Incidental Mutation 'R1216:Plod1'
ID99633
Institutional Source Beutler Lab
Gene Symbol Plod1
Ensembl Gene ENSMUSG00000019055
Gene Nameprocollagen-lysine, 2-oxoglutarate 5-dioxygenase 1
SynonymsLH1, 2410042F05Rik, lysyl hydroxylase 1
MMRRC Submission 039285-MU
Accession Numbers
Is this an essential gene? Probably non essential (E-score: 0.240) question?
Stock #R1216 (G1)
Quality Score225
Status Validated
Chromosome4
Chromosomal Location147909753-147936767 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to T at 147921127 bp
ZygosityHeterozygous
Amino Acid Change Valine to Aspartic acid at position 404 (V404D)
Ref Sequence ENSEMBL: ENSMUSP00000019199 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000019199]
Predicted Effect probably damaging
Transcript: ENSMUST00000019199
AA Change: V404D

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000019199
Gene: ENSMUSG00000019055
AA Change: V404D

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
low complexity region 301 313 N/A INTRINSIC
Blast:P4Hc 444 492 1e-8 BLAST
P4Hc 554 727 4.87e-26 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124041
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124292
Predicted Effect probably benign
Transcript: ENSMUST00000149129
SMART Domains Protein: ENSMUSP00000118857
Gene: ENSMUSG00000019055

DomainStartEndE-ValueType
Blast:P4Hc 31 136 5e-33 BLAST
Blast:P4Hc 141 269 4e-47 BLAST
Meta Mutation Damage Score 0.262 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 96.1%
  • 20x: 92.3%
Validation Efficiency 98% (45/46)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Lysyl hydroxylase is a membrane-bound homodimeric protein localized to the cisternae of the 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 VI have deficiencies in lysyl hydroxylase activity. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
PHENOTYPE: Mice homozygous for a null allele exhibit hypotonia, reduced voluntary movement, abnormal aorta and skin collagen fibers, irregular vascular smooth muscle and premature death associated with thoracic cavity hemorrhage and aortic dissection. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A830018L16Rik A T 1: 11,798,492 D332V probably damaging Het
Akr1c12 T C 13: 4,276,323 Y53C probably benign Het
Arhgap23 T C 11: 97,492,672 probably benign Het
AU040320 T C 4: 126,816,483 probably benign Het
B4galnt2 A G 11: 95,891,941 L15P probably benign Het
Cadps2 A G 6: 23,583,473 probably benign Het
Cul9 C G 17: 46,522,175 A1326P probably damaging Het
Dppa4 T C 16: 48,292,980 F244S possibly damaging Het
Exoc1 A G 5: 76,554,188 K445R probably benign Het
Fam47e A G 5: 92,562,484 E114G probably damaging Het
Fgf12 A T 16: 28,162,450 N171K possibly damaging Het
Fyb2 G A 4: 104,995,706 V528M possibly damaging Het
Ghr A G 15: 3,319,855 S614P probably damaging Het
Gm10985 A C 3: 53,845,253 Y19S probably damaging Het
Gpr152 T A 19: 4,143,555 V365D possibly damaging Het
Guca1a A G 17: 47,395,712 probably benign Het
Hivep1 G A 13: 42,157,521 G1079D probably benign Het
Hnrnpm T C 17: 33,649,713 D580G probably damaging Het
Ints6 A T 14: 62,707,698 D394E probably damaging Het
Kat6b T A 14: 21,622,040 Y339* probably null Het
Kcnj11 C A 7: 46,099,861 V13L probably benign Het
Lama3 C T 18: 12,421,134 probably benign Het
Myo18a A G 11: 77,818,647 T161A probably benign Het
Ncapg G T 5: 45,699,919 S991I possibly damaging Het
Nrde2 G A 12: 100,149,810 probably benign Het
Olfr1262 T A 2: 90,002,478 I24N probably benign Het
Olfr73 T C 2: 88,034,258 R294G probably damaging Het
Pcdhb7 A T 18: 37,343,874 T688S probably damaging Het
Pla2g6 T C 15: 79,306,435 D309G probably benign Het
Ppp2r2a G T 14: 67,028,998 Y71* probably null Het
Prcp A G 7: 92,917,746 N222S probably benign Het
Rad21 T C 15: 51,970,136 T316A possibly damaging Het
Ranbp2 T C 10: 58,483,212 probably benign Het
Rapgef4 C A 2: 72,208,148 P548T possibly damaging Het
Ric1 G T 19: 29,577,735 M416I probably benign Het
Skiv2l2 A G 13: 112,914,342 probably benign Het
Slc9a8 T C 2: 167,424,121 F6S probably benign Het
Smpdl3a T G 10: 57,802,479 I126S probably null Het
Sphkap A T 1: 83,290,977 L98Q probably damaging Het
Spink4 T G 4: 40,924,974 probably benign Het
Taar5 A T 10: 23,971,707 L334F probably damaging Het
Tecta A T 9: 42,377,907 I454K probably benign Het
Ttc7 C T 17: 87,346,578 T561M possibly damaging Het
Vmn2r9 G T 5: 108,847,574 H403N probably damaging Het
Zdbf2 G A 1: 63,303,002 C180Y possibly damaging Het
Other mutations in Plod1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01144:Plod1 APN 4 147932754 missense probably benign 0.12
IGL02312:Plod1 APN 4 147926157 missense probably benign 0.09
IGL02588:Plod1 APN 4 147913290 nonsense probably null
IGL02712:Plod1 APN 4 147918887 missense possibly damaging 0.95
IGL02976:Plod1 APN 4 147913321 missense probably damaging 0.99
IGL03244:Plod1 APN 4 147923123 critical splice donor site probably null
R0393:Plod1 UTSW 4 147918841 missense probably null 0.35
R1897:Plod1 UTSW 4 147926200 missense probably damaging 0.97
R3776:Plod1 UTSW 4 147931277 missense possibly damaging 0.75
R3923:Plod1 UTSW 4 147915823 missense possibly damaging 0.62
R4718:Plod1 UTSW 4 147916244 intron probably benign
R4897:Plod1 UTSW 4 147920279 missense probably benign
R5173:Plod1 UTSW 4 147916301 intron probably benign
R5657:Plod1 UTSW 4 147918781 missense possibly damaging 0.46
R6298:Plod1 UTSW 4 147916315 intron probably benign
R6995:Plod1 UTSW 4 147916218 intron probably benign
R7176:Plod1 UTSW 4 147913287 missense probably benign 0.00
X0013:Plod1 UTSW 4 147927042 missense possibly damaging 0.70
Y5406:Plod1 UTSW 4 147931187 missense probably damaging 1.00
Y5408:Plod1 UTSW 4 147931187 missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ATGGGAGCCCACGACAACTTTCAG -3'
(R):5'- CCATAAAGCCAAGCTATGCGGACAG -3'

Sequencing Primer
(F):5'- TTGAGGTTCAGCTCACCCAG -3'
(R):5'- GCCTAAGGCTCCTGATTGAAC -3'
Posted On2014-01-15