Incidental Mutation 'R5010:Rpap1'
ID 390414
Institutional Source Beutler Lab
Gene Symbol Rpap1
Ensembl Gene ENSMUSG00000034032
Gene Name RNA polymerase II associated protein 1
Synonyms A730023M06Rik, 1190005L06Rik
MMRRC Submission 042601-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.966) question?
Stock # R5010 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 119594440-119618018 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 119600522 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 879 (N879S)
Ref Sequence ENSEMBL: ENSMUSP00000106420 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000048493] [ENSMUST00000099529] [ENSMUST00000110793] [ENSMUST00000136419] [ENSMUST00000184294]
AlphaFold Q80TE0
Predicted Effect probably benign
Transcript: ENSMUST00000048493
AA Change: N879S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000037275
Gene: ENSMUSG00000034032
AA Change: N879S

DomainStartEndE-ValueType
low complexity region 62 81 N/A INTRINSIC
Pfam:RPAP1_N 225 270 2.4e-21 PFAM
Pfam:RPAP1_C 372 438 1.9e-27 PFAM
low complexity region 451 473 N/A INTRINSIC
low complexity region 476 488 N/A INTRINSIC
low complexity region 515 529 N/A INTRINSIC
low complexity region 739 752 N/A INTRINSIC
low complexity region 843 860 N/A INTRINSIC
low complexity region 989 1007 N/A INTRINSIC
low complexity region 1042 1052 N/A INTRINSIC
low complexity region 1097 1108 N/A INTRINSIC
low complexity region 1193 1204 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000099529
AA Change: N879S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000097127
Gene: ENSMUSG00000034032
AA Change: N879S

DomainStartEndE-ValueType
low complexity region 62 81 N/A INTRINSIC
Pfam:RPAP1_N 224 272 1.7e-21 PFAM
Pfam:RPAP1_C 370 440 2.9e-27 PFAM
low complexity region 451 473 N/A INTRINSIC
low complexity region 476 488 N/A INTRINSIC
low complexity region 515 529 N/A INTRINSIC
low complexity region 739 752 N/A INTRINSIC
low complexity region 843 860 N/A INTRINSIC
low complexity region 989 1007 N/A INTRINSIC
low complexity region 1042 1052 N/A INTRINSIC
low complexity region 1097 1108 N/A INTRINSIC
low complexity region 1193 1204 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000110793
AA Change: N879S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000106420
Gene: ENSMUSG00000034032
AA Change: N879S

DomainStartEndE-ValueType
low complexity region 62 81 N/A INTRINSIC
Pfam:RPAP1_N 224 272 1.7e-21 PFAM
Pfam:RPAP1_C 370 440 2.9e-27 PFAM
low complexity region 451 473 N/A INTRINSIC
low complexity region 476 488 N/A INTRINSIC
low complexity region 515 529 N/A INTRINSIC
low complexity region 739 752 N/A INTRINSIC
low complexity region 843 860 N/A INTRINSIC
low complexity region 989 1007 N/A INTRINSIC
low complexity region 1042 1052 N/A INTRINSIC
low complexity region 1097 1108 N/A INTRINSIC
low complexity region 1193 1204 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000136419
SMART Domains Protein: ENSMUSP00000138619
Gene: ENSMUSG00000034032

DomainStartEndE-ValueType
low complexity region 62 81 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139311
Predicted Effect probably benign
Transcript: ENSMUST00000184294
SMART Domains Protein: ENSMUSP00000138873
Gene: ENSMUSG00000034032

DomainStartEndE-ValueType
low complexity region 62 81 N/A INTRINSIC
Pfam:RPAP1_N 224 272 4.8e-22 PFAM
Pfam:RPAP1_C 370 440 1.2e-27 PFAM
low complexity region 451 473 N/A INTRINSIC
low complexity region 476 488 N/A INTRINSIC
low complexity region 515 529 N/A INTRINSIC
low complexity region 739 752 N/A INTRINSIC
low complexity region 843 860 N/A INTRINSIC
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.6%
Validation Efficiency 98% (65/66)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This protein forms part of the RNA polymerase II (RNAPII) enzyme complex and may recruit RNAPII to chromatin through its interaction with acetylated histones. [provided by RefSeq, Jul 2012]
Allele List at MGI
Other mutations in this stock
Total: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1810065E05Rik C T 11: 58,313,630 (GRCm39) A86V possibly damaging Het
9430097D07Rik A G 2: 32,464,440 (GRCm39) probably benign Het
Actr5 T A 2: 158,477,283 (GRCm39) D411E probably benign Het
Ang5 A G 14: 44,200,302 (GRCm39) D122G probably benign Het
Atg9a A T 1: 75,162,704 (GRCm39) probably null Het
Cracd G C 5: 76,805,681 (GRCm39) probably benign Het
Dctd C T 8: 48,590,449 (GRCm39) probably benign Het
Ddx11 G A 17: 66,454,717 (GRCm39) V642M possibly damaging Het
Dis3l2 G A 1: 86,688,043 (GRCm39) V100I probably benign Het
Echdc2 T C 4: 108,029,328 (GRCm39) V111A probably benign Het
Egr1 A G 18: 34,996,711 (GRCm39) T498A probably benign Het
Exosc3 T C 4: 45,317,702 (GRCm39) K200R possibly damaging Het
Exosc8 T C 3: 54,636,644 (GRCm39) D229G probably benign Het
Ext1 T A 15: 52,955,808 (GRCm39) I430F probably damaging Het
Fbxw22 T C 9: 109,232,492 (GRCm39) N31S probably benign Het
Gja8 T C 3: 96,827,165 (GRCm39) T166A probably benign Het
Gm21814 T A 6: 149,485,116 (GRCm39) noncoding transcript Het
Gm21915 T A 9: 40,581,944 (GRCm39) H12Q probably benign Het
Hgsnat G A 8: 26,437,988 (GRCm39) R527* probably null Het
Iqgap2 A G 13: 95,810,251 (GRCm39) F731S probably benign Het
Jchain T C 5: 88,670,364 (GRCm39) H85R probably damaging Het
Kcnb2 T C 1: 15,383,186 (GRCm39) C171R probably benign Het
Kcnk3 C A 5: 30,780,149 (GRCm39) R400S possibly damaging Het
Klhl28 C T 12: 65,004,001 (GRCm39) E171K probably damaging Het
Lrrfip2 T C 9: 111,053,040 (GRCm39) I375T possibly damaging Het
Mccc1 T C 3: 36,033,166 (GRCm39) N326S probably benign Het
Med13l T C 5: 118,731,615 (GRCm39) V97A possibly damaging Het
Mertk C A 2: 128,625,920 (GRCm39) T685K probably benign Het
Msh2 C A 17: 88,030,841 (GRCm39) A906E probably benign Het
Myom2 G A 8: 15,133,310 (GRCm39) V401M probably damaging Het
Nme5 A C 18: 34,711,738 (GRCm39) M1R probably null Het
Nop2 T C 6: 125,110,726 (GRCm39) S68P probably benign Het
Notch1 A T 2: 26,366,126 (GRCm39) D809E possibly damaging Het
Or14c39 T C 7: 86,343,793 (GRCm39) I43T possibly damaging Het
Ppat C T 5: 77,076,525 (GRCm39) probably benign Het
Prss23 T A 7: 89,159,422 (GRCm39) M216L probably benign Het
Psg18 A T 7: 18,083,279 (GRCm39) V171D probably damaging Het
Psg28 A G 7: 18,161,816 (GRCm39) V229A probably damaging Het
Qser1 T C 2: 104,618,176 (GRCm39) N879D possibly damaging Het
Rusc2 T C 4: 43,415,926 (GRCm39) S411P probably damaging Het
Rxfp2 T A 5: 149,990,825 (GRCm39) W519R probably damaging Het
Scpep1 T A 11: 88,832,175 (GRCm39) Q185L probably benign Het
Serpinb11 A G 1: 107,307,379 (GRCm39) N270S probably benign Het
Serpinb6d T A 13: 33,855,427 (GRCm39) M367K probably benign Het
Skint10 T G 4: 112,584,869 (GRCm39) I213L probably benign Het
Skint5 T C 4: 113,403,734 (GRCm39) T1163A unknown Het
Slamf9 A T 1: 172,303,780 (GRCm39) I42L possibly damaging Het
Slc1a3 T C 15: 8,680,330 (GRCm39) probably benign Het
Smad6 T A 9: 63,861,182 (GRCm39) Q371L possibly damaging Het
Snx31 A T 15: 36,555,469 (GRCm39) V26E probably damaging Het
Spata31e5 A G 1: 28,816,943 (GRCm39) I363T possibly damaging Het
Taf4b A G 18: 14,955,229 (GRCm39) N594S possibly damaging Het
Tanc2 T C 11: 105,670,918 (GRCm39) S172P probably damaging Het
Tas2r110 T A 6: 132,845,438 (GRCm39) Y156* probably null Het
Tbc1d20 G A 2: 152,135,856 (GRCm39) probably benign Het
Timm50 A T 7: 28,006,284 (GRCm39) D272E probably benign Het
Ttn T G 2: 76,730,855 (GRCm39) probably benign Het
Vps13c T A 9: 67,823,661 (GRCm39) F1362I probably benign Het
Vwf T C 6: 125,543,220 (GRCm39) S154P probably benign Het
Zfp445 T C 9: 122,681,410 (GRCm39) R844G probably benign Het
Other mutations in Rpap1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01807:Rpap1 APN 2 119,613,189 (GRCm39) missense possibly damaging 0.50
IGL02009:Rpap1 APN 2 119,610,594 (GRCm39) missense possibly damaging 0.51
IGL02068:Rpap1 APN 2 119,613,135 (GRCm39) missense probably benign 0.02
IGL02100:Rpap1 APN 2 119,599,807 (GRCm39) missense probably benign 0.06
IGL02528:Rpap1 APN 2 119,605,431 (GRCm39) splice site probably null
IGL02530:Rpap1 APN 2 119,613,720 (GRCm39) splice site probably benign
IGL02747:Rpap1 APN 2 119,604,609 (GRCm39) missense probably damaging 0.98
IGL03371:Rpap1 APN 2 119,605,538 (GRCm39) splice site probably benign
R0138:Rpap1 UTSW 2 119,595,380 (GRCm39) splice site probably null
R0325:Rpap1 UTSW 2 119,602,321 (GRCm39) missense probably benign
R0616:Rpap1 UTSW 2 119,608,601 (GRCm39) missense probably damaging 1.00
R1081:Rpap1 UTSW 2 119,601,750 (GRCm39) missense probably damaging 1.00
R1657:Rpap1 UTSW 2 119,614,259 (GRCm39) missense possibly damaging 0.53
R1837:Rpap1 UTSW 2 119,600,366 (GRCm39) critical splice donor site probably null
R2307:Rpap1 UTSW 2 119,614,247 (GRCm39) missense probably benign 0.00
R2308:Rpap1 UTSW 2 119,614,247 (GRCm39) missense probably benign 0.00
R2375:Rpap1 UTSW 2 119,600,888 (GRCm39) missense possibly damaging 0.50
R2507:Rpap1 UTSW 2 119,610,535 (GRCm39) critical splice donor site probably null
R2508:Rpap1 UTSW 2 119,610,535 (GRCm39) critical splice donor site probably null
R4155:Rpap1 UTSW 2 119,604,660 (GRCm39) missense probably damaging 1.00
R4156:Rpap1 UTSW 2 119,604,660 (GRCm39) missense probably damaging 1.00
R4157:Rpap1 UTSW 2 119,604,660 (GRCm39) missense probably damaging 1.00
R4657:Rpap1 UTSW 2 119,605,487 (GRCm39) missense probably benign 0.03
R4837:Rpap1 UTSW 2 119,608,732 (GRCm39) missense probably benign 0.32
R4880:Rpap1 UTSW 2 119,614,346 (GRCm39) missense probably damaging 0.97
R5111:Rpap1 UTSW 2 119,601,728 (GRCm39) missense probably damaging 1.00
R5650:Rpap1 UTSW 2 119,604,331 (GRCm39) missense probably benign
R6144:Rpap1 UTSW 2 119,603,128 (GRCm39) nonsense probably null
R6353:Rpap1 UTSW 2 119,607,377 (GRCm39) splice site probably null
R6646:Rpap1 UTSW 2 119,610,612 (GRCm39) missense probably benign 0.03
R6731:Rpap1 UTSW 2 119,608,777 (GRCm39) missense probably benign
R6872:Rpap1 UTSW 2 119,605,850 (GRCm39) missense probably damaging 1.00
R6878:Rpap1 UTSW 2 119,608,657 (GRCm39) missense probably damaging 1.00
R7060:Rpap1 UTSW 2 119,604,043 (GRCm39) missense probably damaging 1.00
R7558:Rpap1 UTSW 2 119,601,735 (GRCm39) missense probably benign
R7640:Rpap1 UTSW 2 119,594,891 (GRCm39) missense possibly damaging 0.63
R7862:Rpap1 UTSW 2 119,605,893 (GRCm39) critical splice acceptor site probably null
R8055:Rpap1 UTSW 2 119,595,284 (GRCm39) missense probably benign 0.13
R8934:Rpap1 UTSW 2 119,599,730 (GRCm39) critical splice donor site probably null
R9032:Rpap1 UTSW 2 119,608,776 (GRCm39) missense probably benign 0.00
R9220:Rpap1 UTSW 2 119,604,669 (GRCm39) missense probably damaging 0.99
R9422:Rpap1 UTSW 2 119,613,519 (GRCm39) intron probably benign
R9651:Rpap1 UTSW 2 119,598,484 (GRCm39) missense probably damaging 1.00
R9776:Rpap1 UTSW 2 119,607,278 (GRCm39) missense probably benign 0.00
X0028:Rpap1 UTSW 2 119,601,543 (GRCm39) missense probably benign
Z1177:Rpap1 UTSW 2 119,614,233 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ACTGATGGGTTCTGGGACTC -3'
(R):5'- GCCTGAGGAAACCCAAATTTC -3'

Sequencing Primer
(F):5'- ATGCCTGGCCTCCAAATG -3'
(R):5'- TTTCCAGCAGGAGCAACC -3'
Posted On 2016-06-06