Incidental Mutation 'R1767:Plod3'
ID 194464
Institutional Source Beutler Lab
Gene Symbol Plod3
Ensembl Gene ENSMUSG00000004846
Gene Name procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3
Synonyms LH3, lysyl hydroxylase 3
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1767 (G1)
Quality Score 225
Status Not validated
Chromosome 5
Chromosomal Location 137015873-137025500 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 137019030 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 305 (V305E)
Ref Sequence ENSEMBL: ENSMUSP00000004968 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000004968] [ENSMUST00000034953] [ENSMUST00000085941] [ENSMUST00000111090] [ENSMUST00000111091] [ENSMUST00000156963] [ENSMUST00000137272]
AlphaFold Q9R0E1
Predicted Effect possibly damaging
Transcript: ENSMUST00000004968
AA Change: V305E

PolyPhen 2 Score 0.893 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
AA Change: V305E

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 probably benign
Transcript: ENSMUST00000034953
SMART Domains Protein: ENSMUSP00000034953
Gene: ENSMUSG00000059518

DomainStartEndE-ValueType
low complexity region 14 26 N/A INTRINSIC
low complexity region 58 73 N/A INTRINSIC
Pfam:zf-HIT 112 141 6.3e-13 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000085941
SMART Domains Protein: ENSMUSP00000083103
Gene: ENSMUSG00000059518

DomainStartEndE-ValueType
low complexity region 15 27 N/A INTRINSIC
low complexity region 59 74 N/A INTRINSIC
Pfam:zf-HIT 113 142 3e-13 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000102285
Predicted Effect probably benign
Transcript: ENSMUST00000111090
SMART Domains Protein: ENSMUSP00000106719
Gene: ENSMUSG00000059518

DomainStartEndE-ValueType
low complexity region 14 26 N/A INTRINSIC
low complexity region 58 73 N/A INTRINSIC
Pfam:zf-HIT 112 141 2.2e-14 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000111091
SMART Domains Protein: ENSMUSP00000106720
Gene: ENSMUSG00000059518

DomainStartEndE-ValueType
low complexity region 19 31 N/A INTRINSIC
low complexity region 63 78 N/A INTRINSIC
Pfam:zf-HIT 117 146 2.1e-13 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144784
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129896
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151642
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137419
Predicted Effect probably benign
Transcript: ENSMUST00000127100
SMART Domains Protein: ENSMUSP00000123550
Gene: ENSMUSG00000004846

DomainStartEndE-ValueType
Blast:P4Hc 2 35 2e-11 BLAST
P4Hc 38 200 3.04e-4 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000156963
SMART Domains Protein: ENSMUSP00000115929
Gene: ENSMUSG00000059518

DomainStartEndE-ValueType
low complexity region 14 26 N/A INTRINSIC
low complexity region 58 73 N/A INTRINSIC
Pfam:zf-HIT 112 141 6.7e-13 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000137272
SMART Domains Protein: ENSMUSP00000120331
Gene: ENSMUSG00000059518

DomainStartEndE-ValueType
low complexity region 19 31 N/A INTRINSIC
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 96.9%
  • 10x: 95.4%
  • 20x: 92.8%
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. [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: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110065P20Rik T C 4: 124,743,754 (GRCm39) N128S possibly damaging Het
Adam26b T A 8: 43,972,948 (GRCm39) I685F probably benign Het
Adgrf5 A T 17: 43,761,455 (GRCm39) Y1050F possibly damaging Het
Alcam A T 16: 52,091,077 (GRCm39) N480K probably damaging Het
Alk T A 17: 72,207,693 (GRCm39) H1014L possibly damaging Het
Arhgef2 A G 3: 88,551,260 (GRCm39) Q778R probably damaging Het
Arhgef6 T C X: 56,383,922 (GRCm39) M5V probably benign Het
Ascc3 T A 10: 50,594,472 (GRCm39) I1189N probably damaging Het
AU040320 G A 4: 126,734,517 (GRCm39) G713D probably damaging Het
Bmpr1a A G 14: 34,169,727 (GRCm39) probably null Het
Bpifa6 A G 2: 153,829,147 (GRCm39) T225A possibly damaging Het
Cacna1g T C 11: 94,350,628 (GRCm39) S406G probably benign Het
Ccdc198 G A 14: 49,473,341 (GRCm39) T128I probably benign Het
Ccdc40 T A 11: 119,121,522 (GRCm39) probably null Het
Cckbr A T 7: 105,083,758 (GRCm39) I229F possibly damaging Het
Cers3 A G 7: 66,433,151 (GRCm39) K156R probably damaging Het
Chd1 T A 17: 15,990,565 (GRCm39) W1706R probably damaging Het
Col11a2 T A 17: 34,282,869 (GRCm39) probably benign Het
Coq10b A G 1: 55,100,513 (GRCm39) R66G probably damaging Het
Cpn2 A T 16: 30,078,485 (GRCm39) Y405* probably null Het
Dis3 A T 14: 99,321,578 (GRCm39) Y590N probably damaging Het
Dpy19l1 T C 9: 24,373,880 (GRCm39) H270R probably benign Het
Dync1h1 G A 12: 110,602,943 (GRCm39) E2195K probably benign Het
Ephx1 C T 1: 180,822,242 (GRCm39) G101S probably damaging Het
Flg A T 3: 93,187,220 (GRCm39) Y224F possibly damaging Het
Focad G T 4: 88,275,705 (GRCm39) V1105L unknown Het
Fzd1 A G 5: 4,806,812 (GRCm39) Y257H probably benign Het
Gm11116 T C 5: 88,259,311 (GRCm39) probably benign Het
Gm11938 G A 11: 99,494,071 (GRCm39) S8F unknown Het
Grin3a A T 4: 49,844,423 (GRCm39) V220E probably damaging Het
Gstt2 T C 10: 75,670,098 (GRCm39) D8G probably damaging Het
Gtf3c3 C T 1: 54,456,937 (GRCm39) A488T probably damaging Het
Hook3 A G 8: 26,561,084 (GRCm39) probably null Het
Itpr2 T C 6: 146,251,566 (GRCm39) D993G possibly damaging Het
Jhy T C 9: 40,872,444 (GRCm39) R22G probably benign Het
Krt13 A C 11: 100,011,926 (GRCm39) H132Q possibly damaging Het
Krtap27-1 G A 16: 88,468,199 (GRCm39) S115L probably damaging Het
L1td1 T C 4: 98,625,686 (GRCm39) V627A probably benign Het
Lrrn4cl A G 19: 8,829,135 (GRCm39) T38A probably benign Het
Ly96 A G 1: 16,776,399 (GRCm39) T112A probably benign Het
Meltf G T 16: 31,702,747 (GRCm39) C158F probably damaging Het
Mycbp2 A T 14: 103,485,841 (GRCm39) H1040Q probably damaging Het
Npas4 G A 19: 5,038,211 (GRCm39) P199L probably benign Het
Or12j3 T C 7: 139,953,389 (GRCm39) I45V possibly damaging Het
Or52r1 T A 7: 102,536,833 (GRCm39) I176F probably damaging Het
Or8k3b A G 2: 86,520,728 (GRCm39) M197T probably benign Het
Pcdh10 A T 3: 45,338,612 (GRCm39) H923L probably damaging Het
Pias3 T C 3: 96,608,719 (GRCm39) S228P probably damaging Het
Pign A G 1: 105,580,917 (GRCm39) V154A probably benign Het
Prkra G T 2: 76,477,584 (GRCm39) H40Q possibly damaging Het
Prss22 T A 17: 24,215,331 (GRCm39) E148D probably benign Het
Psg17 A G 7: 18,550,727 (GRCm39) V376A possibly damaging Het
Retnlg A T 16: 48,693,991 (GRCm39) D49V possibly damaging Het
Rnf26rt A T 6: 76,474,588 (GRCm39) N9K unknown Het
Rtp1 A G 16: 23,250,124 (GRCm39) E163G probably damaging Het
Slc6a20a T A 9: 123,466,165 (GRCm39) I522F probably damaging Het
Slco5a1 T C 1: 13,059,839 (GRCm39) D294G probably damaging Het
Slco6d1 A G 1: 98,418,274 (GRCm39) T487A possibly damaging Het
Smarcc2 A T 10: 128,304,951 (GRCm39) D262V possibly damaging Het
Sned1 G A 1: 93,209,376 (GRCm39) V830M possibly damaging Het
Ssbp3 G T 4: 106,904,612 (GRCm39) D336Y probably damaging Het
Sun2 A G 15: 79,609,758 (GRCm39) S694P probably benign Het
Tdp1 G A 12: 99,857,602 (GRCm39) probably null Het
Tfap2a A T 13: 40,878,613 (GRCm39) I204N probably damaging Het
Tfip11 T A 5: 112,482,298 (GRCm39) W519R probably damaging Het
Tie1 T C 4: 118,333,373 (GRCm39) E831G possibly damaging Het
Tjp1 A G 7: 64,962,301 (GRCm39) probably null Het
Tln2 C T 9: 67,193,796 (GRCm39) A1773T probably benign Het
Tmem39b A C 4: 129,586,976 (GRCm39) I78M possibly damaging Het
Trank1 T C 9: 111,220,547 (GRCm39) V2428A probably benign Het
Trim35 A G 14: 66,541,617 (GRCm39) E247G probably damaging Het
Tsc22d1 T C 14: 76,655,542 (GRCm39) S674P probably damaging Het
Tsn A T 1: 118,228,618 (GRCm39) D201E probably damaging Het
Usp42 A T 5: 143,700,621 (GRCm39) V1134E possibly damaging Het
Uvrag A G 7: 98,748,601 (GRCm39) I117T probably damaging Het
Vmn1r192 A G 13: 22,371,441 (GRCm39) S260P probably benign Het
Vmn2r110 C T 17: 20,800,840 (GRCm39) A531T possibly damaging Het
Wdsub1 A T 2: 59,689,058 (GRCm39) I388N probably damaging Het
Wnt10b A T 15: 98,670,556 (GRCm39) L228Q probably damaging Het
Zbtb34 A C 2: 33,301,348 (GRCm39) S398A possibly damaging 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
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
R5159:Plod3 UTSW 5 137,023,932 (GRCm39) intron probably benign
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'- ATTCTGCAACCAGACCCTGAGGAC -3'
(R):5'- TCGTGGTACACCTCCTGAAGATGG -3'

Sequencing Primer
(F):5'- GACCCTGAGGACACTCCC -3'
(R):5'- GGGATACACTGACGGTCTG -3'
Posted On 2014-05-23