Incidental Mutation 'R5279:Plod2'
ID 404119
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 042839-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5279 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 92424276-92490481 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 92463376 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 154 (Y154H)
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: Y154H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000068611
Gene: ENSMUSG00000032374
AA Change: Y154H

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 noncoding transcript
Transcript: ENSMUST00000160142
Predicted Effect probably damaging
Transcript: ENSMUST00000160359
AA Change: Y154H

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000125373
Gene: ENSMUSG00000032374
AA Change: Y154H

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
Meta Mutation Damage Score 0.5370 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.4%
Validation Efficiency 99% (73/74)
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: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca17 C A 17: 24,508,388 (GRCm39) G1049V probably damaging Het
Afdn G A 17: 14,109,214 (GRCm39) R1579H probably damaging Het
Ankrd28 T A 14: 31,456,963 (GRCm39) N386Y probably damaging Het
Atf7ip T A 6: 136,580,377 (GRCm39) Y1100* probably null Het
Atp9b T A 18: 80,956,073 (GRCm39) E3V probably damaging Het
AW554918 T G 18: 25,308,488 (GRCm39) D60E possibly damaging Het
Baz2b G T 2: 59,762,496 (GRCm39) Q927K probably damaging Het
Birc6 A G 17: 74,957,042 (GRCm39) R3659G probably damaging Het
C8a T G 4: 104,703,185 (GRCm39) N291H probably damaging Het
Calcoco1 G A 15: 102,619,420 (GRCm39) L390F probably damaging Het
Carmil3 A G 14: 55,739,028 (GRCm39) D894G probably damaging Het
Cdc20 A G 4: 118,290,711 (GRCm39) Y430H probably damaging Het
Cdc6 A T 11: 98,803,088 (GRCm39) I316F probably damaging Het
Ceacam23 T A 7: 17,607,214 (GRCm39) noncoding transcript Het
Cenpu T A 8: 47,031,945 (GRCm39) probably null Het
Csmd2 T A 4: 128,350,707 (GRCm39) V1592D probably benign Het
Csmd3 G T 15: 48,655,340 (GRCm39) probably null Het
Dnah7c T C 1: 46,558,429 (GRCm39) F512L probably benign Het
Fam136a T A 6: 86,343,686 (GRCm39) L61Q probably damaging Het
Fpgs A C 2: 32,582,779 (GRCm39) probably benign Het
Fzd4 G A 7: 89,056,881 (GRCm39) M309I probably benign Het
Gad2 A G 2: 22,563,969 (GRCm39) T391A probably benign Het
Gm11563 A T 11: 99,549,539 (GRCm39) S72T unknown Het
Gon4l A G 3: 88,794,944 (GRCm39) I716V probably benign Het
Itga9 T C 9: 118,457,273 (GRCm39) V128A probably damaging Het
Kat6a CGCAGCAGCAGCAGCAGCA CGCAGCAGCAGCA 8: 23,429,664 (GRCm39) probably benign Het
Lrrc9 T A 12: 72,542,368 (GRCm39) D1063E possibly damaging Het
Lyst T A 13: 13,823,387 (GRCm39) L1453* probably null Het
Mcm3ap T C 10: 76,343,373 (GRCm39) V1755A probably damaging Het
Mrc1 T C 2: 14,314,869 (GRCm39) S985P probably damaging Het
Mst1 A C 9: 107,959,414 (GRCm39) K233N probably damaging Het
Nr2c2ap G A 8: 70,584,653 (GRCm39) D42N probably damaging Het
Ntn1 A G 11: 68,276,538 (GRCm39) S137P probably benign Het
Pard3 T C 8: 128,186,867 (GRCm39) probably null Het
Pcdh15 T A 10: 74,430,015 (GRCm39) D1210E probably damaging Het
Pcdhga5 T C 18: 37,827,774 (GRCm39) L74P probably benign Het
Pcsk5 T C 19: 17,573,022 (GRCm39) probably null Het
Pdia3 T C 2: 121,244,484 (GRCm39) probably benign Het
Pikfyve A T 1: 65,235,858 (GRCm39) R177* probably null Het
Pklr A G 3: 89,050,566 (GRCm39) E409G probably damaging Het
Psmc3 T A 2: 90,884,667 (GRCm39) D6E probably benign Het
Ptpru T A 4: 131,547,334 (GRCm39) N205I possibly damaging Het
Rbm6 T C 9: 107,655,213 (GRCm39) E1006G probably benign Het
Rgl2 T C 17: 34,154,922 (GRCm39) V642A probably benign Het
Rnf8 T A 17: 29,845,680 (GRCm39) H104Q possibly damaging Het
Robo4 CGG CG 9: 37,322,786 (GRCm39) probably null Het
Rpa1 T C 11: 75,204,170 (GRCm39) N269S probably damaging Het
Sdk2 A G 11: 113,757,857 (GRCm39) M519T probably benign Het
Snx30 A G 4: 59,885,070 (GRCm39) S237G probably benign Het
Spx A G 6: 142,359,766 (GRCm39) N36S probably damaging Het
Stard7 T C 2: 127,137,416 (GRCm39) Y289H probably damaging Het
Sugp2 T C 8: 70,709,757 (GRCm39) probably benign Het
Susd4 C T 1: 182,715,043 (GRCm39) T288I probably damaging Het
Tceanc2 T A 4: 107,034,826 (GRCm39) probably null Het
Tm4sf4 T G 3: 57,341,159 (GRCm39) V97G probably benign Het
Tmtc1 C T 6: 148,256,629 (GRCm39) probably benign Het
Trappc11 C T 8: 47,958,339 (GRCm39) probably benign Het
Triobp G T 15: 78,878,591 (GRCm39) V398F possibly damaging Het
Ttll9 T A 2: 152,804,464 (GRCm39) S2T possibly damaging Het
Ttn T C 2: 76,731,320 (GRCm39) probably benign Het
Tyw3 A G 3: 154,300,108 (GRCm39) C80R probably damaging Het
Usp24 T C 4: 106,242,621 (GRCm39) V1177A possibly damaging Het
Vmn1r65 A G 7: 6,011,754 (GRCm39) V160A probably damaging Het
Vmn2r104 T A 17: 20,262,146 (GRCm39) H328L probably benign Het
Vmn2r65 A C 7: 84,589,849 (GRCm39) I689S probably damaging Het
Wrn A G 8: 33,731,129 (GRCm39) Y1068H probably damaging Het
Xpo4 C A 14: 57,850,866 (GRCm39) S346I probably benign Het
Zc3h3 T A 15: 75,711,439 (GRCm39) T341S probably benign Het
Zxdc T C 6: 90,347,419 (GRCm39) M260T possibly 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
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
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'- CAAATGTAGTTCCTGTGATGTGAG -3'
(R):5'- TGCCTAGATACACAGGTAGTCC -3'

Sequencing Primer
(F):5'- GGTTGCCTGCTGTGTTCTCTAAAC -3'
(R):5'- TCCAAGGGAAATGGTTTTCAAGC -3'
Posted On 2016-07-22