Incidental Mutation 'R2318:Plod3'
ID 245551
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 # R2318 (G1)
Quality Score 225
Status Not validated
Chromosome 5
Chromosomal Location 137015873-137025500 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to C at 137017000 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Proline at position 50 (A50P)
Ref Sequence ENSEMBL: ENSMUSP00000004968 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000004968] [ENSMUST00000034953] [ENSMUST00000085941] [ENSMUST00000111090] [ENSMUST00000111091] [ENSMUST00000156963] [ENSMUST00000137272]
AlphaFold Q9R0E1
Predicted Effect probably benign
Transcript: ENSMUST00000004968
AA Change: A50P

PolyPhen 2 Score 0.382 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000004968
Gene: ENSMUSG00000004846
AA Change: A50P

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: ENSMUST00000137419
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151642
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129896
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
Meta Mutation Damage Score 0.1039 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.0%
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: 24 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Arhgef10 G A 8: 14,978,855 (GRCm39) A41T probably damaging Het
Car15 T C 16: 17,654,463 (GRCm39) M158V probably benign Het
Cinp C A 12: 110,840,443 (GRCm39) W113L probably damaging Het
Col4a3 T A 1: 82,626,290 (GRCm39) probably null Het
Csnk2b T C 17: 35,337,037 (GRCm39) Y101C possibly damaging Het
Ddb1 C T 19: 10,603,992 (GRCm39) R900C probably damaging Het
Eif4g2 A G 7: 110,673,065 (GRCm39) F876L possibly damaging Het
F11 A G 8: 45,701,675 (GRCm39) S353P probably damaging Het
H4c4 A G 13: 23,765,739 (GRCm39) Y52C probably damaging Het
Mast1 T C 8: 85,647,754 (GRCm39) D540G probably damaging Het
Mis18bp1 C T 12: 65,187,617 (GRCm39) V829M possibly damaging Het
Mtus2 C T 5: 148,043,892 (GRCm39) R827* probably null Het
Nlrp9a G A 7: 26,273,277 (GRCm39) V860M probably damaging Het
Prr14l T C 5: 32,987,422 (GRCm39) E691G probably benign Het
Rad1 A G 15: 10,490,495 (GRCm39) N154S probably benign Het
Sanbr A G 11: 23,538,701 (GRCm39) Y66H probably damaging Het
Slc10a4-ps T C 5: 72,743,638 (GRCm39) T27A probably benign Het
Smc2 T C 4: 52,446,030 (GRCm39) S133P probably damaging Het
Sstr1 T A 12: 58,259,562 (GRCm39) S62T possibly damaging Het
Thsd7a T C 6: 12,405,146 (GRCm39) Y766C probably damaging Het
Timm44 A G 8: 4,318,307 (GRCm39) V129A probably benign Het
Tinag T C 9: 76,952,693 (GRCm39) Y97C probably damaging Het
Tns2 C T 15: 102,017,369 (GRCm39) R281C probably damaging Het
Ubap2 A G 4: 41,251,542 (GRCm39) V30A probably 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
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
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'- CTTCTGGAGATCAAATGTGCTG -3'
(R):5'- AACTGTTCGAGCCACATCAC -3'

Sequencing Primer
(F):5'- TGTGCTGAAAGAACTTTAGTGAAG -3'
(R):5'- CCCAGGGTCTGCAGGAAAGATC -3'
Posted On 2014-10-30