Incidental Mutation 'R5159:Plod3'
ID 396870
Institutional Source Beutler Lab
Gene Symbol Plod3
Ensembl Gene ENSMUSG00000004846
Gene Name procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3
Synonyms LH3, lysyl hydroxylase 3
MMRRC Submission 042741-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5159 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 137015873-137025500 bp(+) (GRCm39)
Type of Mutation intron
DNA Base Change (assembly) T to A at 137023932 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000004968 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000004968]
AlphaFold Q9R0E1
Predicted Effect probably benign
Transcript: ENSMUST00000004968
SMART Domains Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
low complexity region 312 324 N/A INTRINSIC
Blast:P4Hc 456 502 2e-8 BLAST
P4Hc 567 740 1.43e-23 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000102285
Predicted Effect unknown
Transcript: ENSMUST00000127100
AA Change: L167Q
SMART Domains Protein: ENSMUSP00000123550
Gene: ENSMUSG00000004846
AA Change: L167Q

DomainStartEndE-ValueType
Blast:P4Hc 2 35 2e-11 BLAST
P4Hc 38 200 3.04e-4 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129896
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131667
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137419
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151642
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144784
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.7%
Validation Efficiency 100% (63/63)
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. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous null mice display embryonic lethality, reduced embryonic growth, fragility, and fragmented basement membranes. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9930111J21Rik1 T C 11: 48,839,352 (GRCm39) T412A probably benign Het
Aldh5a1 T A 13: 25,097,776 (GRCm39) M420L possibly damaging Het
Armc2 A G 10: 41,884,711 (GRCm39) S77P probably damaging Het
Avil A G 10: 126,856,317 (GRCm39) probably null Het
Bltp3a A G 17: 28,100,530 (GRCm39) H323R probably damaging Het
Bmp5 T A 9: 75,801,035 (GRCm39) F388L probably damaging Het
Brca2 T G 5: 150,465,573 (GRCm39) V1779G possibly damaging Het
Cblb T A 16: 51,932,483 (GRCm39) S147T probably damaging Het
Cblc T C 7: 19,519,233 (GRCm39) E409G probably benign Het
Cdc34b C T 11: 94,632,886 (GRCm39) R29W probably damaging Het
Clic6 T A 16: 92,324,954 (GRCm39) Y371N probably benign Het
Col5a2 A G 1: 45,425,991 (GRCm39) probably null Het
Coro1a A T 7: 126,302,221 (GRCm39) V42D probably damaging Het
Cpa3 C T 3: 20,281,387 (GRCm39) C173Y probably damaging Het
Crb1 A C 1: 139,170,756 (GRCm39) V817G probably damaging Het
Cyp2c39 A G 19: 39,549,378 (GRCm39) T299A possibly damaging Het
Dock5 G A 14: 68,029,738 (GRCm39) R1019C probably benign Het
Exoc8 T C 8: 125,622,952 (GRCm39) T472A probably benign Het
Fancc A G 13: 63,469,679 (GRCm39) probably null Het
Fcgbpl1 T A 7: 27,852,733 (GRCm39) M1340K probably benign Het
Inpp5d T C 1: 87,604,064 (GRCm39) L244P probably damaging Het
Ireb2 A G 9: 54,799,831 (GRCm39) N424S probably benign Het
Krt35 T C 11: 99,984,875 (GRCm39) D261G probably damaging Het
Lipc T A 9: 70,720,192 (GRCm39) I272L probably benign Het
Lpcat3 A G 6: 124,676,357 (GRCm39) probably benign Het
Lzts1 T C 8: 69,591,236 (GRCm39) D304G probably benign Het
Mdn1 A G 4: 32,774,008 (GRCm39) I5540V possibly damaging Het
Msln T C 17: 25,970,563 (GRCm39) S231G probably benign Het
Mup8 G A 4: 60,221,062 (GRCm39) T101M probably benign Het
Myh8 T C 11: 67,179,179 (GRCm39) I524T probably damaging Het
Pappa2 A G 1: 158,589,189 (GRCm39) C1679R probably damaging Het
Pcdhb1 T C 18: 37,399,416 (GRCm39) S456P possibly damaging Het
Pcdhga5 A G 18: 37,828,719 (GRCm39) N389S probably benign Het
Pitrm1 C A 13: 6,617,507 (GRCm39) S620R probably benign Het
Por A T 5: 135,759,771 (GRCm39) Q194L probably benign Het
Prkag3 A T 1: 74,780,646 (GRCm39) Y396N probably damaging Het
R3hcc1 T C 14: 69,935,053 (GRCm39) probably null Het
Rcan3 C T 4: 135,152,592 (GRCm39) S43N probably damaging Het
Rhot1 A G 11: 80,111,098 (GRCm39) T31A probably damaging Het
Rnps1 T G 17: 24,637,486 (GRCm39) S43A unknown Het
Rp1 T C 1: 4,416,426 (GRCm39) D1562G possibly damaging Het
Rps19-ps13 A G 18: 40,859,428 (GRCm39) noncoding transcript Het
Serpina3c A T 12: 104,115,771 (GRCm39) S258T possibly damaging Het
Smc2 G A 4: 52,460,181 (GRCm39) R519Q possibly damaging Het
Sorbs2 A T 8: 46,248,767 (GRCm39) T593S probably benign Het
Sptbn2 A G 19: 4,787,885 (GRCm39) T955A probably benign Het
Stfa3 T C 16: 36,272,581 (GRCm39) K40E probably damaging Het
Tmem87b A G 2: 128,666,378 (GRCm39) E75G probably benign Het
Tmprss15 T C 16: 78,800,298 (GRCm39) Q595R probably benign Het
Trak1 A T 9: 121,289,478 (GRCm39) I597F probably damaging Het
Trat1 T C 16: 48,555,300 (GRCm39) D144G probably damaging Het
Trim25 T C 11: 88,890,358 (GRCm39) V15A probably benign Het
Tulp1 A C 17: 28,578,034 (GRCm39) probably null Het
Txndc15 T A 13: 55,865,734 (GRCm39) M66K probably benign Het
Vmn1r206 T A 13: 22,804,775 (GRCm39) N144I probably damaging Het
Wwc2 T C 8: 48,353,796 (GRCm39) T113A probably benign Het
Xpo5 A C 17: 46,528,535 (GRCm39) E313D probably damaging Het
Zfp790 C T 7: 29,529,192 (GRCm39) H626Y probably benign Het
Other mutations in Plod3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00507:Plod3 APN 5 137,025,030 (GRCm39) missense possibly damaging 0.78
IGL01090:Plod3 APN 5 137,019,090 (GRCm39) missense probably benign 0.37
IGL01443:Plod3 APN 5 137,019,075 (GRCm39) missense probably benign 0.17
IGL01583:Plod3 APN 5 137,025,002 (GRCm39) missense probably benign 0.02
R0544:Plod3 UTSW 5 137,020,465 (GRCm39) missense probably benign 0.09
R0747:Plod3 UTSW 5 137,017,049 (GRCm39) missense probably benign 0.34
R0764:Plod3 UTSW 5 137,018,437 (GRCm39) unclassified probably benign
R1520:Plod3 UTSW 5 137,020,165 (GRCm39) missense probably damaging 0.99
R1631:Plod3 UTSW 5 137,017,847 (GRCm39) missense probably damaging 1.00
R1751:Plod3 UTSW 5 137,019,030 (GRCm39) missense possibly damaging 0.89
R1767:Plod3 UTSW 5 137,019,030 (GRCm39) missense possibly damaging 0.89
R1984:Plod3 UTSW 5 137,019,707 (GRCm39) splice site probably null
R1985:Plod3 UTSW 5 137,019,707 (GRCm39) splice site probably null
R2137:Plod3 UTSW 5 137,017,571 (GRCm39) missense probably damaging 1.00
R2148:Plod3 UTSW 5 137,016,627 (GRCm39) nonsense probably null
R2179:Plod3 UTSW 5 137,019,862 (GRCm39) missense possibly damaging 0.77
R2318:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R2319:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R2512:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R2513:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R2696:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R2891:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R2893:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R3030:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R3439:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R3957:Plod3 UTSW 5 137,023,046 (GRCm39) missense probably damaging 1.00
R4080:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R4081:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R4342:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R4344:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R4345:Plod3 UTSW 5 137,017,000 (GRCm39) missense probably benign 0.38
R4546:Plod3 UTSW 5 137,017,801 (GRCm39) missense possibly damaging 0.94
R4799:Plod3 UTSW 5 137,019,654 (GRCm39) missense probably benign 0.00
R4843:Plod3 UTSW 5 137,019,854 (GRCm39) nonsense probably null
R4956:Plod3 UTSW 5 137,018,772 (GRCm39) missense probably damaging 1.00
R5162:Plod3 UTSW 5 137,020,161 (GRCm39) missense probably damaging 1.00
R5328:Plod3 UTSW 5 137,018,537 (GRCm39) missense probably damaging 1.00
R5427:Plod3 UTSW 5 137,020,642 (GRCm39) missense probably damaging 1.00
R6627:Plod3 UTSW 5 137,017,310 (GRCm39) missense probably damaging 0.99
R7003:Plod3 UTSW 5 137,018,498 (GRCm39) missense probably damaging 1.00
R7132:Plod3 UTSW 5 137,023,971 (GRCm39) missense
R7376:Plod3 UTSW 5 137,019,335 (GRCm39) missense probably benign 0.00
R7404:Plod3 UTSW 5 137,023,901 (GRCm39) missense probably benign
R7827:Plod3 UTSW 5 137,018,835 (GRCm39) missense probably benign
R8062:Plod3 UTSW 5 137,019,123 (GRCm39) missense possibly damaging 0.87
R8506:Plod3 UTSW 5 137,017,830 (GRCm39) missense probably damaging 1.00
R8772:Plod3 UTSW 5 137,017,773 (GRCm39) missense probably damaging 0.99
R9108:Plod3 UTSW 5 137,018,017 (GRCm39) missense probably damaging 0.99
R9439:Plod3 UTSW 5 137,023,036 (GRCm39) missense probably benign 0.03
R9788:Plod3 UTSW 5 137,019,911 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AAAGGGCTAGCCTTGGCG -3'
(R):5'- TCACCAGTGGAGTCCTGGG -3'

Sequencing Primer
(F):5'- TAGCCTTGGCGTGCCCTG -3'
(R):5'- AAGCAGCATCATGGCTTCTG -3'
Posted On 2016-06-21