Incidental Mutation 'R5764:Plod2'
| ID |
446178 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Plod2
|
| Ensembl Gene |
ENSMUSG00000032374 |
| Gene Name |
procollagen lysine, 2-oxoglutarate 5-dioxygenase 2 |
| Synonyms |
Plod-2, LH2, lysyl hydroxylase 2, D530025C14Rik |
| MMRRC Submission |
043365-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5764 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
9 |
| Chromosomal Location |
92424276-92490481 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 92485074 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Arginine
at position 525
(H525R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000068611
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070522]
[ENSMUST00000160359]
|
| AlphaFold |
Q9R0B9 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000070522
AA Change: H525R
PolyPhen 2
Score 0.967 (Sensitivity: 0.77; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000068611
Gene: ENSMUSG00000032374
AA Change: H525R
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
27 |
N/A |
INTRINSIC |
|
low complexity region
|
181 |
193 |
N/A |
INTRINSIC |
|
low complexity region
|
307 |
321 |
N/A |
INTRINSIC |
|
Blast:P4Hc
|
453 |
500 |
1e-22 |
BLAST |
|
P4Hc
|
563 |
736 |
6.38e-21 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160359
AA Change: H546R
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000125373
Gene: ENSMUSG00000032374
AA Change: H546R
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
27 |
N/A |
INTRINSIC |
|
low complexity region
|
181 |
193 |
N/A |
INTRINSIC |
|
low complexity region
|
307 |
321 |
N/A |
INTRINSIC |
|
Blast:P4Hc
|
453 |
500 |
1e-22 |
BLAST |
|
P4Hc
|
584 |
757 |
6.38e-21 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161906
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000190075
|
| Meta Mutation Damage Score |
0.1201 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.8%
- 10x: 97.6%
- 20x: 96.1%
|
| Validation Efficiency |
98% (53/54) |
| 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. Mutations in the coding region of this gene are associated with Bruck syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgrb1 |
G |
A |
15: 74,413,423 (GRCm39) |
V536I |
possibly damaging |
Het |
| Arap2 |
T |
C |
5: 62,800,197 (GRCm39) |
T1277A |
probably damaging |
Het |
| Cep85l |
A |
T |
10: 53,225,090 (GRCm39) |
D166E |
probably benign |
Het |
| Cope |
T |
C |
8: 70,759,231 (GRCm39) |
S125P |
probably damaging |
Het |
| Dzip3 |
A |
G |
16: 48,747,724 (GRCm39) |
|
probably benign |
Het |
| Endou |
G |
A |
15: 97,612,488 (GRCm39) |
R253C |
probably damaging |
Het |
| Entpd1 |
A |
T |
19: 40,727,417 (GRCm39) |
|
probably null |
Het |
| Fhip1a |
A |
G |
3: 85,573,172 (GRCm39) |
Y926H |
probably damaging |
Het |
| Grk3 |
A |
G |
5: 113,114,776 (GRCm39) |
|
probably null |
Het |
| Hba-a2 |
T |
A |
11: 32,247,156 (GRCm39) |
|
probably null |
Het |
| Hecw1 |
C |
T |
13: 14,497,094 (GRCm39) |
V305I |
probably damaging |
Het |
| Hspg2 |
C |
A |
4: 137,289,032 (GRCm39) |
T3735K |
probably damaging |
Het |
| Htr4 |
G |
A |
18: 62,570,613 (GRCm39) |
A223T |
probably damaging |
Het |
| Iglv1 |
T |
C |
16: 18,904,190 (GRCm39) |
I7M |
unknown |
Het |
| Jag1 |
C |
T |
2: 136,931,167 (GRCm39) |
C655Y |
probably damaging |
Het |
| Jmjd1c |
C |
T |
10: 67,062,291 (GRCm39) |
T1548I |
probably damaging |
Het |
| Kif5a |
GGGTTGGT |
GGGT |
10: 127,066,898 (GRCm39) |
|
probably null |
Het |
| Klra6 |
T |
A |
6: 129,999,692 (GRCm39) |
Q92L |
possibly damaging |
Het |
| Lrp1 |
T |
C |
10: 127,431,187 (GRCm39) |
N325S |
probably benign |
Het |
| Ly75 |
C |
T |
2: 60,148,783 (GRCm39) |
R1182H |
probably benign |
Het |
| Map2 |
T |
C |
1: 66,454,034 (GRCm39) |
S975P |
probably damaging |
Het |
| Med13l |
T |
A |
5: 118,866,707 (GRCm39) |
L587Q |
probably damaging |
Het |
| Mpdz |
A |
G |
4: 81,274,683 (GRCm39) |
F180L |
probably benign |
Het |
| Myadm |
G |
A |
7: 3,345,768 (GRCm39) |
V177I |
possibly damaging |
Het |
| Ngly1 |
T |
A |
14: 16,260,799 (GRCm38) |
M161K |
probably benign |
Het |
| Nup153 |
A |
G |
13: 46,840,803 (GRCm39) |
M255T |
probably damaging |
Het |
| Pgm1 |
C |
T |
4: 99,822,043 (GRCm39) |
A303V |
probably damaging |
Het |
| Pgr |
A |
T |
9: 8,900,538 (GRCm39) |
I24F |
probably benign |
Het |
| Pigq |
A |
T |
17: 26,151,093 (GRCm39) |
I412N |
probably damaging |
Het |
| Polq |
T |
G |
16: 36,837,706 (GRCm39) |
M206R |
probably damaging |
Het |
| Psap |
T |
A |
10: 60,129,186 (GRCm39) |
S100T |
probably benign |
Het |
| Psme4 |
G |
A |
11: 30,722,364 (GRCm39) |
|
probably benign |
Het |
| Serpina1d |
T |
A |
12: 103,732,080 (GRCm39) |
M260L |
probably benign |
Het |
| Serpinf2 |
A |
G |
11: 75,328,230 (GRCm39) |
L106P |
possibly damaging |
Het |
| Sumf1 |
C |
T |
6: 108,095,424 (GRCm39) |
|
probably benign |
Het |
| Tcp1 |
A |
G |
17: 13,135,489 (GRCm39) |
T13A |
probably benign |
Het |
| Tfap2a |
A |
C |
13: 40,881,831 (GRCm39) |
I185S |
possibly damaging |
Het |
| Tlr2 |
A |
C |
3: 83,745,819 (GRCm39) |
I88S |
probably damaging |
Het |
| Tmc4 |
A |
T |
7: 3,675,022 (GRCm39) |
F283L |
probably damaging |
Het |
| Tox4 |
T |
C |
14: 52,523,277 (GRCm39) |
V79A |
probably damaging |
Het |
| Trim10 |
A |
T |
17: 37,181,073 (GRCm39) |
E101D |
probably damaging |
Het |
| Troap |
T |
A |
15: 98,973,300 (GRCm39) |
I22N |
probably damaging |
Het |
| Unc13c |
C |
T |
9: 73,441,185 (GRCm39) |
|
probably null |
Het |
| Utp4 |
T |
G |
8: 107,644,248 (GRCm39) |
V529G |
possibly damaging |
Het |
| Zeb2 |
T |
C |
2: 44,886,931 (GRCm39) |
M664V |
possibly damaging |
Het |
| Zfp180 |
A |
G |
7: 23,800,909 (GRCm39) |
Y53C |
possibly damaging |
Het |
|
| Other mutations in Plod2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00715:Plod2
|
APN |
9 |
92,480,667 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL00945:Plod2
|
APN |
9 |
92,466,549 (GRCm39) |
missense |
probably benign |
0.08 |
|
IGL01386:Plod2
|
APN |
9 |
92,488,655 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL01519:Plod2
|
APN |
9 |
92,477,348 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01836:Plod2
|
APN |
9 |
92,488,551 (GRCm39) |
splice site |
probably benign |
|
|
IGL02490:Plod2
|
APN |
9 |
92,468,895 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02496:Plod2
|
APN |
9 |
92,489,147 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02699:Plod2
|
APN |
9 |
92,489,195 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02735:Plod2
|
APN |
9 |
92,477,442 (GRCm39) |
splice site |
probably benign |
|
|
IGL03106:Plod2
|
APN |
9 |
92,455,620 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R0270:Plod2
|
UTSW |
9 |
92,466,574 (GRCm39) |
missense |
probably benign |
0.10 |
|
R0546:Plod2
|
UTSW |
9 |
92,477,388 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0589:Plod2
|
UTSW |
9 |
92,475,799 (GRCm39) |
missense |
probably benign |
|
|
R0707:Plod2
|
UTSW |
9 |
92,487,480 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R1491:Plod2
|
UTSW |
9 |
92,488,637 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1572:Plod2
|
UTSW |
9 |
92,485,120 (GRCm39) |
splice site |
probably benign |
|
|
R1731:Plod2
|
UTSW |
9 |
92,466,657 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1895:Plod2
|
UTSW |
9 |
92,489,188 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1917:Plod2
|
UTSW |
9 |
92,463,310 (GRCm39) |
missense |
probably benign |
|
|
R1946:Plod2
|
UTSW |
9 |
92,489,188 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3850:Plod2
|
UTSW |
9 |
92,424,598 (GRCm39) |
missense |
probably benign |
0.28 |
|
R3973:Plod2
|
UTSW |
9 |
92,480,672 (GRCm39) |
nonsense |
probably null |
|
|
R3974:Plod2
|
UTSW |
9 |
92,480,672 (GRCm39) |
nonsense |
probably null |
|
|
R4289:Plod2
|
UTSW |
9 |
92,485,041 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R4423:Plod2
|
UTSW |
9 |
92,484,042 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4647:Plod2
|
UTSW |
9 |
92,487,503 (GRCm39) |
nonsense |
probably null |
|
|
R4754:Plod2
|
UTSW |
9 |
92,488,584 (GRCm39) |
nonsense |
probably null |
|
|
R4769:Plod2
|
UTSW |
9 |
92,477,325 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5279:Plod2
|
UTSW |
9 |
92,463,376 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5535:Plod2
|
UTSW |
9 |
92,488,622 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5654:Plod2
|
UTSW |
9 |
92,475,876 (GRCm39) |
missense |
probably benign |
|
|
R5885:Plod2
|
UTSW |
9 |
92,488,709 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5940:Plod2
|
UTSW |
9 |
92,473,450 (GRCm39) |
missense |
probably benign |
0.39 |
|
R6917:Plod2
|
UTSW |
9 |
92,475,823 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R7109:Plod2
|
UTSW |
9 |
92,455,650 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7221:Plod2
|
UTSW |
9 |
92,466,580 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7311:Plod2
|
UTSW |
9 |
92,466,611 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7963:Plod2
|
UTSW |
9 |
92,487,499 (GRCm39) |
missense |
probably benign |
0.07 |
|
R8205:Plod2
|
UTSW |
9 |
92,424,371 (GRCm39) |
start gained |
probably benign |
|
|
R8794:Plod2
|
UTSW |
9 |
92,482,801 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8873:Plod2
|
UTSW |
9 |
92,489,112 (GRCm39) |
intron |
probably benign |
|
|
R9044:Plod2
|
UTSW |
9 |
92,489,273 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R9071:Plod2
|
UTSW |
9 |
92,485,048 (GRCm39) |
missense |
probably benign |
0.09 |
|
R9120:Plod2
|
UTSW |
9 |
92,424,380 (GRCm39) |
start gained |
probably benign |
|
|
Z1088:Plod2
|
UTSW |
9 |
92,485,088 (GRCm39) |
missense |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GAAGCCCAGTCCTCTCTTTCAG -3'
(R):5'- AACCCCAAGTCACTAAGGTCTTTC -3'
Sequencing Primer
(F):5'- CAGTTGACACTTAGTGCTATTTTCTG -3'
(R):5'- AAGTCACTAAGGTCTTTCTCCAC -3'
|
| Posted On |
2016-11-21 |
Incidental Mutation