Incidental Mutation 'R9108:Plod3'
ID 692071
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
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9108 (G1)
Quality Score 225.009
Status Validated
Chromosome 5
Chromosomal Location 137015873-137025500 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 137018017 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 221 (I221T)
Ref Sequence ENSEMBL: ENSMUSP00000004968 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000004968] [ENSMUST00000034953] [ENSMUST00000085941] [ENSMUST00000111090] [ENSMUST00000111091] [ENSMUST00000137272] [ENSMUST00000156963]
AlphaFold Q9R0E1
Predicted Effect probably damaging
Transcript: ENSMUST00000004968
AA Change: I221T

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
AA Change: I221T

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 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 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: ENSMUST00000137272
SMART Domains Protein: ENSMUSP00000120331
Gene: ENSMUSG00000059518

DomainStartEndE-ValueType
low complexity region 19 31 N/A INTRINSIC
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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.2%
Validation Efficiency 100% (65/65)
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: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921524L21Rik G A 18: 6,638,794 (GRCm39) V398M probably benign Het
4930568D16Rik G A 2: 35,244,942 (GRCm39) P137S probably damaging Het
Abcb9 T C 5: 124,228,176 (GRCm39) T22A possibly damaging Het
Abcg8 A C 17: 85,000,243 (GRCm39) I268L probably benign Het
Acvrl1 A G 15: 101,039,038 (GRCm39) Q445R probably damaging Het
Adam17 T C 12: 21,380,132 (GRCm39) N625D probably benign Het
Adamts9 C T 6: 92,857,721 (GRCm39) V856M probably damaging Het
Adar T C 3: 89,643,474 (GRCm39) C452R probably damaging Het
Adgra3 G T 5: 50,136,295 (GRCm39) A730D probably damaging Het
Adnp2 C T 18: 80,185,925 (GRCm39) R16Q probably damaging Het
Aox1 T C 1: 58,321,851 (GRCm39) C48R probably damaging Het
Cabin1 T C 10: 75,492,973 (GRCm39) E1774G possibly damaging Het
Capsl A T 15: 9,465,910 (GRCm39) I199F possibly damaging Het
Ccdc191 T A 16: 43,718,512 (GRCm39) D36E possibly damaging Het
Cep170 T A 1: 176,616,051 (GRCm39) K86* probably null Het
Cnnm1 T C 19: 43,464,649 (GRCm39) F736S possibly damaging Het
Col11a2 T A 17: 34,276,634 (GRCm39) V532E probably benign Het
Dnmt3l T C 10: 77,892,756 (GRCm39) probably null Het
Dync1h1 T A 12: 110,622,706 (GRCm39) probably benign Het
Dzank1 C A 2: 144,364,391 (GRCm39) V69L probably benign Het
Epor T G 9: 21,870,875 (GRCm39) E335A probably damaging Het
Fbxo46 A T 7: 18,870,308 (GRCm39) Y309F probably damaging Het
Fra10ac1 A T 19: 38,202,779 (GRCm39) probably benign Het
Gid8 G T 2: 180,352,132 (GRCm39) probably benign Het
Gm57858 T G 3: 36,080,036 (GRCm39) *240C probably null Het
Gnptab C T 10: 88,269,400 (GRCm39) S701L Het
Ifnl3 T C 7: 28,223,704 (GRCm39) L180P probably benign Het
Ikzf2 T A 1: 69,577,956 (GRCm39) I518F probably damaging Het
Ildr1 A G 16: 36,535,919 (GRCm39) T145A probably benign Het
Kiss1r A T 10: 79,754,336 (GRCm39) probably benign Het
Lhpp A G 7: 132,252,018 (GRCm39) D219G probably damaging Het
Lrp1 A T 10: 127,390,206 (GRCm39) M3071K probably damaging Het
Map6 T C 7: 98,986,103 (GRCm39) L872P probably damaging Het
Mgst2 T A 3: 51,589,233 (GRCm39) L82Q probably damaging Het
Mier2 A T 10: 79,377,756 (GRCm39) V399E probably benign Het
Nms T C 1: 38,985,147 (GRCm39) V91A possibly damaging Het
Nt5dc2 T A 14: 30,857,016 (GRCm39) Y145* probably null Het
Olfml2a A T 2: 38,831,753 (GRCm39) M111L probably benign Het
Or5p63 T C 7: 107,810,846 (GRCm39) N297D probably damaging Het
Or5p75-ps1 T A 7: 108,107,779 (GRCm39) L172Q unknown Het
Polm T C 11: 5,779,872 (GRCm39) Q342R probably benign Het
Ppp2r5c A T 12: 110,521,303 (GRCm39) L275F probably damaging Het
Prdm12 C T 2: 31,533,929 (GRCm39) T182M possibly damaging Het
Rasgrp2 G A 19: 6,458,890 (GRCm39) V440M probably damaging Het
Rnf111 C T 9: 70,336,846 (GRCm39) G947D probably damaging Het
Runx3 A T 4: 134,882,692 (GRCm39) M143L probably damaging Het
Samd9l T C 6: 3,373,104 (GRCm39) S1386G possibly damaging Het
Saxo2 C T 7: 82,284,082 (GRCm39) V259I probably benign Het
Shroom3 T C 5: 93,087,975 (GRCm39) S242P probably damaging Het
Slc35e1 G A 8: 73,246,030 (GRCm39) P134L Het
Spata31d1a A G 13: 59,850,982 (GRCm39) V382A probably benign Het
Tanc2 T A 11: 105,810,580 (GRCm39) probably benign Het
Tenm3 A T 8: 48,766,271 (GRCm39) probably null Het
Trip10 C T 17: 57,560,519 (GRCm39) A123V probably damaging Het
Trmt13 A G 3: 116,375,129 (GRCm39) S460P probably damaging Het
Trpd52l3 A G 19: 29,981,329 (GRCm39) N28S probably benign Het
Tubb4a A G 17: 57,388,232 (GRCm39) F265L probably benign Het
Uba6 A T 5: 86,282,934 (GRCm39) C581S possibly damaging Het
Uckl1 A G 2: 181,211,293 (GRCm39) V512A probably damaging Het
Usp34 A T 11: 23,320,528 (GRCm39) M957L Het
Vmn2r57 T C 7: 41,078,192 (GRCm39) I89V possibly damaging Het
Zfp1005 T A 2: 150,109,969 (GRCm39) C220S possibly damaging Het
Zfp322a T C 13: 23,541,437 (GRCm39) I102V probably benign Het
Zzef1 A G 11: 72,790,604 (GRCm39) D2186G 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
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
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'- CACTCAACTGTACCTGGACC -3'
(R):5'- CGGTAGATCGAGCTCCAAACAC -3'

Sequencing Primer
(F):5'- CCAGGGCTGCGGGTAGG -3'
(R):5'- GGGTTTCTGTATGCTAGACACACTC -3'
Posted On 2021-12-30