Incidental Mutation 'R1018:P3h1'
ID 96559
Institutional Source Beutler Lab
Gene Symbol P3h1
Ensembl Gene ENSMUSG00000028641
Gene Name prolyl 3-hydroxylase 1
Synonyms 2410024C15Rik, Lepre1, Leprecan, Gros1
MMRRC Submission 039122-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1018 (G1)
Quality Score 225
Status Validated
Chromosome 4
Chromosomal Location 119090112-119106172 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 119095104 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Lysine at position 287 (T287K)
Ref Sequence ENSEMBL: ENSMUSP00000119695 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030393] [ENSMUST00000081606] [ENSMUST00000102662] [ENSMUST00000121111] [ENSMUST00000136278]
AlphaFold Q3V1T4
Predicted Effect probably benign
Transcript: ENSMUST00000030393
AA Change: T287K

PolyPhen 2 Score 0.103 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000030393
Gene: ENSMUSG00000028641
AA Change: T287K

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
low complexity region 60 84 N/A INTRINSIC
low complexity region 117 127 N/A INTRINSIC
internal_repeat_1 136 213 2.49e-12 PROSPERO
internal_repeat_1 294 369 2.49e-12 PROSPERO
Blast:P4Hc 419 462 2e-14 BLAST
P4Hc 479 687 5.96e-53 SMART
low complexity region 714 725 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000081606
AA Change: T108K

PolyPhen 2 Score 0.752 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000080312
Gene: ENSMUSG00000028641
AA Change: T108K

DomainStartEndE-ValueType
SCOP:d1hxia_ 80 195 4e-5 SMART
Blast:P4Hc 125 206 2e-11 BLAST
Blast:P4Hc 233 276 1e-14 BLAST
P4Hc 293 501 5.96e-53 SMART
low complexity region 528 539 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000102662
AA Change: T287K

PolyPhen 2 Score 0.046 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000099723
Gene: ENSMUSG00000028641
AA Change: T287K

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
low complexity region 60 84 N/A INTRINSIC
low complexity region 117 127 N/A INTRINSIC
internal_repeat_1 136 213 1.9e-12 PROSPERO
internal_repeat_1 294 369 1.9e-12 PROSPERO
Blast:P4Hc 412 455 2e-14 BLAST
P4Hc 472 680 5.96e-53 SMART
low complexity region 707 718 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000121111
AA Change: T287K

PolyPhen 2 Score 0.752 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000112504
Gene: ENSMUSG00000028641
AA Change: T287K

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
low complexity region 60 84 N/A INTRINSIC
low complexity region 117 127 N/A INTRINSIC
internal_repeat_1 136 213 2.32e-12 PROSPERO
internal_repeat_1 294 369 2.32e-12 PROSPERO
Blast:P4Hc 412 455 2e-14 BLAST
P4Hc 472 680 5.96e-53 SMART
low complexity region 707 718 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000123963
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126056
Predicted Effect probably damaging
Transcript: ENSMUST00000136278
AA Change: T287K

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000119695
Gene: ENSMUSG00000028641
AA Change: T287K

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
low complexity region 60 84 N/A INTRINSIC
low complexity region 117 127 N/A INTRINSIC
internal_repeat_1 136 198 6.76e-13 PROSPERO
internal_repeat_1 294 356 6.76e-13 PROSPERO
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131875
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153940
Meta Mutation Damage Score 0.1229 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 95.9%
  • 20x: 91.7%
Validation Efficiency 100% (50/50)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an enzyme that is a member of the collagen prolyl hydroxylase family. These enzymes are localized to the endoplasmic reticulum and their activity is required for proper collagen synthesis and assembly. Mutations in this gene are associated with osteogenesis imperfecta type VIII. Three alternatively spliced transcript variants encoding different isoforms have been described. Other variants may exist, but their biological validity has not been determined. [provided by RefSeq, Aug 2011]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit reduced size, disproportional reduction in long bone length, decreased bone density, decreased bone mineral density, reduced body fat, delayed ossification, and abnormal collagen networks in the skin and tendons. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca7 G T 10: 79,837,325 (GRCm39) C403F probably damaging Het
Adam20 C T 8: 41,249,146 (GRCm39) Q419* probably null Het
Ankrd36 C T 11: 5,596,876 (GRCm39) probably benign Het
Arl8b T A 6: 108,795,572 (GRCm39) I170K probably damaging Het
Atp5pb A T 3: 105,861,488 (GRCm39) V78E possibly damaging Het
Car9 G T 4: 43,512,439 (GRCm39) probably null Het
Cgnl1 A G 9: 71,633,340 (GRCm39) Y4H probably damaging Het
Cnn2 T C 10: 79,829,397 (GRCm39) C176R probably damaging Het
Dst A G 1: 34,233,174 (GRCm39) D3392G probably damaging Het
Eed T C 7: 89,617,019 (GRCm39) probably benign Het
Efl1 T A 7: 82,412,221 (GRCm39) V870E possibly damaging Het
Epx T C 11: 87,760,129 (GRCm39) N495S probably benign Het
Fbxw20 T A 9: 109,050,404 (GRCm39) Y407F probably benign Het
Gbp9 T A 5: 105,228,126 (GRCm39) Q552L probably benign Het
Hspa13 C A 16: 75,558,164 (GRCm39) V134L possibly damaging Het
Il16 T C 7: 83,323,746 (GRCm39) N268S probably damaging Het
Kif14 G A 1: 136,423,579 (GRCm39) probably benign Het
Lrig1 G A 6: 94,599,583 (GRCm39) probably benign Het
Myo7a T A 7: 97,756,212 (GRCm39) D29V probably damaging Het
Nsd2 A G 5: 34,000,585 (GRCm39) K34R probably damaging Het
Or4a15 C A 2: 89,193,523 (GRCm39) L83F possibly damaging Het
Pkhd1 A T 1: 20,271,483 (GRCm39) H3023Q possibly damaging Het
Plxna1 A G 6: 89,319,942 (GRCm39) L535P probably damaging Het
Prom1 A T 5: 44,187,056 (GRCm39) S400R probably benign Het
Psap T G 10: 60,136,590 (GRCm39) L523R probably damaging Het
Psme4 C T 11: 30,754,310 (GRCm39) T189I probably damaging Het
Ptpn12 A T 5: 21,234,867 (GRCm39) S39T possibly damaging Het
Qtrt2 T A 16: 43,698,363 (GRCm39) H98L possibly damaging Het
Rad54l2 C A 9: 106,589,589 (GRCm39) C601F probably benign Het
Saxo4 A T 19: 10,456,824 (GRCm39) probably benign Het
Sfswap A G 5: 129,631,640 (GRCm39) K756R possibly damaging Het
Slc24a5 T C 2: 124,910,827 (GRCm39) V86A probably damaging Het
Srrm2 T C 17: 24,041,514 (GRCm39) S2575P probably damaging Het
Stam T C 2: 14,122,185 (GRCm39) probably benign Het
Tbx6 T A 7: 126,382,364 (GRCm39) probably benign Het
Tmem131 A C 1: 36,833,900 (GRCm39) F1727V probably damaging Het
Tpr T A 1: 150,317,934 (GRCm39) H2147Q possibly damaging Het
Trio T A 15: 27,871,257 (GRCm39) H620L probably damaging Het
Uba5 T C 9: 103,927,102 (GRCm39) T292A probably benign Het
Unc5a T A 13: 55,138,765 (GRCm39) V48E possibly damaging Het
Upf1 G T 8: 70,791,556 (GRCm39) H514Q possibly damaging Het
Usp9y A G Y: 1,341,414 (GRCm39) probably benign Het
Vmn2r6 T A 3: 64,464,261 (GRCm39) D191V probably benign Het
Wapl T C 14: 34,413,863 (GRCm39) Y242H possibly damaging Het
Zfp341 A T 2: 154,487,972 (GRCm39) N812Y probably damaging Het
Zfp358 C A 8: 3,546,843 (GRCm39) S475* probably null Het
Zfp957 C A 14: 79,450,182 (GRCm39) C539F probably damaging Het
Other mutations in P3h1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01622:P3h1 APN 4 119,092,480 (GRCm39) missense probably damaging 1.00
IGL01623:P3h1 APN 4 119,092,480 (GRCm39) missense probably damaging 1.00
IGL01645:P3h1 APN 4 119,093,980 (GRCm39) missense probably damaging 1.00
IGL02140:P3h1 APN 4 119,095,062 (GRCm39) missense probably damaging 1.00
IGL02415:P3h1 APN 4 119,105,152 (GRCm39) missense probably benign
IGL02543:P3h1 APN 4 119,095,053 (GRCm39) splice site probably benign
IGL02870:P3h1 APN 4 119,104,768 (GRCm39) missense probably damaging 1.00
IGL02972:P3h1 APN 4 119,105,157 (GRCm39) missense possibly damaging 0.75
IGL03067:P3h1 APN 4 119,092,477 (GRCm39) missense probably damaging 0.99
IGL03077:P3h1 APN 4 119,093,983 (GRCm39) missense probably damaging 1.00
woohoo UTSW 4 119,098,329 (GRCm39) nonsense probably null
R0194:P3h1 UTSW 4 119,095,149 (GRCm39) missense probably damaging 1.00
R0523:P3h1 UTSW 4 119,098,727 (GRCm39) missense probably benign 0.32
R0734:P3h1 UTSW 4 119,095,885 (GRCm39) missense probably damaging 1.00
R0944:P3h1 UTSW 4 119,095,956 (GRCm39) missense probably benign 0.00
R1978:P3h1 UTSW 4 119,105,173 (GRCm39) missense probably null 0.00
R2697:P3h1 UTSW 4 119,104,377 (GRCm39) missense probably damaging 1.00
R5668:P3h1 UTSW 4 119,101,243 (GRCm39) missense possibly damaging 0.89
R5750:P3h1 UTSW 4 119,095,863 (GRCm39) missense probably damaging 0.96
R5965:P3h1 UTSW 4 119,105,424 (GRCm39) missense probably benign 0.00
R5987:P3h1 UTSW 4 119,103,862 (GRCm39) missense probably damaging 1.00
R6111:P3h1 UTSW 4 119,098,329 (GRCm39) nonsense probably null
R6786:P3h1 UTSW 4 119,095,151 (GRCm39) missense possibly damaging 0.65
R7142:P3h1 UTSW 4 119,104,358 (GRCm39) missense probably benign 0.00
R8068:P3h1 UTSW 4 119,094,059 (GRCm39) missense probably damaging 1.00
R8304:P3h1 UTSW 4 119,104,402 (GRCm39) missense probably damaging 1.00
R9502:P3h1 UTSW 4 119,094,008 (GRCm39) missense possibly damaging 0.86
R9680:P3h1 UTSW 4 119,090,428 (GRCm39) missense probably benign 0.17
Predicted Primers PCR Primer
(F):5'- GTTCACACATGCCACATACTTGCAC -3'
(R):5'- GCTTGTGACAAAACACCCAGGAATC -3'

Sequencing Primer
(F):5'- tcaggaggcagaggcag -3'
(R):5'- ACCCAGGAATCATTGGGC -3'
Posted On 2014-01-05