Incidental Mutation 'R8909:Plod1'
| ID |
678498 |
| 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 |
068700-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R8909 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
147994210-148021224 bp(-) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
T to A
at 148011563 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Stop codon
at position 221
(K221*)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000019199
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000019199]
[ENSMUST00000105712]
|
| AlphaFold |
Q9R0E2 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000019199
AA Change: K221*
|
| SMART Domains |
Protein: ENSMUSP00000019199
Gene: ENSMUSG00000019055
AA Change: K221*
| 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 |
probably benign
Transcript: ENSMUST00000105712
|
| SMART Domains |
Protein: ENSMUSP00000101337
Gene: ENSMUSG00000019055
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.8%
|
| Validation Efficiency |
96% (47/49) |
| 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: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aopep |
G |
T |
13: 63,388,111 (GRCm39) |
R698L |
possibly damaging |
Het |
| Btnl10 |
T |
C |
11: 58,813,198 (GRCm39) |
C276R |
probably benign |
Het |
| Calcoco2 |
GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC |
GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC |
11: 95,990,808 (GRCm39) |
|
probably benign |
Het |
| Cavin4 |
G |
A |
4: 48,672,421 (GRCm39) |
G289R |
probably benign |
Het |
| Cdh9 |
T |
C |
15: 16,848,610 (GRCm39) |
F430S |
probably damaging |
Het |
| Cfh |
A |
G |
1: 140,014,086 (GRCm39) |
I1246T |
possibly damaging |
Het |
| Chd8 |
C |
T |
14: 52,450,389 (GRCm39) |
V1490M |
possibly damaging |
Het |
| Clec2g |
A |
G |
6: 128,958,195 (GRCm39) |
N137S |
probably benign |
Het |
| Cntn6 |
T |
A |
6: 104,825,093 (GRCm39) |
S878T |
probably benign |
Het |
| Cryga |
G |
T |
1: 65,142,173 (GRCm39) |
S73R |
probably benign |
Het |
| Dach1 |
T |
C |
14: 98,406,120 (GRCm39) |
D209G |
probably damaging |
Het |
| Dnai4 |
T |
G |
4: 102,944,607 (GRCm39) |
E248A |
possibly damaging |
Het |
| Duox2 |
A |
G |
2: 122,126,862 (GRCm39) |
S218P |
probably benign |
Het |
| Fbn2 |
T |
A |
18: 58,192,508 (GRCm39) |
Q1491L |
possibly damaging |
Het |
| Foxg1 |
CCAGCAGCAGCAGCAGCAGC |
CCAGCAGCAGCAGCAGC |
12: 49,431,475 (GRCm39) |
|
probably benign |
Het |
| Glra3 |
A |
T |
8: 56,444,159 (GRCm39) |
|
probably null |
Het |
| Helz |
A |
G |
11: 107,556,834 (GRCm39) |
D1284G |
possibly damaging |
Het |
| Iqsec3 |
G |
A |
6: 121,390,118 (GRCm39) |
A451V |
unknown |
Het |
| Kat6b |
A |
G |
14: 21,719,214 (GRCm39) |
T1189A |
probably benign |
Het |
| Lama1 |
T |
A |
17: 68,079,736 (GRCm39) |
F1203Y |
|
Het |
| Lingo2 |
A |
G |
4: 35,708,349 (GRCm39) |
S544P |
probably damaging |
Het |
| Llcfc1 |
T |
C |
6: 41,661,525 (GRCm39) |
V25A |
probably benign |
Het |
| Map1a |
A |
C |
2: 121,129,391 (GRCm39) |
H143P |
probably damaging |
Het |
| Mbd5 |
T |
C |
2: 49,169,233 (GRCm39) |
V1468A |
probably benign |
Het |
| Meis3 |
T |
A |
7: 15,919,385 (GRCm39) |
M367K |
possibly damaging |
Het |
| Myo3b |
G |
A |
2: 70,083,440 (GRCm39) |
A698T |
probably damaging |
Het |
| Nbn |
A |
T |
4: 15,970,833 (GRCm39) |
D272V |
probably damaging |
Het |
| Or51a43 |
A |
G |
7: 103,718,032 (GRCm39) |
S69P |
probably damaging |
Het |
| Or56a5 |
C |
T |
7: 104,793,249 (GRCm39) |
V84I |
probably benign |
Het |
| Or7g20 |
G |
T |
9: 18,946,888 (GRCm39) |
M156I |
probably benign |
Het |
| Or8k27 |
C |
T |
2: 86,276,082 (GRCm39) |
M81I |
possibly damaging |
Het |
| Os9 |
C |
A |
10: 126,956,825 (GRCm39) |
|
probably null |
Het |
| Pard3b |
A |
G |
1: 62,383,294 (GRCm39) |
D796G |
probably benign |
Het |
| Peg10 |
T |
TCCG |
6: 4,756,451 (GRCm39) |
|
probably benign |
Het |
| Pkp4 |
A |
G |
2: 59,184,758 (GRCm39) |
E1180G |
possibly damaging |
Het |
| Ppp6r3 |
T |
C |
19: 3,509,461 (GRCm39) |
T795A |
probably benign |
Het |
| Pramel15 |
T |
C |
4: 144,103,553 (GRCm39) |
Q191R |
probably benign |
Het |
| Prokr2 |
T |
C |
2: 132,215,723 (GRCm39) |
E246G |
probably damaging |
Het |
| Psmb7 |
A |
G |
2: 38,503,481 (GRCm39) |
M178T |
probably damaging |
Het |
| Rbm39 |
C |
T |
2: 156,019,697 (GRCm39) |
|
probably benign |
Het |
| Saa1 |
T |
C |
7: 46,390,773 (GRCm39) |
N46S |
probably benign |
Het |
| Samd12 |
A |
G |
15: 53,521,853 (GRCm39) |
L119P |
probably damaging |
Het |
| Sdc3 |
A |
G |
4: 130,546,094 (GRCm39) |
E151G |
unknown |
Het |
| Serpina1a |
T |
C |
12: 103,820,938 (GRCm39) |
K370E |
probably damaging |
Het |
| Slc49a3 |
C |
T |
5: 108,592,432 (GRCm39) |
V253I |
probably benign |
Het |
| Tnrc18 |
C |
A |
5: 142,762,131 (GRCm39) |
S681I |
|
Het |
| Ulk2 |
C |
T |
11: 61,690,380 (GRCm39) |
G636R |
probably benign |
Het |
| V1ra8 |
T |
C |
6: 90,179,938 (GRCm39) |
L47P |
possibly damaging |
Het |
| Wasf3 |
T |
C |
5: 146,392,410 (GRCm39) |
L160P |
|
Het |
| Zbtb34 |
A |
C |
2: 33,301,701 (GRCm39) |
V280G |
possibly damaging |
Het |
| Zfp646 |
T |
C |
7: 127,478,515 (GRCm39) |
Y231H |
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 |
|
|
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 |
|
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'- AGAGGACCCCAAACAGTGTC -3'
(R):5'- TGGCAAGGTGTTCTCTTACC -3'
Sequencing Primer
(F):5'- AAACAGTGTCACTCCCTCCCTC -3'
(R):5'- GCCTCTGCCTATTAGGATTAAAGGC -3'
|
| Posted On |
2021-08-02 |
Incidental Mutation