Incidental Mutation 'R5057:Prim2'
ID 390881
Institutional Source Beutler Lab
Gene Symbol Prim2
Ensembl Gene ENSMUSG00000026134
Gene Name DNA primase, p58 subunit
Synonyms
MMRRC Submission 042647-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.932) question?
Stock # R5057 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 33492891-33708876 bp(-) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) A to T at 33669441 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Stop codon at position 178 (L178*)
Ref Sequence ENSEMBL: ENSMUSP00000027312 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000027312]
AlphaFold P33610
Predicted Effect probably null
Transcript: ENSMUST00000027312
AA Change: L178*
SMART Domains Protein: ENSMUSP00000027312
Gene: ENSMUSG00000026134
AA Change: L178*

DomainStartEndE-ValueType
Pfam:DNA_primase_lrg 182 448 6.2e-99 PFAM
low complexity region 482 503 N/A INTRINSIC
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.2%
  • 20x: 92.0%
Validation Efficiency 97% (118/122)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the 58 kilodalton subunit of DNA primase, an enzyme that plays a key role in the replication of DNA. The encoded protein forms a heterodimer with a 49 kilodalton subunit. This heterodimer functions as a DNA-directed RNA polymerase to synthesize small RNA primers that are used to create Okazaki fragments on the lagging strand of the DNA. Alternative splicing of this gene results in multiple transcript variants. This gene has a related pseudogene, which is also present on chromosome 6. [provided by RefSeq, Apr 2014]
Allele List at MGI
Other mutations in this stock
Total: 120 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933427D14Rik A T 11: 72,057,581 (GRCm39) H739Q probably benign Het
Acad12 T A 5: 121,748,152 (GRCm39) T89S probably benign Het
Adgb A G 10: 10,233,722 (GRCm39) C1252R probably benign Het
Ankef1 A G 2: 136,392,280 (GRCm39) probably null Het
Ankfy1 T C 11: 72,650,745 (GRCm39) L976P probably damaging Het
Ankib1 T A 5: 3,784,011 (GRCm39) I322F possibly damaging Het
Ankrd61 T A 5: 143,831,613 (GRCm39) T64S probably benign Het
Anxa6 T G 11: 54,892,062 (GRCm39) E298A possibly damaging Het
Apc2 A G 10: 80,144,903 (GRCm39) S605G probably damaging Het
Arih1 T C 9: 59,393,515 (GRCm39) N39S unknown Het
Bicc1 A G 10: 70,783,713 (GRCm39) S393P possibly damaging Het
Bptf A T 11: 106,973,354 (GRCm39) F693L probably damaging Het
Cacng4 A G 11: 107,685,197 (GRCm39) Y32H probably damaging Het
Ccdc50 T A 16: 27,257,092 (GRCm39) D252E probably benign Het
Ccdc92b C A 11: 74,528,976 (GRCm39) T160K probably damaging Het
Cd163 C T 6: 124,302,247 (GRCm39) T937I probably damaging Het
Cdh22 C A 2: 164,958,063 (GRCm39) V635F probably damaging Het
Cenpe G T 3: 134,926,074 (GRCm39) A243S probably benign Het
Cep295 A T 9: 15,233,979 (GRCm39) H2272Q probably benign Het
Cgnl1 A T 9: 71,632,076 (GRCm39) V425D probably damaging Het
Clec4b2 A T 6: 123,177,915 (GRCm39) S77C probably null Het
Cntnap5a C T 1: 115,612,943 (GRCm39) T26I probably benign Het
Col6a3 T C 1: 90,743,852 (GRCm39) K165R possibly damaging Het
Copb1 A T 7: 113,825,997 (GRCm39) N662K probably benign Het
Crybg1 T A 10: 43,865,104 (GRCm39) R1458* probably null Het
Cspp1 T A 1: 10,145,186 (GRCm39) probably benign Het
Dhtkd1 A G 2: 5,924,324 (GRCm39) C430R probably damaging Het
Dlg5 T C 14: 24,186,690 (GRCm39) E1847G probably damaging Het
Dync2i1 A T 12: 116,177,033 (GRCm39) N856K probably benign Het
Eif1ad16 A T 12: 87,985,481 (GRCm39) S21T unknown Het
Ephb3 A G 16: 21,039,197 (GRCm39) D351G probably damaging Het
Exd2 T A 12: 80,543,564 (GRCm39) N582K probably damaging Het
Fam161a T A 11: 22,970,397 (GRCm39) C192S probably damaging Het
Fbn1 A G 2: 125,308,615 (GRCm39) V149A probably benign Het
Fbxw16 A G 9: 109,270,232 (GRCm39) S170P probably damaging Het
Fndc1 T A 17: 7,990,802 (GRCm39) R965* probably null Het
Frem2 T C 3: 53,442,617 (GRCm39) D2640G probably benign Het
Gfm1 T C 3: 67,380,877 (GRCm39) V664A probably damaging Het
Gm10803 A C 2: 93,394,517 (GRCm39) L96F probably damaging Het
Gm14569 T C X: 35,694,470 (GRCm39) D1413G probably benign Het
Gm44501 A G 17: 40,889,563 (GRCm39) T26A probably benign Het
Gpc4 G A X: 51,163,440 (GRCm39) R148C probably damaging Het
Gpsm1 G A 2: 26,215,369 (GRCm39) R277Q probably damaging Het
Inmt T A 6: 55,151,883 (GRCm39) H29L probably benign Het
Insrr T A 3: 87,722,572 (GRCm39) C1265S probably benign Het
Kctd12 A G 14: 103,219,045 (GRCm39) F278L possibly damaging Het
Klk14 G A 7: 43,341,501 (GRCm39) C51Y probably damaging Het
Lag3 T A 6: 124,882,318 (GRCm39) I393F possibly damaging Het
Lama2 C T 10: 27,040,982 (GRCm39) C1447Y probably damaging Het
Lama3 G A 18: 12,665,005 (GRCm39) G2275S probably null Het
Lrrc17 A T 5: 21,780,307 (GRCm39) H427L probably benign Het
Med13l T A 5: 118,856,558 (GRCm39) S164T probably damaging Het
Milr1 A G 11: 106,657,791 (GRCm39) D131G possibly damaging Het
Myo5c A T 9: 75,208,155 (GRCm39) T1630S probably damaging Het
Nbeal2 A T 9: 110,460,073 (GRCm39) N1848K probably damaging Het
Ncor2 A T 5: 125,125,130 (GRCm39) V307E possibly damaging Het
Ndufs3 C A 2: 90,729,004 (GRCm39) A161S probably benign Het
Neo1 T C 9: 58,897,554 (GRCm39) D134G probably damaging Het
Nexmif A T X: 103,130,956 (GRCm39) N320K probably damaging Het
Nipal3 T A 4: 135,194,167 (GRCm39) I289F probably damaging Het
Nrg4 A G 9: 55,189,880 (GRCm39) probably benign Het
Nrxn3 A T 12: 89,221,804 (GRCm39) I528F probably damaging Het
Or11h23 A C 14: 50,948,669 (GRCm39) N294T probably damaging Het
Or3a10 T A 11: 73,935,881 (GRCm39) D73V probably damaging Het
Pate2 T C 9: 35,597,407 (GRCm39) probably benign Het
Pcnx2 T C 8: 126,581,930 (GRCm39) I935M possibly damaging Het
Pik3c2a G T 7: 115,975,518 (GRCm39) T683K possibly damaging Het
Pip5k1c G A 10: 81,146,723 (GRCm39) probably null Het
Pkd1l2 G A 8: 117,781,747 (GRCm39) T766I probably benign Het
Polr3c C A 3: 96,619,373 (GRCm39) L508F probably damaging Het
Por A G 5: 135,759,756 (GRCm39) D189G probably damaging Het
Potefam1 A T 2: 111,055,766 (GRCm39) F207I probably benign Het
Prima1 C A 12: 103,168,864 (GRCm39) probably null Het
Ptpn21 G A 12: 98,645,666 (GRCm39) R1091C probably damaging Het
Ptpn23 G A 9: 110,217,624 (GRCm39) T744I probably benign Het
Rad21 A T 15: 51,830,102 (GRCm39) I503K probably benign Het
Rbm12 A T 2: 155,938,806 (GRCm39) C489S probably benign Het
Rpl10a A T 17: 28,549,607 (GRCm39) H140L probably benign Het
Rpl7-ps8 A T 15: 59,083,004 (GRCm39) noncoding transcript Het
Rtbdn T C 8: 85,681,638 (GRCm39) F143S probably damaging Het
Scamp3 T A 3: 89,089,600 (GRCm39) probably benign Het
Setd5 A G 6: 113,114,922 (GRCm39) S848G probably damaging Het
Sez6 T C 11: 77,863,979 (GRCm39) V487A probably damaging Het
Shc2 G A 10: 79,459,706 (GRCm39) P413S probably benign Het
Sipa1l3 T C 7: 29,070,618 (GRCm39) N966S probably damaging Het
Slc39a8 A G 3: 135,554,790 (GRCm39) E78G probably benign Het
Slc8a3 A G 12: 81,246,332 (GRCm39) V900A probably damaging Het
Slitrk3 T C 3: 72,957,981 (GRCm39) T264A probably benign Het
Spire2 G A 8: 124,084,940 (GRCm39) R260H probably damaging Het
Stk39 T A 2: 68,051,292 (GRCm39) I518F probably damaging Het
Tardbp T A 4: 148,703,813 (GRCm39) probably null Het
Tep1 A G 14: 51,066,456 (GRCm39) Y2335H probably benign Het
Tesl1 G A X: 23,773,480 (GRCm39) G327E probably damaging Het
Tll2 A G 19: 41,105,705 (GRCm39) V358A probably benign Het
Tmem268 C G 4: 63,486,777 (GRCm39) S100C probably damaging Het
Tnfsf9 A G 17: 57,412,444 (GRCm39) T5A probably benign Het
Trappc10 G T 10: 78,052,994 (GRCm39) F260L possibly damaging Het
Trim5 A G 7: 103,914,630 (GRCm39) Y480H probably damaging Het
Trmt112 T C 19: 6,888,121 (GRCm39) V91A probably benign Het
Ttn T A 2: 76,577,379 (GRCm39) K22759* probably null Het
Ttn C A 2: 76,748,988 (GRCm39) L4020F probably benign Het
Ubash3b A G 9: 40,948,755 (GRCm39) C187R possibly damaging Het
Ube3b T C 5: 114,544,318 (GRCm39) F572L probably benign Het
Ubr5 A G 15: 38,004,353 (GRCm39) V1332A probably damaging Het
Ubtd2 C A 11: 32,466,320 (GRCm39) R180S probably damaging Het
Ubtf A G 11: 102,197,913 (GRCm39) S673P probably damaging Het
Ubtfl1 A T 9: 18,320,487 (GRCm39) D5V possibly damaging Het
Usp17la G A 7: 104,510,330 (GRCm39) V312I possibly damaging Het
Usp17ld G T 7: 102,899,655 (GRCm39) H426N probably benign Het
Usp34 A G 11: 23,408,086 (GRCm39) probably benign Het
Vmn1r199 A T 13: 22,567,575 (GRCm39) T290S possibly damaging Het
Vmn1r33 T C 6: 66,589,089 (GRCm39) N155S probably benign Het
Vmn2r28 T A 7: 5,489,463 (GRCm39) I459L probably benign Het
Vmn2r6 T A 3: 64,445,207 (GRCm39) K839N probably damaging Het
Vmn2r65 A G 7: 84,589,819 (GRCm39) I699T probably damaging Het
Vps16 A G 2: 130,281,372 (GRCm39) S235G probably benign Het
Vwde T C 6: 13,192,641 (GRCm39) I421V possibly damaging Het
Xiap T C X: 41,183,342 (GRCm39) F23L probably benign Het
Xkr7 A G 2: 152,896,300 (GRCm39) T385A probably benign Het
Znfx1 T C 2: 166,881,746 (GRCm39) Y217C probably damaging Het
Other mutations in Prim2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00921:Prim2 APN 1 33,551,241 (GRCm39) missense probably damaging 1.00
IGL02576:Prim2 APN 1 33,523,798 (GRCm39) missense probably damaging 1.00
R0398:Prim2 UTSW 1 33,523,757 (GRCm39) splice site probably benign
R0686:Prim2 UTSW 1 33,553,270 (GRCm39) missense probably benign
R1452:Prim2 UTSW 1 33,669,485 (GRCm39) missense probably benign
R3925:Prim2 UTSW 1 33,572,380 (GRCm39) missense probably damaging 1.00
R4398:Prim2 UTSW 1 33,551,192 (GRCm39) missense probably damaging 1.00
R4831:Prim2 UTSW 1 33,709,217 (GRCm39) unclassified probably benign
R4832:Prim2 UTSW 1 33,503,145 (GRCm39) missense probably benign
R5240:Prim2 UTSW 1 33,519,397 (GRCm39) intron probably benign
R5294:Prim2 UTSW 1 33,707,974 (GRCm39) missense probably benign 0.11
R5771:Prim2 UTSW 1 33,493,232 (GRCm39) missense unknown
R5807:Prim2 UTSW 1 33,519,487 (GRCm39) intron probably benign
R6307:Prim2 UTSW 1 33,701,373 (GRCm39) missense probably benign 0.00
R7165:Prim2 UTSW 1 33,667,474 (GRCm39) critical splice donor site probably null
R8904:Prim2 UTSW 1 33,669,513 (GRCm39) missense possibly damaging 0.90
R9435:Prim2 UTSW 1 33,523,876 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GCAATGCCAGGCTTTTCTTC -3'
(R):5'- GCCTTCCTTAGGGTTAGGAATG -3'

Sequencing Primer
(F):5'- CCAGGCTTTTCTTCAACAGGATGAAC -3'
(R):5'- CAATCACTGGAAATGATGGGATAATC -3'
Posted On 2016-06-06