Incidental Mutation 'R1946:Plod2'
ID 216692
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 039964-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1946 (G1)
Quality Score 225
Status Not validated
Chromosome 9
Chromosomal Location 92424276-92490481 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 92489188 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Glycine at position 707 (S707G)
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: S707G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000068611
Gene: ENSMUSG00000032374
AA Change: S707G

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 probably benign
Transcript: ENSMUST00000160359
AA Change: S728G

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000125373
Gene: ENSMUSG00000032374
AA Change: S728G

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: ENSMUST00000190075
Meta Mutation Damage Score 0.0921 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.8%
Validation Efficiency
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: 76 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aasdh A G 5: 77,039,551 (GRCm39) S253P probably damaging Het
Adamts5 C A 16: 85,696,131 (GRCm39) C342F probably damaging Het
Adgrv1 C T 13: 81,522,368 (GRCm39) C5923Y probably damaging Het
Aen G C 7: 78,552,420 (GRCm39) E32Q probably damaging Het
Apba2 T C 7: 64,394,378 (GRCm39) probably null Het
Arhgap44 A G 11: 64,902,922 (GRCm39) M509T probably damaging Het
Arpc1b A G 5: 145,059,443 (GRCm39) T56A probably null Het
Atoh1 T C 6: 64,706,443 (GRCm39) V46A probably benign Het
Bmpr2 T C 1: 59,907,556 (GRCm39) V883A possibly damaging Het
Bpifa1 A T 2: 153,987,554 (GRCm39) I135F probably damaging Het
Bsn A G 9: 107,991,850 (GRCm39) F1301L probably damaging Het
Capn13 T C 17: 73,657,520 (GRCm39) E240G possibly damaging Het
Ccdc18 A G 5: 108,376,861 (GRCm39) E1434G probably damaging Het
Coq8b G A 7: 26,939,299 (GRCm39) V150I possibly damaging Het
Cpn1 G A 19: 43,944,957 (GRCm39) T450M probably benign Het
Dlg4 A G 11: 69,930,401 (GRCm39) Y432C probably damaging Het
Dnah8 C A 17: 30,931,359 (GRCm39) T1458K probably benign Het
Dock5 A T 14: 68,023,765 (GRCm39) M1132K probably damaging Het
Dsg2 A G 18: 20,713,605 (GRCm39) D192G probably damaging Het
F930017D23Rik G A 10: 43,469,440 (GRCm39) noncoding transcript Het
Fndc11 A T 2: 180,863,627 (GRCm39) D144V probably benign Het
Fut2 A G 7: 45,300,748 (GRCm39) F8S probably damaging Het
Gad2 A T 2: 22,575,440 (GRCm39) T515S probably benign Het
Ganab T A 19: 8,888,172 (GRCm39) D439E probably damaging Het
Gm10228 C A 16: 88,838,241 (GRCm39) G21V unknown Het
Grm3 A G 5: 9,562,123 (GRCm39) W576R probably damaging Het
Gsdmc4 C A 15: 63,774,629 (GRCm39) D51Y probably benign Het
Hmcn2 T C 2: 31,295,647 (GRCm39) S2619P probably damaging Het
Kcnq2 T A 2: 180,730,244 (GRCm39) D446V probably benign Het
Kera A G 10: 97,445,009 (GRCm39) K123E probably benign Het
Kmt2c A T 5: 25,520,152 (GRCm39) V1986E probably benign Het
Lrp11 T C 10: 7,499,540 (GRCm39) Y244H probably damaging Het
Lrp1b T A 2: 40,555,159 (GRCm39) D320V unknown Het
Lrrcc1 A G 3: 14,615,453 (GRCm39) R394G probably benign Het
Lrrk2 G A 15: 91,620,864 (GRCm39) probably null Het
Map4k5 A T 12: 69,892,529 (GRCm39) D133E probably damaging Het
Megf11 A T 9: 64,586,558 (GRCm39) D461V probably damaging Het
Msrb3 A G 10: 120,687,913 (GRCm39) V54A probably damaging Het
Muc21 A T 17: 35,933,416 (GRCm39) probably benign Het
Ncoa3 T A 2: 165,901,097 (GRCm39) N896K possibly damaging Het
Ncor2 G A 5: 125,111,476 (GRCm39) T1314I probably damaging Het
Nes A G 3: 87,885,821 (GRCm39) Q1316R possibly damaging Het
Nfe2l3 A C 6: 51,434,295 (GRCm39) Q285P probably damaging Het
Nkd1 C T 8: 89,318,745 (GRCm39) H357Y probably damaging Het
Nmt2 T A 2: 3,323,672 (GRCm39) I355N probably benign Het
Or10ak11 T C 4: 118,687,223 (GRCm39) N139S probably benign Het
Or1n1b A T 2: 36,780,458 (GRCm39) M134K possibly damaging Het
Or5ae1 T C 7: 84,565,487 (GRCm39) S167P probably benign Het
Or5b3 T C 19: 13,388,143 (GRCm39) V70A possibly damaging Het
Or7a38 T A 10: 78,752,758 (GRCm39) I28N probably damaging Het
Or8b3 T A 9: 38,314,182 (GRCm39) M1K probably null Het
Otx1 G T 11: 21,948,482 (GRCm39) T46K probably damaging Het
Panx1 A G 9: 14,918,822 (GRCm39) C346R probably benign Het
Pcdhb16 T A 18: 37,611,952 (GRCm39) L304* probably null Het
Plet1 A G 9: 50,415,652 (GRCm39) probably null Het
Plscr4 G A 9: 92,365,889 (GRCm39) V120I probably damaging Het
Ppp1r12b A G 1: 134,820,008 (GRCm39) V245A probably damaging Het
Ppp2r2d A G 7: 138,470,196 (GRCm39) D19G probably damaging Het
Pramel31 T A 4: 144,088,435 (GRCm39) V77E probably benign Het
Rimbp3 G A 16: 17,028,291 (GRCm39) V572I probably benign Het
Ror2 T C 13: 53,285,885 (GRCm39) I110V probably damaging Het
Sec24d A T 3: 123,147,043 (GRCm39) H667L probably benign Het
Sema3d A G 5: 12,623,810 (GRCm39) Q573R probably damaging Het
Snx19 T A 9: 30,343,620 (GRCm39) N593K probably damaging Het
Sulf1 T C 1: 12,867,131 (GRCm39) V105A probably benign Het
Syngr3 T C 17: 24,906,680 (GRCm39) N45S probably benign Het
Tenm4 A T 7: 96,385,015 (GRCm39) H524L probably damaging Het
Tex30 C T 1: 44,130,564 (GRCm39) G68D probably damaging Het
Tmem43 A T 6: 91,463,891 (GRCm39) I389F probably benign Het
Trpm1 A T 7: 63,873,556 (GRCm39) N488Y probably damaging Het
Usf2 T C 7: 30,655,663 (GRCm39) T1A probably null Het
Vill A T 9: 118,887,560 (GRCm39) H108L probably benign Het
Vmn1r16 T C 6: 57,299,885 (GRCm39) I246V probably benign Het
Vmn1r188 T G 13: 22,272,815 (GRCm39) S256R possibly damaging Het
Zfp12 G A 5: 143,231,133 (GRCm39) E487K probably damaging Het
Zfp24 AC A 18: 24,147,476 (GRCm39) probably null 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
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
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'- ATGGAAAAGGCTCTGCTGATATTTG -3'
(R):5'- GCCCAAAGTGATGTTGTTCTG -3'

Sequencing Primer
(F):5'- GCCATTTAGATGGCACAGT -3'
(R):5'- CCCAAAGTGATGTTGTTCTGTTGAC -3'
Posted On 2014-08-01