Incidental Mutation 'R5896:Polr2a'
ID 457539
Institutional Source Beutler Lab
Gene Symbol Polr2a
Ensembl Gene ENSMUSG00000005198
Gene Name polymerase (RNA) II (DNA directed) polypeptide A
Synonyms Rpo2-1, 220kDa
MMRRC Submission 044095-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.968) question?
Stock # R5896 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 69624823-69649459 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 69627086 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 1457 (N1457K)
Ref Sequence ENSEMBL: ENSMUSP00000071200 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000058470] [ENSMUST00000071213]
AlphaFold P08775
Predicted Effect probably damaging
Transcript: ENSMUST00000058470
AA Change: N1457K

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000050771
Gene: ENSMUSG00000005198
AA Change: N1457K

DomainStartEndE-ValueType
Blast:RPOLA_N 110 179 5e-37 BLAST
RPOLA_N 246 549 7.02e-203 SMART
Pfam:RNA_pol_Rpb1_4 716 823 3.6e-39 PFAM
Pfam:RNA_pol_Rpb1_5 830 1428 2e-101 PFAM
Pfam:RNA_pol_Rpb1_6 896 1079 1.7e-70 PFAM
Pfam:RNA_pol_Rpb1_7 1164 1299 1.7e-57 PFAM
Pfam:RNA_pol_Rpb1_R 1555 1568 2.1e-3 PFAM
Pfam:RNA_pol_Rpb1_R 1616 1629 8.8e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1630 1643 1.9e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1644 1657 2.3e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1658 1671 2.2e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1672 1685 2.4e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1686 1699 2.5e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1700 1713 2.5e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1714 1727 2.5e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1728 1741 2.6e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1742 1755 5.3e-6 PFAM
Pfam:RNA_pol_Rpb1_R 1757 1769 5.8e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1784 1797 2.6e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1798 1811 4.8e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1826 1839 4.3e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1841 1853 2e-3 PFAM
Pfam:RNA_pol_Rpb1_R 1854 1867 6.9e-6 PFAM
Pfam:RNA_pol_Rpb1_R 1868 1881 3.7e-6 PFAM
Pfam:RNA_pol_Rpb1_R 1882 1895 1.2e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1896 1909 5e-6 PFAM
Pfam:RNA_pol_Rpb1_R 1910 1923 2.5e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1924 1936 2e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1931 1954 2.6e-3 PFAM
Pfam:RNA_pol_Rpb1_R 1948 1960 2.5e-3 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000071213
AA Change: N1457K

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000071200
Gene: ENSMUSG00000005198
AA Change: N1457K

DomainStartEndE-ValueType
Blast:RPOLA_N 110 179 5e-37 BLAST
RPOLA_N 246 549 7.02e-203 SMART
Pfam:RNA_pol_Rpb1_4 716 823 1.8e-41 PFAM
Pfam:RNA_pol_Rpb1_5 830 1428 4.8e-104 PFAM
Pfam:RNA_pol_Rpb1_6 896 1079 5.2e-74 PFAM
Pfam:RNA_pol_Rpb1_7 1164 1299 1.4e-55 PFAM
low complexity region 1503 1522 N/A INTRINSIC
low complexity region 1524 1549 N/A INTRINSIC
Pfam:RNA_pol_Rpb1_R 1578 1591 2.7e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1592 1605 2.5e-6 PFAM
Pfam:RNA_pol_Rpb1_R 1606 1619 2.7e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1620 1633 2.5e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1634 1647 2.5e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1648 1661 2.4e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1662 1675 2.4e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1676 1689 2.6e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1690 1703 2.3e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1704 1717 5.2e-7 PFAM
Pfam:RNA_pol_Rpb1_R 1718 1731 5.5e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1732 1745 1.6e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1746 1759 8.6e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1760 1773 2e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1788 1801 3.3e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1802 1815 2.4e-4 PFAM
Pfam:RNA_pol_Rpb1_R 1816 1829 8.3e-7 PFAM
Pfam:RNA_pol_Rpb1_R 1830 1843 2.2e-6 PFAM
Pfam:RNA_pol_Rpb1_R 1844 1857 1.6e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1858 1871 2.8e-6 PFAM
Pfam:RNA_pol_Rpb1_R 1872 1885 6e-7 PFAM
Pfam:RNA_pol_Rpb1_R 1886 1899 4.6e-6 PFAM
Pfam:RNA_pol_Rpb1_R 1893 1909 4.8e-5 PFAM
Pfam:RNA_pol_Rpb1_R 1903 1916 2.8e-6 PFAM
Pfam:RNA_pol_Rpb1_R 1910 1923 1.6e-4 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156588
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.3%
  • 20x: 91.5%
Validation Efficiency 99% (86/87)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. The product of this gene contains a carboxy terminal domain composed of heptapeptide repeats that are essential for polymerase activity. These repeats contain serine and threonine residues that are phosphorylated in actively transcribing RNA polymerase. In addition, this subunit, in combination with several other polymerase subunits, forms the DNA binding domain of the polymerase, a groove in which the DNA template is transcribed into RNA. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a reporter allele show prenatal lethality. Homozygotes for a small deletion in the C-terminal domain are viable, fertile and developmentally normal. Homozygotes for a larger deletion show reduced fetal size and partial postnatal lethality; survivors are small but otherwise normal. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310061N02Rik A T 16: 88,504,321 (GRCm39) S159T probably damaging Het
2610028H24Rik T A 10: 76,288,664 (GRCm39) M53K probably benign Het
3425401B19Rik G A 14: 32,383,632 (GRCm39) Q778* probably null Het
Abhd16a T A 17: 35,310,701 (GRCm39) probably benign Het
Acp6 A G 3: 97,075,810 (GRCm39) K226R probably benign Het
Ankfy1 A G 11: 72,650,811 (GRCm39) D998G probably damaging Het
Apbb1 G T 7: 105,223,432 (GRCm39) P60T probably damaging Het
Apol9a T A 15: 77,288,705 (GRCm39) I221F probably benign Het
Arhgap29 A G 3: 121,805,736 (GRCm39) E947G possibly damaging Het
B430218F22Rik A T 13: 118,523,934 (GRCm39) probably benign Het
Carmil3 ACCCCC ACCCCCCC 14: 55,741,456 (GRCm39) probably null Het
Ccdc69 C T 11: 54,943,716 (GRCm39) probably null Het
Ccdc93 G T 1: 121,390,849 (GRCm39) V274L possibly damaging Het
Cdc25a A G 9: 109,713,433 (GRCm39) D191G probably benign Het
Cimip2a A T 2: 25,110,578 (GRCm39) M129L probably benign Het
Cmya5 A G 13: 93,182,373 (GRCm39) probably null Het
Crebzf TGGAGGAGGAGGAGGAGGA TGGAGGAGGAGGAGGA 7: 90,092,479 (GRCm39) probably benign Het
Csde1 T C 3: 102,947,859 (GRCm39) probably benign Het
Ctdp1 A G 18: 80,502,003 (GRCm39) L177P probably damaging Het
Dnah5 T A 15: 28,272,206 (GRCm39) H1003Q probably benign Het
Epb41l2 T A 10: 25,369,494 (GRCm39) N604K probably damaging Het
Fig4 T A 10: 41,130,881 (GRCm39) N465Y possibly damaging Het
Gemin7 G A 7: 19,299,223 (GRCm39) S124F probably damaging Het
Gli3 G A 13: 15,900,765 (GRCm39) R1384K probably benign Het
Gm12258 G A 11: 58,750,457 (GRCm39) C544Y probably damaging Het
Grm1 C T 10: 10,956,294 (GRCm39) probably benign Het
H2-T15 T A 17: 36,367,236 (GRCm39) M329L probably benign Het
Hps4 C T 5: 112,517,351 (GRCm39) T246I probably benign Het
Ifngr2 A T 16: 91,358,653 (GRCm39) E284D possibly damaging Het
Impdh2 A G 9: 108,441,165 (GRCm39) T148A probably benign Het
Irx3 T C 8: 92,527,763 (GRCm39) S36G probably benign Het
Itga5 T A 15: 103,259,514 (GRCm39) K667N probably benign Het
Itgad G A 7: 127,773,188 (GRCm39) C15Y probably benign Het
Ly75 T G 2: 60,213,490 (GRCm39) E29A probably benign Het
Magi1 T A 6: 93,685,180 (GRCm39) S506C probably damaging Het
Map4 G A 9: 109,901,702 (GRCm39) V781M possibly damaging Het
Med23 T C 10: 24,778,043 (GRCm39) L797P probably damaging Het
Naip1 C T 13: 100,559,636 (GRCm39) G1123R probably benign Het
Ncor1 G T 11: 62,274,016 (GRCm39) P55Q probably damaging Het
Odr4 A T 1: 150,256,111 (GRCm39) N211K probably benign Het
Ofcc1 T A 13: 40,334,060 (GRCm39) I344F probably benign Het
Or4a74 C A 2: 89,439,667 (GRCm39) V260F probably damaging Het
Or4d5 A T 9: 40,012,189 (GRCm39) M199K probably damaging Het
Or5d35 A G 2: 87,855,465 (GRCm39) Y133C probably damaging Het
Or5k1 G A 16: 58,618,095 (GRCm39) T38I probably damaging Het
Otub2 C T 12: 103,369,687 (GRCm39) probably benign Het
Parva A G 7: 112,143,960 (GRCm39) M83V probably benign Het
Pcdha8 T A 18: 37,126,572 (GRCm39) N351K probably benign Het
Pcdhb5 T A 18: 37,455,732 (GRCm39) L704* probably null Het
Pkd1l3 T A 8: 110,353,468 (GRCm39) L683H probably damaging Het
Plekhn1 C T 4: 156,308,331 (GRCm39) R288H probably benign Het
Ppp1r12b A G 1: 134,693,719 (GRCm39) S981P probably damaging Het
Ppp1r9a A G 6: 5,159,648 (GRCm39) K1062E probably damaging Het
Ptpre A T 7: 135,276,007 (GRCm39) T498S probably benign Het
Pus7l C T 15: 94,427,332 (GRCm39) probably null Het
Rptn C T 3: 93,305,639 (GRCm39) Q991* probably null Het
Rsu1 T G 2: 13,229,170 (GRCm39) E76A probably damaging Het
Septin11 T A 5: 93,304,824 (GRCm39) F214I probably damaging Het
Slc1a7 G T 4: 107,869,587 (GRCm39) A551S probably benign Het
Slc45a2 T A 15: 11,000,941 (GRCm39) Y13* probably null Het
Slc7a14 T G 3: 31,311,719 (GRCm39) L100F probably damaging Het
Slit3 A G 11: 35,598,932 (GRCm39) E1512G probably damaging Het
Stat5a A G 11: 100,767,883 (GRCm39) Q458R possibly damaging Het
Svep1 T C 4: 58,084,906 (GRCm39) T1811A possibly damaging Het
Tarbp1 A G 8: 127,179,667 (GRCm39) F624L probably benign Het
Tfeb T G 17: 48,070,433 (GRCm39) probably null Het
Tnxb G A 17: 34,891,126 (GRCm39) G490R probably damaging Het
Tra2b T C 16: 22,077,953 (GRCm39) Y32C probably damaging Het
Trpv4 C T 5: 114,760,708 (GRCm39) probably benign Het
Uvrag A T 7: 98,637,414 (GRCm39) L138* probably null Het
Vwf A T 6: 125,655,725 (GRCm39) probably null Het
Wdr47 G A 3: 108,526,322 (GRCm39) D282N probably damaging Het
Xirp2 A G 2: 67,340,290 (GRCm39) N844D possibly damaging Het
Xirp2 A G 2: 67,339,042 (GRCm39) M428V probably benign Het
Znfx1 G A 2: 166,880,920 (GRCm39) T288I probably damaging Het
Other mutations in Polr2a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00987:Polr2a APN 11 69,634,620 (GRCm39) splice site probably benign
IGL01067:Polr2a APN 11 69,638,840 (GRCm39) missense possibly damaging 0.94
IGL01547:Polr2a APN 11 69,635,768 (GRCm39) missense probably damaging 0.99
IGL01589:Polr2a APN 11 69,632,020 (GRCm39) missense probably benign
IGL01955:Polr2a APN 11 69,632,674 (GRCm39) missense probably damaging 1.00
IGL02457:Polr2a APN 11 69,634,076 (GRCm39) splice site probably benign
IGL02526:Polr2a APN 11 69,630,293 (GRCm39) missense probably benign 0.03
IGL02792:Polr2a APN 11 69,636,938 (GRCm39) missense probably damaging 0.99
IGL03058:Polr2a APN 11 69,635,873 (GRCm39) splice site probably null
IGL03083:Polr2a APN 11 69,635,872 (GRCm39) critical splice acceptor site probably null
IGL03198:Polr2a APN 11 69,638,107 (GRCm39) splice site probably null
IGL03201:Polr2a APN 11 69,636,516 (GRCm39) nonsense probably null
Leastest UTSW 11 69,638,118 (GRCm39) splice site probably null
PIT4260001:Polr2a UTSW 11 69,626,793 (GRCm39) missense possibly damaging 0.93
R0126:Polr2a UTSW 11 69,638,251 (GRCm39) missense probably damaging 0.99
R0254:Polr2a UTSW 11 69,634,497 (GRCm39) missense possibly damaging 0.75
R0313:Polr2a UTSW 11 69,625,906 (GRCm39) missense unknown
R0336:Polr2a UTSW 11 69,627,719 (GRCm39) missense possibly damaging 0.92
R0453:Polr2a UTSW 11 69,631,845 (GRCm39) missense possibly damaging 0.65
R0762:Polr2a UTSW 11 69,625,943 (GRCm39) missense unknown
R1101:Polr2a UTSW 11 69,638,897 (GRCm39) missense probably benign 0.23
R1509:Polr2a UTSW 11 69,638,039 (GRCm39) missense possibly damaging 0.93
R1547:Polr2a UTSW 11 69,625,381 (GRCm39) missense probably benign 0.39
R1567:Polr2a UTSW 11 69,636,857 (GRCm39) missense probably benign 0.07
R1597:Polr2a UTSW 11 69,630,755 (GRCm39) missense possibly damaging 0.88
R1614:Polr2a UTSW 11 69,634,199 (GRCm39) missense possibly damaging 0.75
R1698:Polr2a UTSW 11 69,630,703 (GRCm39) critical splice donor site probably null
R1735:Polr2a UTSW 11 69,633,222 (GRCm39) missense probably damaging 0.99
R1743:Polr2a UTSW 11 69,630,329 (GRCm39) missense probably damaging 0.96
R1899:Polr2a UTSW 11 69,634,772 (GRCm39) missense probably damaging 0.99
R1900:Polr2a UTSW 11 69,634,772 (GRCm39) missense probably damaging 0.99
R1931:Polr2a UTSW 11 69,626,201 (GRCm39) missense unknown
R2217:Polr2a UTSW 11 69,633,511 (GRCm39) critical splice donor site probably null
R2218:Polr2a UTSW 11 69,633,511 (GRCm39) critical splice donor site probably null
R2245:Polr2a UTSW 11 69,626,009 (GRCm39) missense unknown
R3123:Polr2a UTSW 11 69,626,536 (GRCm39) missense possibly damaging 0.92
R3124:Polr2a UTSW 11 69,626,536 (GRCm39) missense possibly damaging 0.92
R4018:Polr2a UTSW 11 69,625,885 (GRCm39) missense unknown
R4025:Polr2a UTSW 11 69,634,485 (GRCm39) missense possibly damaging 0.95
R4197:Polr2a UTSW 11 69,626,162 (GRCm39) missense unknown
R4462:Polr2a UTSW 11 69,637,229 (GRCm39) missense probably damaging 1.00
R4508:Polr2a UTSW 11 69,633,385 (GRCm39) critical splice acceptor site probably null
R4746:Polr2a UTSW 11 69,626,500 (GRCm39) missense probably benign 0.05
R5069:Polr2a UTSW 11 69,627,561 (GRCm39) splice site probably null
R5102:Polr2a UTSW 11 69,637,771 (GRCm39) missense possibly damaging 0.93
R5195:Polr2a UTSW 11 69,634,905 (GRCm39) missense probably damaging 1.00
R5234:Polr2a UTSW 11 69,627,666 (GRCm39) missense probably benign 0.03
R5330:Polr2a UTSW 11 69,638,101 (GRCm39) missense probably benign 0.01
R5331:Polr2a UTSW 11 69,638,101 (GRCm39) missense probably benign 0.01
R5910:Polr2a UTSW 11 69,637,696 (GRCm39) missense probably damaging 0.99
R6128:Polr2a UTSW 11 69,627,803 (GRCm39) missense probably damaging 1.00
R6238:Polr2a UTSW 11 69,638,047 (GRCm39) missense possibly damaging 0.95
R6244:Polr2a UTSW 11 69,635,052 (GRCm39) missense probably damaging 1.00
R6303:Polr2a UTSW 11 69,637,739 (GRCm39) missense probably damaging 1.00
R6338:Polr2a UTSW 11 69,630,505 (GRCm39) splice site probably null
R6361:Polr2a UTSW 11 69,634,163 (GRCm39) missense probably damaging 0.99
R6374:Polr2a UTSW 11 69,627,758 (GRCm39) missense probably damaging 0.98
R6630:Polr2a UTSW 11 69,626,339 (GRCm39) missense possibly damaging 0.93
R6631:Polr2a UTSW 11 69,626,339 (GRCm39) missense possibly damaging 0.93
R6633:Polr2a UTSW 11 69,626,339 (GRCm39) missense possibly damaging 0.93
R6897:Polr2a UTSW 11 69,626,787 (GRCm39) missense probably benign 0.12
R6923:Polr2a UTSW 11 69,626,787 (GRCm39) missense probably benign 0.12
R6933:Polr2a UTSW 11 69,630,293 (GRCm39) missense probably benign 0.03
R6933:Polr2a UTSW 11 69,627,003 (GRCm39) missense probably damaging 0.99
R6953:Polr2a UTSW 11 69,632,537 (GRCm39) missense probably damaging 0.99
R6974:Polr2a UTSW 11 69,638,026 (GRCm39) missense probably damaging 0.98
R7033:Polr2a UTSW 11 69,638,039 (GRCm39) missense possibly damaging 0.93
R7085:Polr2a UTSW 11 69,634,706 (GRCm39) missense probably damaging 0.99
R7112:Polr2a UTSW 11 69,626,135 (GRCm39) missense unknown
R7124:Polr2a UTSW 11 69,628,288 (GRCm39) nonsense probably null
R7307:Polr2a UTSW 11 69,638,118 (GRCm39) splice site probably null
R7319:Polr2a UTSW 11 69,637,196 (GRCm39) missense possibly damaging 0.95
R7350:Polr2a UTSW 11 69,631,886 (GRCm39) missense possibly damaging 0.92
R7369:Polr2a UTSW 11 69,636,803 (GRCm39) missense probably benign 0.01
R7585:Polr2a UTSW 11 69,630,828 (GRCm39) missense probably damaging 0.99
R7882:Polr2a UTSW 11 69,627,000 (GRCm39) missense possibly damaging 0.86
R7935:Polr2a UTSW 11 69,638,330 (GRCm39) missense probably benign 0.00
R8080:Polr2a UTSW 11 69,625,874 (GRCm39) missense unknown
R8140:Polr2a UTSW 11 69,637,202 (GRCm39) missense probably benign 0.12
R8221:Polr2a UTSW 11 69,628,344 (GRCm39) missense probably benign 0.24
R8245:Polr2a UTSW 11 69,630,779 (GRCm39) missense probably damaging 0.99
R8274:Polr2a UTSW 11 69,638,882 (GRCm39) missense probably damaging 0.99
R8275:Polr2a UTSW 11 69,638,882 (GRCm39) missense probably damaging 0.99
R8276:Polr2a UTSW 11 69,638,882 (GRCm39) missense probably damaging 0.99
R8277:Polr2a UTSW 11 69,638,882 (GRCm39) missense probably damaging 0.99
R8311:Polr2a UTSW 11 69,628,282 (GRCm39) missense probably null 0.20
R8477:Polr2a UTSW 11 69,626,312 (GRCm39) missense probably benign 0.00
R8677:Polr2a UTSW 11 69,626,381 (GRCm39) missense possibly damaging 0.85
R8976:Polr2a UTSW 11 69,638,037 (GRCm39) missense possibly damaging 0.92
R9296:Polr2a UTSW 11 69,625,562 (GRCm39) missense probably benign 0.39
R9659:Polr2a UTSW 11 69,625,654 (GRCm39) missense unknown
R9731:Polr2a UTSW 11 69,638,043 (GRCm39) missense possibly damaging 0.88
Predicted Primers PCR Primer
(F):5'- TAAAGGCACGCACTCCCTTG -3'
(R):5'- ATTGAAAGAAGGGAGCTTGTCTCAG -3'

Sequencing Primer
(F):5'- TATGTCTACCCTTAAGCATGACCCAG -3'
(R):5'- CTCAGTAGTGAGCGTGCAG -3'
Posted On 2017-02-15