Incidental Mutation 'R4289:Plod2'
ID 322341
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 041654-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4289 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 92424276-92490481 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 92485041 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Glutamine at position 514 (R514Q)
Ref Sequence ENSEMBL: ENSMUSP00000068611 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070522] [ENSMUST00000160359]
AlphaFold Q9R0B9
Predicted Effect possibly damaging
Transcript: ENSMUST00000070522
AA Change: R514Q

PolyPhen 2 Score 0.895 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000068611
Gene: ENSMUSG00000032374
AA Change: R514Q

DomainStartEndE-ValueType
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 possibly damaging
Transcript: ENSMUST00000160359
AA Change: R535Q

PolyPhen 2 Score 0.884 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000125373
Gene: ENSMUSG00000032374
AA Change: R535Q

DomainStartEndE-ValueType
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 0.1795 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.5%
Validation Efficiency 100% (56/56)
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: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actl6a C T 3: 32,766,263 (GRCm39) T39M possibly damaging Het
Arhgdib T C 6: 136,901,156 (GRCm39) N191S probably benign Het
Arhgef39 A G 4: 43,497,353 (GRCm39) probably benign Het
Baz1a G A 12: 54,947,233 (GRCm39) R1139C probably damaging Het
Cdhr5 A T 7: 140,852,752 (GRCm39) I78N probably damaging Het
Cfap97 T A 8: 46,645,698 (GRCm39) N525K probably benign Het
Cntn2 T A 1: 132,455,481 (GRCm39) Y252F probably benign Het
Cyp3a57 G A 5: 145,286,207 (GRCm39) G48S probably damaging Het
Cyp4v3 A C 8: 45,781,260 (GRCm39) F73V possibly damaging Het
Ear10 T C 14: 44,160,404 (GRCm39) D141G probably benign Het
Fbn2 T C 18: 58,168,411 (GRCm39) I2309V probably damaging Het
Fcrl5 A G 3: 87,349,531 (GRCm39) D102G probably benign Het
Fdxacb1 A T 9: 50,683,879 (GRCm39) Q614L probably damaging Het
Gm10267 T C 18: 44,290,331 (GRCm39) T59A probably damaging Het
Gm5581 C T 6: 131,144,519 (GRCm39) noncoding transcript Het
Gm5592 G T 7: 40,808,336 (GRCm39) probably benign Het
Gtf2a1l A G 17: 89,001,884 (GRCm39) T200A probably damaging Het
Hspg2 C T 4: 137,246,251 (GRCm39) R1010C probably damaging Het
Ift122 T C 6: 115,900,852 (GRCm39) C1057R probably damaging Het
Kirrel3 A T 9: 34,934,769 (GRCm39) N73I probably benign Het
Kndc1 A G 7: 139,490,798 (GRCm39) I433M probably benign Het
Mks1 T C 11: 87,747,530 (GRCm39) probably benign Het
Mmp14 A T 14: 54,673,665 (GRCm39) K110* probably null Het
Mms19 A G 19: 41,933,992 (GRCm39) L938P probably damaging Het
Mrpl36 A T 13: 73,479,777 (GRCm39) probably null Het
Mypn T C 10: 62,966,961 (GRCm39) E905G probably damaging Het
Ncam1 G T 9: 49,468,472 (GRCm39) T329N probably damaging Het
Nfkbie T C 17: 45,869,516 (GRCm39) L157P probably damaging Het
Or14c45 T A 7: 86,176,262 (GRCm39) I99N probably damaging Het
Or4f47 T A 2: 111,972,319 (GRCm39) S10T probably benign Het
Pappa C T 4: 65,074,100 (GRCm39) A218V probably benign Het
Plekhg5 T C 4: 152,196,884 (GRCm39) Y737H probably benign Het
Plxnb1 C T 9: 108,943,420 (GRCm39) R1888W probably damaging Het
Prss45 A G 9: 110,669,997 (GRCm39) T269A probably benign Het
Ptpn13 A G 5: 103,681,151 (GRCm39) T784A probably damaging Het
Pycr3 T C 15: 75,790,655 (GRCm39) N68S probably benign Het
Rbis T C 3: 14,674,714 (GRCm39) M1V probably null Het
Rdh14 A T 12: 10,444,949 (GRCm39) N267Y probably benign Het
Rph3a G A 5: 121,111,368 (GRCm39) R71C probably damaging Het
Sall2 C A 14: 52,551,260 (GRCm39) R643L probably damaging Het
Spata13 T A 14: 60,928,523 (GRCm39) V27E probably damaging Het
Tbc1d1 T A 5: 64,417,771 (GRCm39) S312T probably damaging Het
Tcp11l2 T C 10: 84,440,937 (GRCm39) probably null Het
Trdn C T 10: 33,340,578 (GRCm39) S604L probably benign Het
Ttn T C 2: 76,640,742 (GRCm39) T13669A probably benign Het
Tyw3 A T 3: 154,302,645 (GRCm39) F30I probably damaging Het
Vmn1r227 G T 17: 20,956,092 (GRCm39) noncoding transcript Het
Vmn2r74 C T 7: 85,606,562 (GRCm39) M261I probably benign Het
Zfp217 C T 2: 169,956,707 (GRCm39) G764S probably benign Het
Zfp267 A G 3: 36,213,747 (GRCm39) N27S possibly damaging Het
Zfp748 T A 13: 67,689,202 (GRCm39) H686L probably damaging Het
Other mutations in Plod2
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
R5764:Plod2 UTSW 9 92,485,074 (GRCm39) missense probably damaging 0.97
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'- ACCCCAAGTCACTAAGGTCTTTC -3'

Sequencing Primer
(F):5'- CAGTTGACACTTAGTGCTATTTTCTG -3'
(R):5'- AAGTCACTAAGGTCTTTCTCCAC -3'
Posted On 2015-06-20