Incidental Mutation 'R0563:Prim1'
ID 46020
Institutional Source Beutler Lab
Gene Symbol Prim1
Ensembl Gene ENSMUSG00000025395
Gene Name DNA primase, p49 subunit
Synonyms
MMRRC Submission 038754-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.960) question?
Stock # R0563 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 127851084-127865899 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 127862423 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 340 (D340G)
Ref Sequence ENSEMBL: ENSMUSP00000136556 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026461] [ENSMUST00000178041]
AlphaFold P20664
Predicted Effect probably damaging
Transcript: ENSMUST00000026461
AA Change: D339G

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000026461
Gene: ENSMUSG00000025395
AA Change: D339G

DomainStartEndE-ValueType
Pfam:DNA_primase_S 108 336 9.7e-59 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133285
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135580
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138330
Predicted Effect probably damaging
Transcript: ENSMUST00000178041
AA Change: D340G

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000136556
Gene: ENSMUSG00000025395
AA Change: D340G

DomainStartEndE-ValueType
Pfam:DNA_primase_S 108 336 3.3e-71 PFAM
Meta Mutation Damage Score 0.4993 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.3%
Validation Efficiency 98% (52/53)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The replication of DNA in eukaryotic cells is carried out by a complex chromosomal replication apparatus, in which DNA polymerase alpha and primase are two key enzymatic components. Primase, which is a heterodimer of a small subunit and a large subunit, synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication. The protein encoded by this gene is the small, 49 kDa primase subunit. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrb3 G T 1: 25,586,635 (GRCm39) P146T probably damaging Het
Ambn A C 5: 88,611,309 (GRCm39) N163T probably benign Het
Ankrd36 A T 11: 5,579,322 (GRCm39) E870D probably benign Het
Cdc123 T C 2: 5,803,212 (GRCm39) N269S probably benign Het
Cdc7 A T 5: 107,120,776 (GRCm39) probably benign Het
Cdh2 A T 18: 16,762,738 (GRCm39) V402D possibly damaging Het
Cwc27 C A 13: 104,797,865 (GRCm39) E365* probably null Het
Dcdc5 G A 2: 106,180,035 (GRCm39) noncoding transcript Het
Eif4g3 T C 4: 137,903,151 (GRCm39) probably benign Het
Elovl4 C T 9: 83,667,087 (GRCm39) probably null Het
Fhl5 T G 4: 25,213,610 (GRCm39) I109L probably damaging Het
Gm16181 A G 17: 35,442,872 (GRCm39) probably benign Het
Gna14 A G 19: 16,585,483 (GRCm39) Y287C probably benign Het
Greb1 A T 12: 16,730,268 (GRCm39) C1720S probably benign Het
Gypa T A 8: 81,236,089 (GRCm39) S165T probably benign Het
Hephl1 T C 9: 14,993,241 (GRCm39) D531G probably damaging Het
Hsf2bp A T 17: 32,226,692 (GRCm39) L221Q probably damaging Het
Itsn1 A G 16: 91,617,684 (GRCm39) probably benign Het
Kif7 T C 7: 79,352,020 (GRCm39) E914G probably benign Het
Lrp1b T C 2: 40,640,926 (GRCm39) D3506G probably benign Het
Lrrc28 T C 7: 67,195,135 (GRCm39) N225S probably damaging Het
Lysmd4 T A 7: 66,875,925 (GRCm39) L196Q probably benign Het
Megf8 T C 7: 25,041,820 (GRCm39) C1245R probably damaging Het
Mgat4f A G 1: 134,317,777 (GRCm39) K183R probably benign Het
Mib2 C T 4: 155,743,917 (GRCm39) G42S probably damaging Het
Mindy2 T A 9: 70,538,334 (GRCm39) I334L possibly damaging Het
Mrm1 A G 11: 84,705,539 (GRCm39) S287P probably damaging Het
Ncor1 A G 11: 62,234,056 (GRCm39) I382T probably damaging Het
Nectin1 A G 9: 43,702,342 (GRCm39) T30A probably benign Het
Nelfe A G 17: 35,073,215 (GRCm39) E250G possibly damaging Het
Nsd1 C A 13: 55,394,391 (GRCm39) T767K possibly damaging Het
Or1i2 G A 10: 78,448,467 (GRCm39) P3S probably benign Het
Or1j18 A T 2: 36,625,013 (GRCm39) K227* probably null Het
Or4e5 T A 14: 52,727,714 (GRCm39) K236* probably null Het
Or5b111 A G 19: 13,291,112 (GRCm39) I179T probably benign Het
Pcnx1 A G 12: 81,964,718 (GRCm39) D295G probably damaging Het
Pex14 A G 4: 149,046,003 (GRCm39) V309A possibly damaging Het
Phf14 C T 6: 11,933,600 (GRCm39) probably benign Het
Pnpla6 A G 8: 3,573,333 (GRCm39) D399G possibly damaging Het
Rb1 A G 14: 73,454,207 (GRCm39) F564L probably damaging Het
Rcc1l G C 5: 134,205,394 (GRCm39) R54G probably benign Het
Rnf151 G A 17: 24,936,430 (GRCm39) probably benign Het
Rnf40 T C 7: 127,192,048 (GRCm39) L398P probably damaging Het
Robo1 C T 16: 72,769,174 (GRCm39) T531I probably benign Het
Rps6ka2 A T 17: 7,521,836 (GRCm39) I198F probably damaging Het
Sgk2 T C 2: 162,846,164 (GRCm39) L264P probably damaging Het
Slc26a6 T A 9: 108,734,869 (GRCm39) I281N probably damaging Het
Tnxb A T 17: 34,935,921 (GRCm39) K2657N probably benign Het
Tor1aip1 G A 1: 155,911,554 (GRCm39) T143M probably damaging Het
Tpr A G 1: 150,284,609 (GRCm39) D358G probably benign Het
Vstm2b T C 7: 40,551,899 (GRCm39) S76P probably damaging Het
Wdr33 A G 18: 32,019,792 (GRCm39) K488R possibly damaging Het
Ythdc2 T A 18: 44,997,915 (GRCm39) probably benign Het
Other mutations in Prim1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01775:Prim1 APN 10 127,865,112 (GRCm39) missense probably benign
IGL01896:Prim1 APN 10 127,858,758 (GRCm39) missense probably damaging 1.00
IGL02505:Prim1 APN 10 127,865,652 (GRCm39) makesense probably null
PIT4403001:Prim1 UTSW 10 127,858,745 (GRCm39) missense probably benign 0.01
R1732:Prim1 UTSW 10 127,851,193 (GRCm39) missense probably damaging 1.00
R1976:Prim1 UTSW 10 127,859,668 (GRCm39) missense probably benign
R2263:Prim1 UTSW 10 127,851,132 (GRCm39) missense probably benign 0.13
R4774:Prim1 UTSW 10 127,862,887 (GRCm39) intron probably benign
R4976:Prim1 UTSW 10 127,851,131 (GRCm39) missense probably damaging 0.97
R5908:Prim1 UTSW 10 127,853,893 (GRCm39) missense probably damaging 1.00
R6356:Prim1 UTSW 10 127,859,704 (GRCm39) missense probably damaging 0.97
R6598:Prim1 UTSW 10 127,856,049 (GRCm39) missense possibly damaging 0.83
R6794:Prim1 UTSW 10 127,854,018 (GRCm39) missense probably damaging 0.97
R7179:Prim1 UTSW 10 127,851,845 (GRCm39) missense probably damaging 1.00
R7325:Prim1 UTSW 10 127,858,788 (GRCm39) missense probably null 0.13
R7432:Prim1 UTSW 10 127,851,885 (GRCm39) missense probably damaging 1.00
R7542:Prim1 UTSW 10 127,853,903 (GRCm39) missense probably damaging 1.00
R7659:Prim1 UTSW 10 127,862,458 (GRCm39) critical splice donor site probably null
R8382:Prim1 UTSW 10 127,856,138 (GRCm39) splice site probably null
R8828:Prim1 UTSW 10 127,859,761 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGGCTAAGGATTGAACCCAGGACC -3'
(R):5'- TGTATACCACAACACCGGCTGTTAC -3'

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