Incidental Mutation 'IGL03106:Plod2'
ID 418966
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Plod2
Ensembl Gene ENSMUSG00000032374
Gene Name procollagen lysine, 2-oxoglutarate 5-dioxygenase 2
Synonyms D530025C14Rik, Plod-2, LH2, lysyl hydroxylase 2
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock # IGL03106
Quality Score
Status
Chromosome 9
Chromosomal Location 92542223-92608428 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to C at 92573567 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 100 (Y100H)
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: Y100H

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000068611
Gene: ENSMUSG00000032374
AA Change: Y100H

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: Y100H

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000125373
Gene: ENSMUSG00000032374
AA Change: Y100H

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
Coding Region Coverage
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: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam3 G T 8: 24,715,119 probably benign Het
Adgrv1 T C 13: 81,472,899 N3911S probably benign Het
Alox12b C T 11: 69,168,876 Q585* probably null Het
Amtn A G 5: 88,378,085 Q36R probably benign Het
Arg2 G A 12: 79,149,891 G129S probably damaging Het
Arhgef28 A C 13: 97,957,793 Y948D probably damaging Het
Atp10b T C 11: 43,247,477 V1195A probably benign Het
Bet1l G T 7: 140,854,610 T42K probably benign Het
Cabin1 G A 10: 75,733,628 T875I probably benign Het
Ccdc17 A G 4: 116,596,836 probably null Het
Crebrf A G 17: 26,771,319 E612G probably damaging Het
Cyp2c67 A T 19: 39,643,675 M83K probably benign Het
Dgkz A G 2: 91,940,859 S414P probably damaging Het
Dock10 G T 1: 80,568,834 H411N probably damaging Het
Dpyd A T 3: 119,195,134 T749S probably benign Het
Dsc1 C T 18: 20,086,644 probably null Het
Echdc1 A T 10: 29,322,280 M74L probably damaging Het
Edn1 C A 13: 42,305,023 T104K possibly damaging Het
Fat2 T A 11: 55,311,901 T116S probably benign Het
Fcrl5 A T 3: 87,435,883 probably null Het
Fpgt C T 3: 155,087,122 G423R probably damaging Het
Gprc5b A T 7: 118,984,193 V151E probably damaging Het
Grm5 A G 7: 88,036,070 Y465C probably damaging Het
Idh3b T A 2: 130,284,401 N6I probably benign Het
Ighmbp2 T C 19: 3,273,022 K308R possibly damaging Het
Lrch1 A T 14: 74,835,762 S146T possibly damaging Het
Lyl1 C T 8: 84,702,671 P3L possibly damaging Het
Mterf3 T C 13: 66,930,157 K16R probably damaging Het
Ncapg T A 5: 45,695,668 H825Q probably damaging Het
Olfr1095 A C 2: 86,851,614 L28R possibly damaging Het
Olfr1138 A T 2: 87,738,118 S69T probably benign Het
Olfr1392 T A 11: 49,294,161 I280N probably damaging Het
Olfr1443 G A 19: 12,680,923 V272M possibly damaging Het
Olfr31 G A 14: 14,328,851 V247I probably damaging Het
Olfr984 A G 9: 40,100,734 V252A probably damaging Het
Pald1 A T 10: 61,347,105 M355K probably benign Het
Phc1 A G 6: 122,323,469 probably benign Het
Phkb T A 8: 86,018,466 probably benign Het
Pkn3 G T 2: 30,085,245 R506L probably damaging Het
Prl7b1 G T 13: 27,606,935 Q56K probably benign Het
Rhot1 T A 11: 80,242,581 C229* probably null Het
Sema3a G A 5: 13,599,488 R735Q probably damaging Het
Slc18b1 A G 10: 23,826,659 *460W probably null Het
Slco6c1 T A 1: 97,066,023 probably benign Het
Slu7 T A 11: 43,442,630 V359D possibly damaging Het
Suco T C 1: 161,834,480 Y794C possibly damaging Het
Sult3a2 T C 10: 33,779,773 N70S probably benign Het
Taar2 A T 10: 23,941,297 D245V probably damaging Het
Taf1d A G 9: 15,309,941 H181R possibly damaging Het
Tmem33 T C 5: 67,263,796 S38P probably damaging Het
Traf3ip1 T C 1: 91,522,887 S519P probably benign Het
Ttc12 T C 9: 49,458,062 K253E possibly damaging Het
Other mutations in Plod2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00715:Plod2 APN 9 92598614 missense probably damaging 0.99
IGL00945:Plod2 APN 9 92584496 missense probably benign 0.08
IGL01386:Plod2 APN 9 92606602 missense probably damaging 0.99
IGL01519:Plod2 APN 9 92595295 missense probably benign 0.00
IGL01836:Plod2 APN 9 92606498 splice site probably benign
IGL02490:Plod2 APN 9 92586842 missense probably benign 0.00
IGL02496:Plod2 APN 9 92607094 missense probably damaging 1.00
IGL02699:Plod2 APN 9 92607142 missense probably damaging 1.00
IGL02735:Plod2 APN 9 92595389 splice site probably benign
R0270:Plod2 UTSW 9 92584521 missense probably benign 0.10
R0546:Plod2 UTSW 9 92595335 missense probably damaging 1.00
R0589:Plod2 UTSW 9 92593746 missense probably benign
R0707:Plod2 UTSW 9 92605427 missense possibly damaging 0.91
R1491:Plod2 UTSW 9 92606584 missense probably benign 0.00
R1572:Plod2 UTSW 9 92603067 splice site probably benign
R1731:Plod2 UTSW 9 92584604 critical splice donor site probably null
R1895:Plod2 UTSW 9 92607135 missense probably damaging 1.00
R1917:Plod2 UTSW 9 92581257 missense probably benign
R1946:Plod2 UTSW 9 92607135 missense probably damaging 1.00
R3850:Plod2 UTSW 9 92542545 missense probably benign 0.28
R3973:Plod2 UTSW 9 92598619 nonsense probably null
R3974:Plod2 UTSW 9 92598619 nonsense probably null
R4289:Plod2 UTSW 9 92602988 missense possibly damaging 0.89
R4423:Plod2 UTSW 9 92601989 missense probably benign 0.00
R4647:Plod2 UTSW 9 92605450 nonsense probably null
R4754:Plod2 UTSW 9 92606531 nonsense probably null
R4769:Plod2 UTSW 9 92595272 missense probably damaging 1.00
R5279:Plod2 UTSW 9 92581323 missense probably damaging 1.00
R5535:Plod2 UTSW 9 92606569 missense probably damaging 1.00
R5654:Plod2 UTSW 9 92593823 missense probably benign
R5764:Plod2 UTSW 9 92603021 missense probably damaging 0.97
R5885:Plod2 UTSW 9 92606656 critical splice donor site probably null
R5940:Plod2 UTSW 9 92591397 missense probably benign 0.39
R6917:Plod2 UTSW 9 92593770 missense possibly damaging 0.87
R7109:Plod2 UTSW 9 92573597 missense probably damaging 1.00
R7221:Plod2 UTSW 9 92584527 missense probably damaging 1.00
R7311:Plod2 UTSW 9 92584558 missense probably damaging 1.00
R7963:Plod2 UTSW 9 92605446 missense probably benign 0.07
R8205:Plod2 UTSW 9 92542318 start gained probably benign
R8794:Plod2 UTSW 9 92600748 missense probably damaging 0.98
R8873:Plod2 UTSW 9 92607059 intron probably benign
R9044:Plod2 UTSW 9 92607220 missense probably damaging 0.97
R9071:Plod2 UTSW 9 92602995 missense probably benign 0.09
R9120:Plod2 UTSW 9 92542327 start gained probably benign
Z1088:Plod2 UTSW 9 92603035 missense probably benign
Posted On 2016-08-02