) |
T161A |
probably benign |
Het |
| Ncapg |
G |
T |
5: 45,857,261 (GRCm39) |
S991I |
possibly damaging |
Het |
| Nrde2 |
G |
A |
12: 100,116,069 (GRCm39) |
|
probably benign |
Het |
| Or4c127 |
T |
A |
2: 89,832,822 (GRCm39) |
I24N |
probably benign |
Het |
| Or5d18 |
T |
C |
2: 87,864,602 (GRCm39) |
R294G |
probably damaging |
Het |
| Pcdhb7 |
A |
T |
18: 37,476,927 (GRCm39) |
T688S |
probably damaging |
Het |
| Pla2g6 |
T |
C |
15: 79,190,635 (GRCm39) |
D309G |
probably benign |
Het |
| Ppp2r2a |
G |
T |
14: 67,266,447 (GRCm39) |
Y71* |
probably null |
Het |
| Prcp |
A |
G |
7: 92,566,954 (GRCm39) |
N222S |
probably benign |
Het |
| Rad21 |
T |
C |
15: 51,833,532 (GRCm39) |
T316A |
possibly damaging |
Het |
| Ranbp2 |
T |
C |
10: 58,319,034 (GRCm39) |
|
probably benign |
Het |
| Rapgef4 |
C |
A |
2: 72,038,492 (GRCm39) |
P548T |
possibly damaging |
Het |
| Ric1 |
G |
T |
19: 29,555,135 (GRCm39) |
M416I |
probably benign |
Het |
| Slc9a8 |
T |
C |
2: 167,266,041 (GRCm39) |
F6S |
probably benign |
Het |
| Smpdl3a |
T |
G |
10: 57,678,575 (GRCm39) |
I126S |
probably null |
Het |
| Sphkap |
A |
T |
1: 83,268,698 (GRCm39) |
L98Q |
probably damaging |
Het |
| Spink4 |
T |
G |
4: 40,924,974 (GRCm39) |
|
probably benign |
Het |
| Taar5 |
A |
T |
10: 23,847,605 (GRCm39) |
L334F |
probably damaging |
Het |
| Tecta |
A |
T |
9: 42,289,203 (GRCm39) |
I454K |
probably benign |
Het |
| Ttc7 |
C |
T |
17: 87,654,006 (GRCm39) |
T561M |
possibly damaging |
Het |
| Vmn2r9 |
G |
T |
5: 108,995,440 (GRCm39) |
H403N |
probably damaging |
Het |
| Zdbf2 |
G |
A |
1: 63,342,161 (GRCm39) |
C180Y |
possibly damaging |
Het |
|
| Other mutations in Plod1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01144:Plod1
|
APN |
4 |
148,017,211 (GRCm39) |
missense |
probably benign |
0.12 |
|
IGL02312:Plod1
|
APN |
4 |
148,010,614 (GRCm39) |
missense |
probably benign |
0.09 |
|
IGL02588:Plod1
|
APN |
4 |
147,997,747 (GRCm39) |
nonsense |
probably null |
|
|
IGL02712:Plod1
|
APN |
4 |
148,003,344 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL02976:Plod1
|
APN |
4 |
147,997,778 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL03244:Plod1
|
APN |
4 |
148,007,580 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0393:Plod1
|
UTSW |
4 |
148,003,298 (GRCm39) |
missense |
probably null |
0.35 |
|
R1897:Plod1
|
UTSW |
4 |
148,010,657 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R3776:Plod1
|
UTSW |
4 |
148,015,734 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R3923:Plod1
|
UTSW |
4 |
148,000,280 (GRCm39) |
missense |
possibly damaging |
0.62 |
|
R4718:Plod1
|
UTSW |
4 |
148,000,701 (GRCm39) |
intron |
probably benign |
|
|
R4897:Plod1
|
UTSW |
4 |
148,004,736 (GRCm39) |
missense |
probably benign |
|
|
R5173:Plod1
|
UTSW |
4 |
148,000,758 (GRCm39) |
intron |
probably benign |
|
|
R5657:Plod1
|
UTSW |
4 |
148,003,238 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R6298:Plod1
|
UTSW |
4 |
148,000,772 (GRCm39) |
intron |
probably benign |
|
|
R6995:Plod1
|
UTSW |
4 |
148,000,675 (GRCm39) |
intron |
probably benign |
|
|
R7176:Plod1
|
UTSW |
4 |
147,997,744 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7632:Plod1
|
UTSW |
4 |
148,011,481 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8059:Plod1
|
UTSW |
4 |
148,012,941 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8167:Plod1
|
UTSW |
4 |
148,004,658 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8804:Plod1
|
UTSW |
4 |
147,997,778 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8909:Plod1
|
UTSW |
4 |
148,011,563 (GRCm39) |
nonsense |
probably null |
|
|
R8986:Plod1
|
UTSW |
4 |
147,997,734 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9245:Plod1
|
UTSW |
4 |
148,010,626 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R9646:Plod1
|
UTSW |
4 |
148,016,112 (GRCm39) |
missense |
probably benign |
0.03 |
|
X0013:Plod1
|
UTSW |
4 |
148,011,499 (GRCm39) |
missense |
possibly damaging |
0.70 |
|
Y5406:Plod1
|
UTSW |
4 |
148,015,644 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Y5408:Plod1
|
UTSW |
4 |
148,015,644 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Plod1
|
UTSW |
4 |
148,007,657 (GRCm39) |
missense |
probably damaging |
0.99 |
|
Z1177:Plod1
|
UTSW |
4 |
148,016,178 (GRCm39) |
missense |
probably benign |
0.02 |
|
| Predicted Primers |
PCR Primer
(F):5'- ATGGGAGCCCACGACAACTTTCAG -3'
(R):5'- CCATAAAGCCAAGCTATGCGGACAG -3'
Sequencing Primer
(F):5'- TTGAGGTTCAGCTCACCCAG -3'
(R):5'- GCCTAAGGCTCCTGATTGAAC -3'
|
| Posted On |
2014-01-15 |
Incidental Mutation