Incidental Mutation 'R0571:Primpol'
ID 46461
Institutional Source Beutler Lab
Gene Symbol Primpol
Ensembl Gene ENSMUSG00000038225
Gene Name primase and polymerase (DNA-directed)
Synonyms Ccdc111
MMRRC Submission 038762-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0571 (G1)
Quality Score 225
Status Validated
Chromosome 8
Chromosomal Location 47028629-47070247 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 47034674 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Alanine at position 418 (D418A)
Ref Sequence ENSEMBL: ENSMUSP00000147574 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034045] [ENSMUST00000040468] [ENSMUST00000093518] [ENSMUST00000135432] [ENSMUST00000136335] [ENSMUST00000209787] [ENSMUST00000211400]
AlphaFold Q6P1E7
Predicted Effect probably benign
Transcript: ENSMUST00000034045
SMART Domains Protein: ENSMUSP00000034045
Gene: ENSMUSG00000031629

DomainStartEndE-ValueType
low complexity region 58 66 N/A INTRINSIC
Pfam:CENP-U 138 312 6.5e-74 PFAM
low complexity region 340 354 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000040468
AA Change: D418A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000036119
Gene: ENSMUSG00000038225
AA Change: D418A

DomainStartEndE-ValueType
Pfam:Herpes_UL52 384 448 1.3e-19 PFAM
low complexity region 465 478 N/A INTRINSIC
low complexity region 491 516 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000093518
SMART Domains Protein: ENSMUSP00000091239
Gene: ENSMUSG00000031629

DomainStartEndE-ValueType
Pfam:CENP-U 39 162 4.6e-61 PFAM
low complexity region 190 204 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000135432
Predicted Effect probably benign
Transcript: ENSMUST00000136335
Predicted Effect noncoding transcript
Transcript: ENSMUST00000136724
Predicted Effect probably damaging
Transcript: ENSMUST00000209787
AA Change: D418A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Predicted Effect probably damaging
Transcript: ENSMUST00000211400
AA Change: D418A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Meta Mutation Damage Score 0.7935 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 96.9%
  • 20x: 94.7%
Validation Efficiency 100% (71/71)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a DNA primase-polymerase that belongs to a superfamily of archaeao-eukaryotic primases. Members of this family have primase activity, catalyzing the synthesis of short RNA primers that serve as starting points for DNA synthesis, as well as DNA polymerase activity. The encoded protein facilitates DNA damage tolerance by mediating uninterrupted fork progression after UV irradiation and reinitiating DNA synthesis. An allelic variant in this gene is associated with myopia 22. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]
PHENOTYPE: Homozygous null mutants are viable and fertile. Mice homozygous for another knock-out allele exhibit selective increase in C to G transversions in B cells. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abhd4 C T 14: 54,500,706 (GRCm39) T165I possibly damaging Het
Acsl5 A G 19: 55,277,343 (GRCm39) probably benign Het
Actl6b C A 5: 137,565,046 (GRCm39) probably benign Het
Atg13 T C 2: 91,509,063 (GRCm39) probably benign Het
Cabyr A G 18: 12,883,909 (GRCm39) E132G probably damaging Het
Cadps2 C T 6: 23,583,411 (GRCm39) V389I probably damaging Het
Capn2 C T 1: 182,298,325 (GRCm39) V647I probably benign Het
Card10 G T 15: 78,671,601 (GRCm39) P621Q possibly damaging Het
Catsperb C G 12: 101,569,033 (GRCm39) H902D possibly damaging Het
Cers3 A G 7: 66,435,805 (GRCm39) M255V possibly damaging Het
Cfh T C 1: 140,030,071 (GRCm39) probably null Het
Chd3 A C 11: 69,252,495 (GRCm39) probably null Het
Chpf2 G T 5: 24,795,425 (GRCm39) R316L probably damaging Het
Clca3a1 T A 3: 144,713,550 (GRCm39) N694Y probably damaging Het
Cplane1 A G 15: 8,289,277 (GRCm39) D2909G unknown Het
Ctbp2 G A 7: 132,616,534 (GRCm39) L44F probably damaging Het
Cttnbp2 T C 6: 18,381,102 (GRCm39) M1365V probably benign Het
D130052B06Rik G A 11: 33,573,922 (GRCm39) R173H probably benign Het
Dchs1 A G 7: 105,421,203 (GRCm39) F406L probably damaging Het
Ddx43 T A 9: 78,321,145 (GRCm39) N384K possibly damaging Het
Drd5 G A 5: 38,477,270 (GRCm39) V88M probably damaging Het
Eefsec A T 6: 88,274,881 (GRCm39) F361Y probably benign Het
Epb41 T C 4: 131,717,215 (GRCm39) D313G probably damaging Het
Etl4 T C 2: 20,748,580 (GRCm39) M104T probably damaging Het
Fabp7 A T 10: 57,661,637 (GRCm39) T37S probably benign Het
Fam186b T C 15: 99,184,834 (GRCm39) T30A probably benign Het
Fam83d G A 2: 158,627,611 (GRCm39) W433* probably null Het
Fmnl2 A T 2: 52,944,503 (GRCm39) T161S probably benign Het
Ghsr C T 3: 27,426,165 (GRCm39) R74C probably damaging Het
Gtf3c3 C T 1: 54,456,937 (GRCm39) A488T probably damaging Het
Gtpbp4 A T 13: 9,040,722 (GRCm39) probably benign Het
Hamp2 A G 7: 30,623,511 (GRCm39) L17P possibly damaging Het
Heatr1 C A 13: 12,445,121 (GRCm39) S1581R probably damaging Het
Hpf1 T C 8: 61,353,147 (GRCm39) V176A probably benign Het
Hydin T A 8: 111,240,735 (GRCm39) probably null Het
Ighg2c G A 12: 113,252,382 (GRCm39) Q57* probably null Het
Itgb4 A G 11: 115,870,594 (GRCm39) N141S possibly damaging Het
Kif13b G T 14: 64,988,977 (GRCm39) R786L probably damaging Het
Lhx3 C A 2: 26,091,136 (GRCm39) W391L probably damaging Het
Map1s T A 8: 71,365,551 (GRCm39) V152D probably damaging Het
Map4 T C 9: 109,865,834 (GRCm39) M608T probably benign Het
Mb21d2 G A 16: 28,748,324 (GRCm39) A31V probably benign Het
Mfn1 T C 3: 32,615,621 (GRCm39) I328T probably damaging Het
Mif-ps9 G A 19: 56,743,675 (GRCm39) noncoding transcript Het
Myh4 A T 11: 67,141,157 (GRCm39) I740F possibly damaging Het
Neo1 A G 9: 58,893,069 (GRCm39) V191A probably benign Het
Nfatc4 T C 14: 56,067,485 (GRCm39) V565A probably damaging Het
Nrxn2 G C 19: 6,523,563 (GRCm39) E525D probably damaging Het
Or12k8 T C 2: 36,975,346 (GRCm39) H138R probably benign Het
Pcdhb12 A T 18: 37,570,261 (GRCm39) D469V probably damaging Het
Pcdhb6 G T 18: 37,468,167 (GRCm39) V363L probably benign Het
Pkd1l2 T C 8: 117,808,957 (GRCm39) T78A probably benign Het
Rbm12b1 G A 4: 12,146,248 (GRCm39) S740N probably benign Het
Rpe65 T C 3: 159,305,986 (GRCm39) L15P probably damaging Het
Rxrb CGCGGCGGCGGCGGCGGCGGC CGCGGCGGCGGCGGCGGC 17: 34,251,106 (GRCm39) probably benign Het
Sectm1a A G 11: 120,959,928 (GRCm39) probably benign Het
Sft2d1 C A 17: 8,545,782 (GRCm39) probably benign Het
Slc22a18 A G 7: 143,045,598 (GRCm39) probably benign Het
Slu7 G A 11: 43,332,405 (GRCm39) probably null Het
Smc4 T C 3: 68,931,622 (GRCm39) V572A probably damaging Het
Spire2 T A 8: 124,080,855 (GRCm39) I33N probably damaging Het
Tbck T A 3: 132,458,403 (GRCm39) C678S probably damaging Het
Tnrc6b T C 15: 80,797,539 (GRCm39) V1362A probably damaging Het
Ttn T C 2: 76,570,326 (GRCm39) K25110E possibly damaging Het
Ugt2b35 A G 5: 87,148,793 (GRCm39) S15G possibly damaging Het
Upf3a T A 8: 13,842,184 (GRCm39) I200K probably damaging Het
Vill G C 9: 118,899,701 (GRCm39) G295A possibly damaging Het
Vmn1r191 A T 13: 22,363,217 (GRCm39) V179D probably damaging Het
Vmn2r74 T C 7: 85,601,629 (GRCm39) T670A probably damaging Het
Zfp169 T C 13: 48,643,166 (GRCm39) T654A possibly damaging Het
Zfp646 A G 7: 127,481,138 (GRCm39) E1105G probably damaging Het
Zyg11b A T 4: 108,117,239 (GRCm39) Y334N probably damaging Het
Other mutations in Primpol
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00832:Primpol APN 8 47,034,632 (GRCm39) missense probably damaging 0.98
IGL02421:Primpol APN 8 47,060,830 (GRCm39) splice site probably benign
IGL02886:Primpol APN 8 47,046,619 (GRCm39) nonsense probably null
IGL03244:Primpol APN 8 47,039,475 (GRCm39) missense probably damaging 1.00
R0243:Primpol UTSW 8 47,052,849 (GRCm39) missense probably damaging 1.00
R0329:Primpol UTSW 8 47,063,496 (GRCm39) missense probably damaging 0.97
R0330:Primpol UTSW 8 47,063,496 (GRCm39) missense probably damaging 0.97
R1266:Primpol UTSW 8 47,046,734 (GRCm39) missense probably damaging 1.00
R1334:Primpol UTSW 8 47,039,426 (GRCm39) missense probably damaging 1.00
R1469:Primpol UTSW 8 47,046,672 (GRCm39) missense probably benign
R1469:Primpol UTSW 8 47,046,672 (GRCm39) missense probably benign
R1524:Primpol UTSW 8 47,039,502 (GRCm39) intron probably benign
R1738:Primpol UTSW 8 47,060,873 (GRCm39) missense probably damaging 0.98
R2144:Primpol UTSW 8 47,039,378 (GRCm39) missense probably damaging 0.99
R3747:Primpol UTSW 8 47,052,848 (GRCm39) missense probably benign 0.34
R3748:Primpol UTSW 8 47,052,848 (GRCm39) missense probably benign 0.34
R3750:Primpol UTSW 8 47,052,848 (GRCm39) missense probably benign 0.34
R4378:Primpol UTSW 8 47,029,218 (GRCm39) utr 3 prime probably benign
R4855:Primpol UTSW 8 47,039,726 (GRCm39) missense probably benign 0.00
R5209:Primpol UTSW 8 47,043,295 (GRCm39) missense probably benign 0.00
R5497:Primpol UTSW 8 47,045,657 (GRCm39) nonsense probably null
R5720:Primpol UTSW 8 47,034,677 (GRCm39) missense probably damaging 1.00
R5963:Primpol UTSW 8 47,046,615 (GRCm39) missense possibly damaging 0.93
R6164:Primpol UTSW 8 47,039,477 (GRCm39) missense probably benign 0.10
R6497:Primpol UTSW 8 47,039,376 (GRCm39) critical splice donor site probably null
R6549:Primpol UTSW 8 47,058,185 (GRCm39) missense probably damaging 1.00
R7595:Primpol UTSW 8 47,063,650 (GRCm39) missense probably benign 0.00
R7775:Primpol UTSW 8 47,039,459 (GRCm39) missense probably damaging 1.00
R7778:Primpol UTSW 8 47,039,459 (GRCm39) missense probably damaging 1.00
R7824:Primpol UTSW 8 47,039,459 (GRCm39) missense probably damaging 1.00
R8055:Primpol UTSW 8 47,032,197 (GRCm39) missense probably benign 0.34
R8840:Primpol UTSW 8 47,046,731 (GRCm39) missense probably damaging 1.00
R8992:Primpol UTSW 8 47,034,597 (GRCm39) splice site probably benign
R9356:Primpol UTSW 8 47,043,318 (GRCm39) missense probably benign 0.00
R9388:Primpol UTSW 8 47,034,605 (GRCm39) missense possibly damaging 0.80
Predicted Primers PCR Primer
(F):5'- CAGACAGGACAGCACCTTGGTTTAC -3'
(R):5'- TTGCACACACGAGTGCTTTGCC -3'

Sequencing Primer
(F):5'- TGCCTCACAGTGTGCTAAAG -3'
(R):5'- GCCATGAGTGTTATTTTTAGCAACC -3'
Posted On 2013-06-11