Incidental Mutation 'R5696:Polr1a'
ID 450661
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
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5696 (G1)
Quality Score 225
Status Not validated
Chromosome 6
Chromosomal Location 71886037-71956419 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 71906410 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Isoleucine at position 409 (F409I)
Ref Sequence ENSEMBL: ENSMUSP00000060858 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000055296] [ENSMUST00000206556]
AlphaFold O35134
Predicted Effect probably benign
Transcript: ENSMUST00000055296
AA Change: F409I

PolyPhen 2 Score 0.052 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000060858
Gene: ENSMUSG00000049553
AA Change: F409I

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: ENSMUST00000205333
Predicted Effect probably benign
Transcript: ENSMUST00000206556
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206753
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206823
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.6%
Validation Efficiency
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: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam8 G A 7: 139,569,159 (GRCm39) R186W probably benign Het
Afg3l2 A G 18: 67,540,529 (GRCm39) I660T probably damaging Het
Amtn T A 5: 88,532,944 (GRCm39) Y186* probably null Het
Atosa A G 9: 74,917,399 (GRCm39) E666G probably benign Het
Atrip A G 9: 108,894,569 (GRCm39) S453P possibly damaging Het
Bahcc1 T C 11: 120,164,813 (GRCm39) L840P probably damaging Het
Capn2 T C 1: 182,306,165 (GRCm39) E527G possibly damaging Het
Caprin2 A T 6: 148,779,316 (GRCm39) Y164N possibly damaging Het
Ccnh T A 13: 85,344,446 (GRCm39) probably null Het
Cdon G T 9: 35,403,162 (GRCm39) V1091F possibly damaging Het
Ceacam14 A G 7: 17,548,267 (GRCm39) Y119C probably damaging Het
Ces2h A G 8: 105,745,611 (GRCm39) K445E possibly damaging Het
Cfap46 A G 7: 139,191,947 (GRCm39) S2357P probably damaging Het
Commd4 A T 9: 57,063,499 (GRCm39) S86R possibly damaging Het
Cpsf6 A T 10: 117,196,934 (GRCm39) probably benign Het
Dag1 A T 9: 108,086,646 (GRCm39) V165E probably benign Het
Dmxl1 A T 18: 50,065,008 (GRCm39) K2618* probably null Het
Dnah17 A G 11: 117,991,882 (GRCm39) Y1229H probably benign Het
Endov T A 11: 119,382,625 (GRCm39) L24Q probably damaging Het
Fap C T 2: 62,332,803 (GRCm39) V717M probably damaging Het
Fbxl2 A G 9: 113,815,546 (GRCm39) L239P probably damaging Het
Fbxl5 A T 5: 43,916,182 (GRCm39) V367D possibly damaging Het
Fkbp10 G T 11: 100,314,352 (GRCm39) W384L probably damaging Het
Gbp8 C T 5: 105,166,682 (GRCm39) V216I possibly damaging Het
Gclm G A 3: 122,059,936 (GRCm39) A239T probably benign Het
Gm11569 C T 11: 99,689,556 (GRCm39) probably benign Het
Gnas C A 2: 174,141,468 (GRCm39) probably benign Het
Grb10 T A 11: 11,883,566 (GRCm39) N508I probably benign Het
Gykl1 T G 18: 52,827,267 (GRCm39) I158M probably benign Het
Ide G A 19: 37,295,420 (GRCm39) T214M unknown Het
Il12rb2 T A 6: 67,272,262 (GRCm39) Q341H possibly damaging Het
Ints1 T C 5: 139,740,744 (GRCm39) E1946G probably benign Het
Kdelr3 T C 15: 79,410,100 (GRCm39) probably null Het
Kif1b A C 4: 149,358,306 (GRCm39) probably null Het
Kri1 A G 9: 21,191,533 (GRCm39) I320T probably damaging Het
Krt9 TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC 11: 100,079,903 (GRCm39) probably benign Het
Lin9 T C 1: 180,486,646 (GRCm39) S111P probably benign Het
Lpcat2b C A 5: 107,580,773 (GRCm39) P34Q probably damaging Het
Ltk T A 2: 119,590,080 (GRCm39) T49S probably benign Het
Map3k9 A T 12: 81,780,896 (GRCm39) H421Q probably benign Het
Mapkbp1 T A 2: 119,852,201 (GRCm39) probably null Het
Mcm4 A G 16: 15,443,434 (GRCm39) S830P probably damaging Het
Nek10 T A 14: 14,860,736 (GRCm38) probably null Het
Nlrp9b A T 7: 19,758,417 (GRCm39) R551S probably benign Het
Nol4l T C 2: 153,260,026 (GRCm39) T143A probably damaging Het
Or1r1 T C 11: 73,875,362 (GRCm39) H24R possibly damaging Het
Or51g1 T A 7: 102,633,748 (GRCm39) T208S probably benign Het
Or6z5 T C 7: 6,477,742 (GRCm39) probably null Het
Or7a39 A T 10: 78,715,919 (GRCm39) R304S probably benign Het
Pde4dip G T 3: 97,616,806 (GRCm39) A1812D probably damaging Het
Plekhb1 C A 7: 100,305,960 (GRCm39) G26C probably damaging Het
Ptpn13 T A 5: 103,702,625 (GRCm39) M1197K probably benign Het
Qrich2 T C 11: 116,335,828 (GRCm39) I2114V probably damaging Het
Rbm27 T C 18: 42,450,731 (GRCm39) Y449H probably damaging Het
Rp1l1 A G 14: 64,267,195 (GRCm39) D927G probably damaging Het
Secisbp2 C A 13: 51,833,857 (GRCm39) Q666K probably damaging Het
Slc45a2 T C 15: 11,001,219 (GRCm39) I106T probably damaging Het
Slx4 G T 16: 3,797,831 (GRCm39) Q1518K probably damaging Het
Smim10l1 T C 6: 133,082,489 (GRCm39) F12S probably damaging Het
Son T C 16: 91,468,301 (GRCm39) V306A possibly damaging Het
Stab1 A G 14: 30,882,178 (GRCm39) S506P probably benign Het
Syne2 A C 12: 76,040,919 (GRCm39) D3859A probably benign Het
Tab1 T A 15: 80,032,930 (GRCm39) Y71* probably null Het
Tarbp1 A C 8: 127,174,079 (GRCm39) M909R probably damaging Het
Tex15 T G 8: 34,063,220 (GRCm39) S1157R probably benign Het
Tnni3 G A 7: 4,523,453 (GRCm39) T120I probably benign Het
Ttn T C 2: 76,747,888 (GRCm39) E4387G probably benign Het
Ugt3a1 G A 15: 9,361,534 (GRCm39) silent Het
Unc5d T C 8: 29,156,870 (GRCm39) I783V probably benign Het
Usp40 T C 1: 87,923,474 (GRCm39) T266A probably benign Het
Vmn2r59 C T 7: 41,695,468 (GRCm39) V315I probably benign Het
Zbtb48 G T 4: 152,105,067 (GRCm39) H532N probably damaging Het
Zfp1005 C T 2: 150,111,394 (GRCm39) H695Y possibly damaging 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
R1460:Polr1a UTSW 6 71,918,368 (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
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'- CTCATTAAGGGCTAGGTTGAGTAAC -3'
(R):5'- GGAACAGGCCTTCCTTCTTC -3'

Sequencing Primer
(F):5'- ATGACTCCTCAGTGGCTA -3'
(R):5'- CTTCTTGCTTCTGAAACAGTGAG -3'
Posted On 2017-01-03