Incidental Mutation 'R5657:Plod1'
ID |
501235 |
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 |
043171-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R5657 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
4 |
Chromosomal Location |
147994210-148021224 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 148003238 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Glutamic Acid to Glycine
at position 529
(E529G)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000019199
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000019199]
|
AlphaFold |
Q9R0E2 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000019199
AA Change: E529G
PolyPhen 2
Score 0.457 (Sensitivity: 0.89; Specificity: 0.90)
|
SMART Domains |
Protein: ENSMUSP00000019199 Gene: ENSMUSG00000019055 AA Change: E529G
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 |
unknown
Transcript: ENSMUST00000149129
AA Change: E115G
|
SMART Domains |
Protein: ENSMUSP00000118857 Gene: ENSMUSG00000019055 AA Change: E115G
Domain | Start | End | E-Value | Type |
Blast:P4Hc
|
31 |
136 |
5e-33 |
BLAST |
Blast:P4Hc
|
141 |
269 |
4e-47 |
BLAST |
|
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.6%
|
Validation Efficiency |
|
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: 38 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Agbl5 |
A |
G |
5: 31,051,390 (GRCm39) |
Y533C |
probably damaging |
Het |
Ahnak |
T |
C |
19: 8,991,979 (GRCm39) |
V4421A |
probably damaging |
Het |
Bach1 |
A |
G |
16: 87,516,173 (GRCm39) |
K238R |
probably benign |
Het |
Bloc1s6 |
T |
A |
2: 122,580,577 (GRCm39) |
V12D |
probably benign |
Het |
Clca3b |
C |
A |
3: 144,533,144 (GRCm39) |
L629F |
probably benign |
Het |
Clhc1 |
A |
G |
11: 29,511,431 (GRCm39) |
I292V |
probably benign |
Het |
Col27a1 |
T |
C |
4: 63,143,547 (GRCm39) |
S412P |
probably damaging |
Het |
Col6a4 |
A |
G |
9: 105,949,397 (GRCm39) |
I746T |
probably damaging |
Het |
Cracr2a |
G |
A |
6: 127,580,970 (GRCm39) |
A49T |
probably damaging |
Het |
Cyb561d1 |
A |
G |
3: 108,108,008 (GRCm39) |
I28T |
possibly damaging |
Het |
Dnah11 |
T |
A |
12: 117,847,352 (GRCm39) |
M4264L |
probably damaging |
Het |
Dnajc13 |
A |
G |
9: 104,105,736 (GRCm39) |
L412S |
probably damaging |
Het |
Dpf3 |
T |
C |
12: 83,371,785 (GRCm39) |
N150S |
probably damaging |
Het |
Epha2 |
T |
C |
4: 141,050,805 (GRCm39) |
C854R |
probably damaging |
Het |
Fat2 |
G |
T |
11: 55,201,507 (GRCm39) |
Y522* |
probably null |
Het |
Foxm1 |
A |
T |
6: 128,350,351 (GRCm39) |
S551C |
possibly damaging |
Het |
Galnt12 |
T |
C |
4: 47,104,150 (GRCm39) |
V136A |
possibly damaging |
Het |
Gm6647 |
T |
G |
5: 13,818,835 (GRCm39) |
|
noncoding transcript |
Het |
Grin2b |
T |
A |
6: 135,710,085 (GRCm39) |
I1154F |
possibly damaging |
Het |
Hmcn1 |
A |
G |
1: 150,534,313 (GRCm39) |
V2987A |
probably benign |
Het |
Jade2 |
A |
G |
11: 51,707,814 (GRCm39) |
S800P |
probably damaging |
Het |
Naip6 |
C |
A |
13: 100,436,909 (GRCm39) |
S538I |
probably benign |
Het |
Or1e33 |
T |
C |
11: 73,738,366 (GRCm39) |
N195S |
probably damaging |
Het |
Plekha6 |
G |
C |
1: 133,200,045 (GRCm39) |
R208P |
possibly damaging |
Het |
Plppr2 |
T |
C |
9: 21,858,911 (GRCm39) |
C343R |
probably damaging |
Het |
Prpf38a |
T |
C |
4: 108,425,621 (GRCm39) |
D219G |
probably damaging |
Het |
Ptpra |
G |
A |
2: 130,346,204 (GRCm39) |
E122K |
probably benign |
Het |
Rabl2 |
T |
C |
15: 89,472,416 (GRCm39) |
M38V |
probably benign |
Het |
Reep1 |
A |
G |
6: 71,738,358 (GRCm39) |
M39V |
possibly damaging |
Het |
Rsf1 |
GC |
GCGGCGGCGTC |
7: 97,229,141 (GRCm39) |
|
probably benign |
Het |
Slc26a10 |
T |
C |
10: 127,010,833 (GRCm39) |
|
probably benign |
Het |
Sun2 |
C |
A |
15: 79,612,150 (GRCm39) |
E510* |
probably null |
Het |
Tanc1 |
A |
G |
2: 59,665,051 (GRCm39) |
|
probably null |
Het |
Ticam1 |
TCACACA |
TCACA |
17: 56,577,629 (GRCm39) |
|
probably null |
Het |
Tor1aip1 |
G |
T |
1: 155,883,234 (GRCm39) |
H205N |
probably damaging |
Het |
Trpc6 |
C |
T |
9: 8,609,808 (GRCm39) |
T92I |
probably benign |
Het |
Vmn2r100 |
T |
A |
17: 19,725,178 (GRCm39) |
F36I |
probably benign |
Het |
Zfp787 |
T |
C |
7: 6,136,053 (GRCm39) |
Y66C |
probably 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 |
R1216:Plod1
|
UTSW |
4 |
148,005,584 (GRCm39) |
missense |
probably damaging |
0.98 |
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 |
|
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'- TCAATTAAGTCATAGCTCCCTGC -3'
(R):5'- GCTGGGAGCACATACTGTACTC -3'
Sequencing Primer
(F):5'- GCTCCCTGCTCCACTAGGTG -3'
(R):5'- ACTCACAGGTCTTTAATCTGGTTG -3'
|
Posted On |
2017-12-01 |