Incidental Mutation 'R1460:Polr1a'
ID 162057
Institutional Source Beutler Lab
Gene Symbol Polr1a
Ensembl Gene ENSMUSG00000049553
Gene Name polymerase (RNA) I polypeptide A
Synonyms 2900087K15Rik, 3010014K16Rik, 194kDa, mRPA1, Rpo1-4, RPA194
MMRRC Submission 039515-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1460 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 71886037-71956419 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 71918368 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Threonine at position 642 (M642T)
Ref Sequence ENSEMBL: ENSMUSP00000060858 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000055296] [ENSMUST00000206556]
AlphaFold O35134
Predicted Effect probably damaging
Transcript: ENSMUST00000055296
AA Change: M642T

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000060858
Gene: ENSMUSG00000049553
AA Change: M642T

DomainStartEndE-ValueType
RPOLA_N 302 649 8.97e-137 SMART
Pfam:RNA_pol_Rpb1_4 846 958 1.3e-26 PFAM
Pfam:RNA_pol_Rpb1_5 965 1669 7e-103 PFAM
low complexity region 1698 1708 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205942
Predicted Effect probably benign
Transcript: ENSMUST00000206556
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206753
Meta Mutation Damage Score 0.6798 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 98.0%
  • 10x: 95.2%
  • 20x: 89.1%
Validation Efficiency 94% (93/99)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is the largest subunit of the RNA polymerase I complex. The encoded protein represents the catalytic subunit of the complex, which transcribes DNA into ribosomal RNA precursors. Defects in this gene are a cause of the Cincinnati type of acrofacial dysostosis. [provided by RefSeq, May 2016]
Allele List at MGI

All alleles(18) : Gene trapped(18)

Other mutations in this stock
Total: 96 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930522H14Rik A T 4: 109,388,407 (GRCm39) probably null Het
Abcb11 A G 2: 69,087,718 (GRCm39) probably benign Het
Abi3bp T C 16: 56,382,780 (GRCm39) V130A probably damaging Het
Adamts4 A G 1: 171,084,009 (GRCm39) probably benign Het
Adgrd1 A G 5: 129,199,627 (GRCm39) T155A possibly damaging Het
Ano3 A T 2: 110,513,103 (GRCm39) S631T probably damaging Het
Ass1 G A 2: 31,404,753 (GRCm39) V345I probably benign Het
Atg7 G A 6: 114,680,325 (GRCm39) A384T probably damaging Het
Atp6v0a1 T A 11: 100,924,824 (GRCm39) I303N probably damaging Het
B3gntl1 T G 11: 121,530,624 (GRCm39) Y149S probably damaging Het
Btnl2 A G 17: 34,585,424 (GRCm39) D475G probably benign Het
Cdcp1 A T 9: 123,009,092 (GRCm39) S529T possibly damaging Het
Cenpt A G 8: 106,575,520 (GRCm39) L194P probably damaging Het
Cfhr4 T A 1: 139,625,934 (GRCm39) I788F probably damaging Het
Chmp4b A G 2: 154,534,515 (GRCm39) D177G possibly damaging Het
Chmp7 C T 14: 69,956,899 (GRCm39) M336I probably benign Het
Cish G T 9: 107,177,596 (GRCm39) E91* probably null Het
Col22a1 T C 15: 71,693,780 (GRCm39) D740G unknown Het
Cplane2 T C 4: 140,945,523 (GRCm39) F125L probably damaging Het
Crocc G A 4: 140,756,551 (GRCm39) Q1025* probably null Het
Ctrc C A 4: 141,566,120 (GRCm39) probably benign Het
Cyb5r2 T A 7: 107,356,450 (GRCm39) D7V probably benign Het
Dhx29 T C 13: 113,101,744 (GRCm39) probably benign Het
Dhx9 A C 1: 153,341,426 (GRCm39) D607E probably benign Het
Dnajb7 C T 15: 81,291,888 (GRCm39) G150R probably benign Het
Dnase1l3 T A 14: 7,974,050 (GRCm38) T214S probably benign Het
Dpm1 A T 2: 168,052,549 (GRCm39) I229N probably damaging Het
Dstn T C 2: 143,780,408 (GRCm39) V36A possibly damaging Het
Entpd1 T C 19: 40,714,632 (GRCm39) V247A probably damaging Het
Ephb3 C A 16: 21,037,672 (GRCm39) H277Q probably benign Het
Etl4 A T 2: 20,793,288 (GRCm39) N671I probably damaging Het
Fabp3 C T 4: 130,206,180 (GRCm39) T57I probably benign Het
Fancd2os G A 6: 113,574,973 (GRCm39) T11I probably damaging Het
Fcrlb G T 1: 170,739,853 (GRCm39) probably benign Het
Fhip1a T C 3: 85,638,183 (GRCm39) I39V probably damaging Het
Gm9991 T C 1: 90,606,780 (GRCm39) noncoding transcript Het
Gstk1 C T 6: 42,223,529 (GRCm39) R40W probably damaging Het
Gstt1 C T 10: 75,620,004 (GRCm39) V190M probably damaging Het
Hectd2 G A 19: 36,592,908 (GRCm39) W691* probably null Het
Hecw2 T C 1: 53,852,404 (GRCm39) T1572A probably damaging Het
Hoxa5 T C 6: 52,180,928 (GRCm39) T135A probably benign Het
Igfl3 T A 7: 17,913,880 (GRCm39) C77S possibly damaging Het
Itgb4 A G 11: 115,874,990 (GRCm39) D449G probably damaging Het
Larp1b T C 3: 40,916,653 (GRCm39) V11A probably benign Het
Lhx9 A G 1: 138,766,447 (GRCm39) probably benign Het
Lig3 G T 11: 82,686,624 (GRCm39) probably benign Het
Lipo4 A C 19: 33,476,718 (GRCm39) F343L probably benign Het
Lyn T A 4: 3,789,908 (GRCm39) Y480* probably null Het
Mib2 C T 4: 155,743,917 (GRCm39) G42S probably damaging Het
Mill1 C A 7: 17,996,595 (GRCm39) A137D probably damaging Het
Mmut T C 17: 41,248,266 (GRCm39) Y98H probably damaging Het
Morc2a A T 11: 3,633,794 (GRCm39) R635S probably benign Het
Mpped2 A G 2: 106,575,237 (GRCm39) probably benign Het
Mug2 T C 6: 122,017,492 (GRCm39) probably benign Het
Mynn C A 3: 30,657,853 (GRCm39) S57Y probably damaging Het
Myo3b G A 2: 70,062,798 (GRCm39) E333K probably benign Het
Myt1 A T 2: 181,444,725 (GRCm39) I514F probably damaging Het
Nlrp4f A G 13: 65,338,082 (GRCm39) C708R probably benign Het
Nod2 A G 8: 89,390,440 (GRCm39) E249G probably damaging Het
Npy2r T C 3: 82,448,251 (GRCm39) I175V probably benign Het
Obscn A T 11: 58,946,792 (GRCm39) V4114D probably damaging Het
Or1l8 A T 2: 36,817,820 (GRCm39) M102K probably damaging Het
Or2y12 T A 11: 49,426,504 (GRCm39) M164K possibly damaging Het
Or4a76 A G 2: 89,460,282 (GRCm39) probably null Het
Or52e7 T A 7: 104,684,915 (GRCm39) I170N possibly damaging Het
Or8g33 A G 9: 39,337,503 (GRCm39) M288T probably benign Het
Pbxip1 T A 3: 89,352,921 (GRCm39) I196N probably damaging Het
Piezo1 G A 8: 123,228,890 (GRCm39) T209M possibly damaging Het
Prdm4 T C 10: 85,743,686 (GRCm39) M190V probably benign Het
Psmd7 G A 8: 108,307,691 (GRCm39) S264L possibly damaging Het
Qrich1 T G 9: 108,410,846 (GRCm39) probably benign Het
Rapgef4 G T 2: 71,861,520 (GRCm39) probably null Het
Rfx5 T C 3: 94,863,636 (GRCm39) I95T probably damaging Het
Rgr G A 14: 36,767,683 (GRCm39) R113C probably damaging Het
Rnf20 T C 4: 49,645,873 (GRCm39) probably benign Het
Rps3a1 G A 3: 86,045,369 (GRCm39) A241V probably benign Het
Rttn A T 18: 89,127,481 (GRCm39) probably benign Het
Scn2a A G 2: 65,532,187 (GRCm39) T600A probably damaging Het
Scyl2 T C 10: 89,493,751 (GRCm39) D339G possibly damaging Het
Sipa1 T A 19: 5,701,475 (GRCm39) H1029L probably benign Het
Slc49a4 T C 16: 35,539,736 (GRCm39) T362A probably benign Het
Snrnp48 A G 13: 38,395,081 (GRCm39) T124A probably benign Het
Sptbn1 A T 11: 30,088,637 (GRCm39) M875K possibly damaging Het
Supt6 A G 11: 78,113,024 (GRCm39) V973A possibly damaging Het
Supv3l1 T C 10: 62,279,162 (GRCm39) probably benign Het
Svep1 G T 4: 58,068,740 (GRCm39) N3015K possibly damaging Het
Tgfb3 A G 12: 86,105,841 (GRCm39) probably benign Het
Trerf1 A G 17: 47,628,771 (GRCm39) noncoding transcript Het
Trim24 T A 6: 37,941,761 (GRCm39) F904I probably damaging Het
Trim30d T A 7: 104,121,311 (GRCm39) Y328F probably benign Het
Ttn T C 2: 76,698,717 (GRCm39) E6G probably damaging Het
Ube2m T C 7: 12,769,762 (GRCm39) probably benign Het
Vmn2r-ps158 A T 7: 42,672,639 (GRCm39) R91S probably benign Het
Wdr90 A T 17: 26,079,422 (GRCm39) S237R possibly damaging Het
Zfp735 A T 11: 73,603,159 (GRCm39) H701L possibly damaging Het
Zp1 T C 19: 10,896,242 (GRCm39) D161G probably benign Het
Other mutations in Polr1a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01363:Polr1a APN 6 71,925,470 (GRCm39) missense probably benign 0.32
IGL01834:Polr1a APN 6 71,925,446 (GRCm39) missense probably benign
IGL01902:Polr1a APN 6 71,940,732 (GRCm39) missense probably damaging 1.00
IGL02101:Polr1a APN 6 71,927,786 (GRCm39) missense probably benign 0.00
IGL02325:Polr1a APN 6 71,897,641 (GRCm39) missense probably benign 0.38
IGL02398:Polr1a APN 6 71,913,540 (GRCm39) splice site probably benign
IGL02528:Polr1a APN 6 71,941,701 (GRCm39) missense probably benign
IGL02555:Polr1a APN 6 71,897,441 (GRCm39) missense probably damaging 0.98
IGL02613:Polr1a APN 6 71,944,304 (GRCm39) missense probably damaging 1.00
IGL02693:Polr1a APN 6 71,940,830 (GRCm39) splice site probably benign
IGL02892:Polr1a APN 6 71,908,680 (GRCm39) missense possibly damaging 0.70
IGL03059:Polr1a APN 6 71,913,496 (GRCm39) missense probably benign
IGL03174:Polr1a APN 6 71,954,331 (GRCm39) missense possibly damaging 0.82
D4043:Polr1a UTSW 6 71,918,401 (GRCm39) missense possibly damaging 0.92
R0092:Polr1a UTSW 6 71,944,439 (GRCm39) splice site probably benign
R0217:Polr1a UTSW 6 71,940,687 (GRCm39) missense probably benign 0.19
R0267:Polr1a UTSW 6 71,951,123 (GRCm39) missense probably damaging 0.99
R0329:Polr1a UTSW 6 71,943,400 (GRCm39) missense possibly damaging 0.96
R0330:Polr1a UTSW 6 71,943,400 (GRCm39) missense possibly damaging 0.96
R0352:Polr1a UTSW 6 71,897,747 (GRCm39) splice site probably benign
R0411:Polr1a UTSW 6 71,955,405 (GRCm39) missense possibly damaging 0.95
R0446:Polr1a UTSW 6 71,927,648 (GRCm39) critical splice donor site probably null
R0846:Polr1a UTSW 6 71,901,627 (GRCm39) missense probably damaging 1.00
R1035:Polr1a UTSW 6 71,944,900 (GRCm39) missense probably benign
R1294:Polr1a UTSW 6 71,889,886 (GRCm39) missense probably damaging 0.99
R1657:Polr1a UTSW 6 71,918,519 (GRCm39) missense probably damaging 1.00
R1846:Polr1a UTSW 6 71,953,172 (GRCm39) missense probably damaging 0.98
R1862:Polr1a UTSW 6 71,886,187 (GRCm39) missense probably damaging 0.96
R1865:Polr1a UTSW 6 71,943,508 (GRCm39) missense probably damaging 1.00
R1903:Polr1a UTSW 6 71,944,898 (GRCm39) missense probably benign 0.02
R1937:Polr1a UTSW 6 71,913,536 (GRCm39) critical splice donor site probably null
R2063:Polr1a UTSW 6 71,913,269 (GRCm39) splice site probably null
R2071:Polr1a UTSW 6 71,953,058 (GRCm39) missense possibly damaging 0.64
R2084:Polr1a UTSW 6 71,927,793 (GRCm39) missense possibly damaging 0.69
R2377:Polr1a UTSW 6 71,949,810 (GRCm39) critical splice donor site probably null
R2410:Polr1a UTSW 6 71,951,866 (GRCm39) missense probably benign
R3001:Polr1a UTSW 6 71,890,000 (GRCm39) missense probably benign 0.01
R3001:Polr1a UTSW 6 71,942,628 (GRCm39) missense probably benign 0.02
R3002:Polr1a UTSW 6 71,942,628 (GRCm39) missense probably benign 0.02
R3002:Polr1a UTSW 6 71,890,000 (GRCm39) missense probably benign 0.01
R3924:Polr1a UTSW 6 71,906,434 (GRCm39) missense probably benign 0.00
R4105:Polr1a UTSW 6 71,953,175 (GRCm39) missense probably damaging 0.98
R4125:Polr1a UTSW 6 71,942,690 (GRCm39) missense probably benign 0.00
R4271:Polr1a UTSW 6 71,930,006 (GRCm39) missense probably benign 0.02
R4440:Polr1a UTSW 6 71,927,832 (GRCm39) missense probably damaging 0.98
R4667:Polr1a UTSW 6 71,894,805 (GRCm39) missense probably benign 0.30
R4769:Polr1a UTSW 6 71,927,852 (GRCm39) missense probably benign 0.01
R4801:Polr1a UTSW 6 71,953,054 (GRCm39) missense probably benign 0.00
R4802:Polr1a UTSW 6 71,953,054 (GRCm39) missense probably benign 0.00
R4828:Polr1a UTSW 6 71,943,385 (GRCm39) missense possibly damaging 0.93
R4911:Polr1a UTSW 6 71,886,213 (GRCm39) missense possibly damaging 0.67
R5071:Polr1a UTSW 6 71,908,693 (GRCm39) missense possibly damaging 0.71
R5165:Polr1a UTSW 6 71,944,909 (GRCm39) missense probably damaging 1.00
R5223:Polr1a UTSW 6 71,944,891 (GRCm39) missense possibly damaging 0.73
R5239:Polr1a UTSW 6 71,890,021 (GRCm39) missense probably damaging 1.00
R5546:Polr1a UTSW 6 71,906,350 (GRCm39) missense possibly damaging 0.64
R5599:Polr1a UTSW 6 71,944,346 (GRCm39) missense possibly damaging 0.95
R5696:Polr1a UTSW 6 71,906,410 (GRCm39) missense probably benign 0.05
R5850:Polr1a UTSW 6 71,903,667 (GRCm39) missense probably benign 0.00
R6274:Polr1a UTSW 6 71,931,874 (GRCm39) splice site probably null
R6526:Polr1a UTSW 6 71,906,427 (GRCm39) missense possibly damaging 0.89
R6578:Polr1a UTSW 6 71,953,025 (GRCm39) missense possibly damaging 0.93
R6660:Polr1a UTSW 6 71,944,358 (GRCm39) missense probably damaging 0.98
R6892:Polr1a UTSW 6 71,941,696 (GRCm39) missense possibly damaging 0.72
R7274:Polr1a UTSW 6 71,897,500 (GRCm39) nonsense probably null
R7291:Polr1a UTSW 6 71,918,440 (GRCm39) missense probably benign 0.02
R7311:Polr1a UTSW 6 71,927,863 (GRCm39) missense possibly damaging 0.53
R7431:Polr1a UTSW 6 71,903,643 (GRCm39) missense probably benign 0.14
R7479:Polr1a UTSW 6 71,913,281 (GRCm39) missense probably damaging 1.00
R7607:Polr1a UTSW 6 71,890,005 (GRCm39) missense probably benign
R7739:Polr1a UTSW 6 71,931,819 (GRCm39) missense possibly damaging 0.94
R7746:Polr1a UTSW 6 71,918,496 (GRCm39) missense probably damaging 1.00
R7764:Polr1a UTSW 6 71,930,054 (GRCm39) missense probably damaging 1.00
R7835:Polr1a UTSW 6 71,892,126 (GRCm39) missense probably benign 0.02
R8029:Polr1a UTSW 6 71,889,940 (GRCm39) nonsense probably null
R8057:Polr1a UTSW 6 71,908,644 (GRCm39) missense possibly damaging 0.95
R8144:Polr1a UTSW 6 71,927,600 (GRCm39) missense probably benign
R8170:Polr1a UTSW 6 71,897,733 (GRCm39) missense probably benign
R8320:Polr1a UTSW 6 71,918,368 (GRCm39) missense probably damaging 0.99
R8328:Polr1a UTSW 6 71,897,718 (GRCm39) missense probably benign
R8331:Polr1a UTSW 6 71,953,163 (GRCm39) missense probably damaging 1.00
R8362:Polr1a UTSW 6 71,941,651 (GRCm39) missense probably benign 0.00
R8511:Polr1a UTSW 6 71,897,504 (GRCm39) missense probably benign 0.01
R8709:Polr1a UTSW 6 71,951,832 (GRCm39) missense probably benign
R8745:Polr1a UTSW 6 71,931,755 (GRCm39) missense probably damaging 1.00
R8784:Polr1a UTSW 6 71,927,612 (GRCm39) missense probably benign
R9055:Polr1a UTSW 6 71,892,053 (GRCm39) missense possibly damaging 0.46
R9088:Polr1a UTSW 6 71,908,767 (GRCm39) missense probably benign 0.26
R9211:Polr1a UTSW 6 71,943,521 (GRCm39) missense probably damaging 1.00
R9228:Polr1a UTSW 6 71,931,755 (GRCm39) missense probably damaging 1.00
R9240:Polr1a UTSW 6 71,940,661 (GRCm39) nonsense probably null
R9267:Polr1a UTSW 6 71,942,542 (GRCm39) missense probably benign
R9302:Polr1a UTSW 6 71,901,683 (GRCm39) critical splice donor site probably null
R9744:Polr1a UTSW 6 71,906,372 (GRCm39) missense probably benign 0.05
Predicted Primers PCR Primer
(F):5'- TGACAGCAGCTTGACCAAACGTAG -3'
(R):5'- AGAAGCCGTGCAACCTGTTCTTAG -3'

Sequencing Primer
(F):5'- ATGTTGAGGCCAGTAGTAACTCC -3'
(R):5'- GCAACCTGTTCTTAGTAGATACACC -3'
Posted On 2014-03-14