Incidental Mutation 'R5279:Rpa1'
ID 404127
Institutional Source Beutler Lab
Gene Symbol Rpa1
Ensembl Gene ENSMUSG00000000751
Gene Name replication protein A1
Synonyms 5031405K23Rik, Rpa, RF-A, 70kDa, RP-A
MMRRC Submission 042839-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5279 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 75191085-75239478 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 75204170 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 269 (N269S)
Ref Sequence ENSEMBL: ENSMUSP00000000767 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000000767] [ENSMUST00000092907]
AlphaFold Q8VEE4
Predicted Effect probably damaging
Transcript: ENSMUST00000000767
AA Change: N269S

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000000767
Gene: ENSMUSG00000000751
AA Change: N269S

DomainStartEndE-ValueType
Pfam:Rep-A_N 5 93 7.2e-30 PFAM
low complexity region 145 175 N/A INTRINSIC
Pfam:tRNA_anti-codon 227 316 5e-13 PFAM
Pfam:REPA_OB_2 335 432 5e-37 PFAM
Pfam:Rep_fac-A_C 491 636 4.5e-57 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000092907
AA Change: N248S

PolyPhen 2 Score 0.770 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000090585
Gene: ENSMUSG00000000751
AA Change: N248S

DomainStartEndE-ValueType
Pfam:Rep-A_N 5 104 4.3e-35 PFAM
low complexity region 124 154 N/A INTRINSIC
Pfam:tRNA_anti-codon 206 295 8.4e-13 PFAM
SCOP:d1fgua2 308 435 8e-46 SMART
Pfam:Rep_fac-A_C 470 615 9.2e-56 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135770
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154894
Meta Mutation Damage Score 0.2068 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.4%
Validation Efficiency 99% (73/74)
MGI Phenotype PHENOTYPE: Homozygous null mice display embryonic lethality before implantation and impaired cell proliferation. Heterozygous null mice display decreased survival, chromosomal instability, impaired double strand break repair, and develop lymphomas. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca17 C A 17: 24,508,388 (GRCm39) G1049V probably damaging Het
Afdn G A 17: 14,109,214 (GRCm39) R1579H probably damaging Het
Ankrd28 T A 14: 31,456,963 (GRCm39) N386Y probably damaging Het
Atf7ip T A 6: 136,580,377 (GRCm39) Y1100* probably null Het
Atp9b T A 18: 80,956,073 (GRCm39) E3V probably damaging Het
AW554918 T G 18: 25,308,488 (GRCm39) D60E possibly damaging Het
Baz2b G T 2: 59,762,496 (GRCm39) Q927K probably damaging Het
Birc6 A G 17: 74,957,042 (GRCm39) R3659G probably damaging Het
C8a T G 4: 104,703,185 (GRCm39) N291H probably damaging Het
Calcoco1 G A 15: 102,619,420 (GRCm39) L390F probably damaging Het
Carmil3 A G 14: 55,739,028 (GRCm39) D894G probably damaging Het
Cdc20 A G 4: 118,290,711 (GRCm39) Y430H probably damaging Het
Cdc6 A T 11: 98,803,088 (GRCm39) I316F probably damaging Het
Ceacam23 T A 7: 17,607,214 (GRCm39) noncoding transcript Het
Cenpu T A 8: 47,031,945 (GRCm39) probably null Het
Csmd2 T A 4: 128,350,707 (GRCm39) V1592D probably benign Het
Csmd3 G T 15: 48,655,340 (GRCm39) probably null Het
Dnah7c T C 1: 46,558,429 (GRCm39) F512L probably benign Het
Fam136a T A 6: 86,343,686 (GRCm39) L61Q probably damaging Het
Fpgs A C 2: 32,582,779 (GRCm39) probably benign Het
Fzd4 G A 7: 89,056,881 (GRCm39) M309I probably benign Het
Gad2 A G 2: 22,563,969 (GRCm39) T391A probably benign Het
Gm11563 A T 11: 99,549,539 (GRCm39) S72T unknown Het
Gon4l A G 3: 88,794,944 (GRCm39) I716V probably benign Het
Itga9 T C 9: 118,457,273 (GRCm39) V128A probably damaging Het
Kat6a CGCAGCAGCAGCAGCAGCA CGCAGCAGCAGCA 8: 23,429,664 (GRCm39) probably benign Het
Lrrc9 T A 12: 72,542,368 (GRCm39) D1063E possibly damaging Het
Lyst T A 13: 13,823,387 (GRCm39) L1453* probably null Het
Mcm3ap T C 10: 76,343,373 (GRCm39) V1755A probably damaging Het
Mrc1 T C 2: 14,314,869 (GRCm39) S985P probably damaging Het
Mst1 A C 9: 107,959,414 (GRCm39) K233N probably damaging Het
Nr2c2ap G A 8: 70,584,653 (GRCm39) D42N probably damaging Het
Ntn1 A G 11: 68,276,538 (GRCm39) S137P probably benign Het
Pard3 T C 8: 128,186,867 (GRCm39) probably null Het
Pcdh15 T A 10: 74,430,015 (GRCm39) D1210E probably damaging Het
Pcdhga5 T C 18: 37,827,774 (GRCm39) L74P probably benign Het
Pcsk5 T C 19: 17,573,022 (GRCm39) probably null Het
Pdia3 T C 2: 121,244,484 (GRCm39) probably benign Het
Pikfyve A T 1: 65,235,858 (GRCm39) R177* probably null Het
Pklr A G 3: 89,050,566 (GRCm39) E409G probably damaging Het
Plod2 T C 9: 92,463,376 (GRCm39) Y154H probably damaging Het
Psmc3 T A 2: 90,884,667 (GRCm39) D6E probably benign Het
Ptpru T A 4: 131,547,334 (GRCm39) N205I possibly damaging Het
Rbm6 T C 9: 107,655,213 (GRCm39) E1006G probably benign Het
Rgl2 T C 17: 34,154,922 (GRCm39) V642A probably benign Het
Rnf8 T A 17: 29,845,680 (GRCm39) H104Q possibly damaging Het
Robo4 CGG CG 9: 37,322,786 (GRCm39) probably null Het
Sdk2 A G 11: 113,757,857 (GRCm39) M519T probably benign Het
Snx30 A G 4: 59,885,070 (GRCm39) S237G probably benign Het
Spx A G 6: 142,359,766 (GRCm39) N36S probably damaging Het
Stard7 T C 2: 127,137,416 (GRCm39) Y289H probably damaging Het
Sugp2 T C 8: 70,709,757 (GRCm39) probably benign Het
Susd4 C T 1: 182,715,043 (GRCm39) T288I probably damaging Het
Tceanc2 T A 4: 107,034,826 (GRCm39) probably null Het
Tm4sf4 T G 3: 57,341,159 (GRCm39) V97G probably benign Het
Tmtc1 C T 6: 148,256,629 (GRCm39) probably benign Het
Trappc11 C T 8: 47,958,339 (GRCm39) probably benign Het
Triobp G T 15: 78,878,591 (GRCm39) V398F possibly damaging Het
Ttll9 T A 2: 152,804,464 (GRCm39) S2T possibly damaging Het
Ttn T C 2: 76,731,320 (GRCm39) probably benign Het
Tyw3 A G 3: 154,300,108 (GRCm39) C80R probably damaging Het
Usp24 T C 4: 106,242,621 (GRCm39) V1177A possibly damaging Het
Vmn1r65 A G 7: 6,011,754 (GRCm39) V160A probably damaging Het
Vmn2r104 T A 17: 20,262,146 (GRCm39) H328L probably benign Het
Vmn2r65 A C 7: 84,589,849 (GRCm39) I689S probably damaging Het
Wrn A G 8: 33,731,129 (GRCm39) Y1068H probably damaging Het
Xpo4 C A 14: 57,850,866 (GRCm39) S346I probably benign Het
Zc3h3 T A 15: 75,711,439 (GRCm39) T341S probably benign Het
Zxdc T C 6: 90,347,419 (GRCm39) M260T possibly damaging Het
Other mutations in Rpa1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01296:Rpa1 APN 11 75,203,141 (GRCm39) missense probably damaging 1.00
IGL01347:Rpa1 APN 11 75,198,111 (GRCm39) missense probably damaging 1.00
IGL02976:Rpa1 APN 11 75,203,628 (GRCm39) missense probably damaging 0.99
IGL03169:Rpa1 APN 11 75,192,183 (GRCm39) missense probably damaging 0.97
nonnae UTSW 11 75,205,721 (GRCm39) missense probably damaging 1.00
vomica UTSW 11 75,231,171 (GRCm39) missense possibly damaging 0.89
FR4976:Rpa1 UTSW 11 75,209,345 (GRCm39) small deletion probably benign
PIT4576001:Rpa1 UTSW 11 75,203,984 (GRCm39) missense probably damaging 1.00
R0017:Rpa1 UTSW 11 75,205,687 (GRCm39) missense probably null 1.00
R0017:Rpa1 UTSW 11 75,205,687 (GRCm39) missense probably null 1.00
R0126:Rpa1 UTSW 11 75,209,355 (GRCm39) missense probably benign 0.00
R0240:Rpa1 UTSW 11 75,219,513 (GRCm39) missense probably benign 0.01
R0240:Rpa1 UTSW 11 75,219,513 (GRCm39) missense probably benign 0.01
R0465:Rpa1 UTSW 11 75,203,921 (GRCm39) missense probably damaging 0.99
R0718:Rpa1 UTSW 11 75,209,227 (GRCm39) splice site probably benign
R0973:Rpa1 UTSW 11 75,203,799 (GRCm39) splice site probably null
R1055:Rpa1 UTSW 11 75,193,558 (GRCm39) missense probably damaging 1.00
R1172:Rpa1 UTSW 11 75,203,219 (GRCm39) missense probably damaging 1.00
R1642:Rpa1 UTSW 11 75,203,517 (GRCm39) critical splice donor site probably null
R1883:Rpa1 UTSW 11 75,209,309 (GRCm39) missense probably benign
R1975:Rpa1 UTSW 11 75,197,002 (GRCm39) missense probably damaging 1.00
R5008:Rpa1 UTSW 11 75,204,125 (GRCm39) critical splice donor site probably null
R6083:Rpa1 UTSW 11 75,205,737 (GRCm39) missense probably damaging 1.00
R6161:Rpa1 UTSW 11 75,205,721 (GRCm39) missense probably damaging 1.00
R6187:Rpa1 UTSW 11 75,201,062 (GRCm39) missense probably benign 0.00
R6762:Rpa1 UTSW 11 75,231,171 (GRCm39) missense possibly damaging 0.89
R6828:Rpa1 UTSW 11 75,205,697 (GRCm39) missense probably damaging 1.00
R7044:Rpa1 UTSW 11 75,203,628 (GRCm39) missense probably damaging 0.99
R7331:Rpa1 UTSW 11 75,203,941 (GRCm39) missense probably damaging 0.98
R7798:Rpa1 UTSW 11 75,203,635 (GRCm39) missense probably damaging 0.96
R7890:Rpa1 UTSW 11 75,198,050 (GRCm39) frame shift probably null
R7938:Rpa1 UTSW 11 75,198,050 (GRCm39) frame shift probably null
R8116:Rpa1 UTSW 11 75,193,501 (GRCm39) missense possibly damaging 0.90
R8258:Rpa1 UTSW 11 75,193,550 (GRCm39) missense probably benign 0.03
R8259:Rpa1 UTSW 11 75,193,550 (GRCm39) missense probably benign 0.03
R8837:Rpa1 UTSW 11 75,204,167 (GRCm39) missense possibly damaging 0.70
R9169:Rpa1 UTSW 11 75,200,999 (GRCm39) nonsense probably null
R9789:Rpa1 UTSW 11 75,203,938 (GRCm39) missense probably damaging 0.97
RF018:Rpa1 UTSW 11 75,209,343 (GRCm39) frame shift probably null
Predicted Primers PCR Primer
(F):5'- CCTGCAAAAGAGGCCAAGTC -3'
(R):5'- AGCTGCTTTTGTTTTACCAGAG -3'

Sequencing Primer
(F):5'- AGTCAGGGCAAGCTACTCAGTC -3'
(R):5'- CTTTTGTTTTACCAGAGCTGATAGC -3'
Posted On 2016-07-22