Incidental Mutation 'R3124:Polr2a'
ID 264204
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 040597-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.968) question?
Stock # R3124 (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 69626536 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 1566 (S1566T)
Ref Sequence ENSEMBL: ENSMUSP00000050771 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000058470] [ENSMUST00000071213]
AlphaFold P08775
Predicted Effect possibly damaging
Transcript: ENSMUST00000058470
AA Change: S1566T

PolyPhen 2 Score 0.922 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000050771
Gene: ENSMUSG00000005198
AA Change: S1566T

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 benign
Transcript: ENSMUST00000071213
AA Change: S1528T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000071200
Gene: ENSMUSG00000005198
AA Change: S1528T

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 0.1795 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.5%
Validation Efficiency 100% (40/40)
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: 37 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abhd16b G A 2: 181,136,319 (GRCm39) R407H possibly damaging Het
Bag4 C T 8: 26,259,516 (GRCm39) A228T probably benign Het
Cadm1 A G 9: 47,710,775 (GRCm39) E226G possibly damaging Het
Caskin2 T C 11: 115,695,623 (GRCm39) D246G probably damaging Het
Cd80 T A 16: 38,294,255 (GRCm39) V46E probably damaging Het
Ctr9 C T 7: 110,652,653 (GRCm39) R984C unknown Het
Dach2 T C X: 112,729,664 (GRCm39) I417T possibly damaging Het
Dcaf8l A T X: 88,448,327 (GRCm39) Y601N probably benign Het
Drd3 T C 16: 43,643,155 (GRCm39) F464L probably damaging Het
Dyrk1a G A 16: 94,469,660 (GRCm39) probably benign Het
Fam227b T C 2: 125,966,006 (GRCm39) T140A probably benign Het
Fam91a1 A G 15: 58,293,738 (GRCm39) I101V probably benign Het
Fem1b T C 9: 62,703,836 (GRCm39) I475V probably benign Het
Glra3 A G 8: 56,578,244 (GRCm39) R434G possibly damaging Het
Hsd17b12 C T 2: 93,864,303 (GRCm39) R268Q probably benign Het
Iglc3 T C 16: 18,884,345 (GRCm39) probably benign Het
Khdrbs2 C A 1: 32,558,858 (GRCm39) R408L probably damaging Het
Loxhd1 A G 18: 77,518,774 (GRCm39) D1860G probably damaging Het
Mcpt8 A T 14: 56,321,398 (GRCm39) I22K probably damaging Het
Myo1h A G 5: 114,466,860 (GRCm39) I303V probably benign Het
Nipsnap2 G A 5: 129,825,098 (GRCm39) probably null Het
Nop2 G A 6: 125,109,164 (GRCm39) probably benign Het
Pthlh A T 6: 147,164,789 (GRCm39) V27E probably damaging Het
Ralgps1 T C 2: 33,048,968 (GRCm39) T314A possibly damaging Het
Robo4 CGG CG 9: 37,322,786 (GRCm39) probably null Het
Skil A G 3: 31,151,487 (GRCm39) N3S probably benign Het
Tas2r129 A G 6: 132,928,411 (GRCm39) N116S probably damaging Het
Tas2r140 T A 6: 133,032,204 (GRCm39) I185L probably benign Het
Tnpo1 GCACCTCTGCTTCCTC GCACCTCTGCTTCCTCACCTCTGCTTCCTC 13: 99,003,637 (GRCm39) probably null Het
Togaram1 G T 12: 65,013,118 (GRCm39) R123L probably damaging Het
Trappc9 G A 15: 72,897,816 (GRCm39) R377W probably damaging Het
Trim12a G T 7: 103,950,063 (GRCm39) T292K probably benign Het
Trim9 C T 12: 70,295,167 (GRCm39) G648R probably damaging Het
Trmt13 T C 3: 116,383,893 (GRCm39) I104V probably benign Het
Vav3 G A 3: 109,535,484 (GRCm39) probably null Het
Vmn1r87 A G 7: 12,865,493 (GRCm39) Y265H probably damaging Het
Zfp574 G T 7: 24,781,026 (GRCm39) A683S possibly 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
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
R5896:Polr2a UTSW 11 69,627,086 (GRCm39) missense probably damaging 0.99
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'- GTAGCTGGGAGACATAGCAC -3'
(R):5'- TGCAATGACACCCTGGAACC -3'

Sequencing Primer
(F):5'- TGGGAGACATAGCACCACCTATAG -3'
(R):5'- TGGAACCAGGGTGCAACTC -3'
Posted On 2015-02-05