Incidental Mutation 'R5940:Plod2'
ID 462505
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 044132-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5940 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 92424276-92490481 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 92473450 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 292 (V292E)
Ref Sequence ENSEMBL: ENSMUSP00000068611 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070522] [ENSMUST00000160359]
AlphaFold Q9R0B9
Predicted Effect probably benign
Transcript: ENSMUST00000070522
AA Change: V292E

PolyPhen 2 Score 0.390 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000068611
Gene: ENSMUSG00000032374
AA Change: V292E

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 benign
Transcript: ENSMUST00000160359
AA Change: V292E

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000125373
Gene: ENSMUSG00000032374
AA Change: V292E

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
Meta Mutation Damage Score 0.1065 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.2%
  • 20x: 95.0%
Validation Efficiency 96% (88/92)
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: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
3425401B19Rik T C 14: 32,384,645 (GRCm39) Y440C possibly damaging Het
Aasdh G T 5: 77,030,745 (GRCm39) S618R probably benign Het
Alpk1 T G 3: 127,464,595 (GRCm39) T1228P probably benign Het
Ank3 T C 10: 69,756,316 (GRCm39) V850A probably benign Het
Apeh A T 9: 107,969,098 (GRCm39) probably null Het
Ash1l C T 3: 88,891,343 (GRCm39) T1074I probably damaging Het
C3 G A 17: 57,517,244 (GRCm39) S1297F possibly damaging Het
Cchcr1 G A 17: 35,835,890 (GRCm39) R284Q probably damaging Het
Cd93 A T 2: 148,284,152 (GRCm39) I398N probably benign Het
Cdcp3 A T 7: 130,839,992 (GRCm39) D638V probably damaging Het
Chrd G T 16: 20,553,336 (GRCm39) R226L probably null Het
Clvs1 A T 4: 9,449,443 (GRCm39) N344I possibly damaging Het
Cyp4v3 A T 8: 45,774,821 (GRCm39) I111N probably damaging Het
Cysltr2 T A 14: 73,267,389 (GRCm39) Y107F probably damaging Het
Cysltr2 T C 14: 73,266,931 (GRCm39) K260E probably benign Het
Czib A G 4: 107,750,485 (GRCm39) probably benign Het
Defb47 A T 14: 63,238,359 (GRCm39) E28D probably benign Het
Dnajc30 T A 5: 135,093,413 (GRCm39) Y103* probably null Het
Drap1 T C 19: 5,473,028 (GRCm39) T160A probably benign Het
Dsp A G 13: 38,380,002 (GRCm39) E2249G possibly damaging Het
E2f8 T A 7: 48,520,825 (GRCm39) I499F probably benign Het
Ebf1 T A 11: 44,512,048 (GRCm39) Y116N probably damaging Het
Ecrg4 C T 1: 43,776,401 (GRCm39) R41* probably null Het
Ect2 C A 3: 27,169,614 (GRCm39) E746D probably benign Het
Enpep T A 3: 129,106,227 (GRCm39) Y333F probably damaging Het
Fat4 T C 3: 38,943,798 (GRCm39) V897A probably benign Het
Gja3 T A 14: 57,273,317 (GRCm39) S352C probably damaging Het
Gpr153 C A 4: 152,367,832 (GRCm39) P561Q probably benign Het
Hlcs T C 16: 93,935,571 (GRCm39) M574V probably damaging Het
Hmcn1 A G 1: 150,532,973 (GRCm39) V3070A probably benign Het
Hsd3b2 G T 3: 98,619,287 (GRCm39) N219K probably benign Het
Htra3 T C 5: 35,810,324 (GRCm39) I453V possibly damaging Het
Klrc1 A T 6: 129,651,898 (GRCm39) M220K possibly damaging Het
Kntc1 T G 5: 123,924,258 (GRCm39) I1048S probably benign Het
Lrrc37 T C 11: 103,504,712 (GRCm39) S243G probably benign Het
Macf1 T A 4: 123,326,674 (GRCm39) D2822V probably damaging Het
Mcu T A 10: 59,292,554 (GRCm39) I42F possibly damaging Het
Mkln1 T A 6: 31,466,307 (GRCm39) D521E probably damaging Het
Ms4a13 T C 19: 11,170,330 (GRCm39) N5D possibly damaging Het
Msh3 T G 13: 92,386,351 (GRCm39) N838T probably damaging Het
Msl2 T A 9: 100,978,290 (GRCm39) C221* probably null Het
Ncapd2 A G 6: 125,145,832 (GRCm39) S1310P probably benign Het
Ncoa6 A T 2: 155,257,785 (GRCm39) M586K probably damaging Het
Ndel1 C T 11: 68,713,397 (GRCm39) probably benign Het
Ndst4 T C 3: 125,355,068 (GRCm39) probably benign Het
Nes T G 3: 87,883,259 (GRCm39) V506G probably damaging Het
Nrg1 T C 8: 32,339,372 (GRCm39) K200E probably damaging Het
Nt5c1b A G 12: 10,425,515 (GRCm39) K295E probably damaging Het
Or4f54 G A 2: 111,122,729 (GRCm39) V39M possibly damaging Het
Or5b123 T A 19: 13,596,517 (GRCm39) probably null Het
Or6s1 T A 14: 51,308,179 (GRCm39) I224L probably damaging Het
Or8b4 C T 9: 37,830,733 (GRCm39) T260I probably damaging Het
Or8g51 G T 9: 38,609,007 (GRCm39) Y218* probably null Het
Or8k38 A T 2: 86,488,394 (GRCm39) M136K probably damaging Het
Otx1 C A 11: 21,947,037 (GRCm39) A91S probably damaging Het
Pde1a A G 2: 79,718,183 (GRCm39) probably null Het
Pds5a A G 5: 65,801,328 (GRCm39) probably benign Het
Plbd1 A T 6: 136,590,719 (GRCm39) probably benign Het
Polg A G 7: 79,103,819 (GRCm39) V879A possibly damaging Het
Ppargc1a C T 5: 51,631,253 (GRCm39) A459T probably damaging Het
Prorp T A 12: 55,351,659 (GRCm39) W323R probably damaging Het
Psip1 T C 4: 83,394,559 (GRCm39) E83G probably damaging Het
Rhbdf1 T C 11: 32,159,847 (GRCm39) D843G probably benign Het
Rnpepl1 G T 1: 92,845,434 (GRCm39) C451F probably damaging Het
Rrp1 T C 10: 78,241,249 (GRCm39) D206G probably damaging Het
Setbp1 A T 18: 78,798,703 (GRCm39) D1492E probably damaging Het
Sh3bp5 C A 14: 31,099,452 (GRCm39) R265L probably benign Het
Slc16a6 C T 11: 109,364,022 (GRCm39) probably benign Homo
Slc7a6os A G 8: 106,937,437 (GRCm39) S37P probably damaging Het
Tenm4 T A 7: 96,495,102 (GRCm39) S1140T probably damaging Het
Thoc6 C A 17: 23,889,315 (GRCm39) R115L probably benign Het
Tmem63c C T 12: 87,121,946 (GRCm39) H385Y probably benign Het
Trpm8 G T 1: 88,279,137 (GRCm39) E649* probably null Het
Usf1 A G 1: 171,245,347 (GRCm39) E253G possibly damaging Het
Vps13d T C 4: 144,801,545 (GRCm39) T443A probably benign Het
Wdr86 T C 5: 24,927,660 (GRCm39) Y93C probably damaging Het
Zfp597 A T 16: 3,683,685 (GRCm39) I357N probably damaging Het
Zfp709 A G 8: 72,644,064 (GRCm39) I497V possibly damaging Het
Zxdc T C 6: 90,347,307 (GRCm39) S223P 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
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
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'- AGAATGCTGTGGAGCTATGG -3'
(R):5'- ATGCTGTCAATGCTCAATTCCC -3'

Sequencing Primer
(F):5'- AGAATGCTGTGGAGCTATGGGTATC -3'
(R):5'- GGCTGTTAGTGGTTTCAAAACAATTC -3'
Posted On 2017-02-28