Incidental Mutation 'YA93:Rpap3'
ID 86
Institutional Source Beutler Lab
Gene Symbol Rpap3
Ensembl Gene ENSMUSG00000022466
Gene Name RNA polymerase II associated protein 3
Synonyms D15Ertd682e, 2310042P20Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # YA93 of strain inept
Quality Score
Status Validated
Chromosome 15
Chromosomal Location 97572978-97603706 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 97591114 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Valine at position 241 (E241V)
Ref Sequence ENSEMBL: ENSMUSP00000023104 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023104]
AlphaFold Q9D706
Predicted Effect possibly damaging
Transcript: ENSMUST00000023104
AA Change: E241V

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000023104
Gene: ENSMUSG00000022466
AA Change: E241V

DomainStartEndE-ValueType
coiled coil region 9 45 N/A INTRINSIC
low complexity region 63 78 N/A INTRINSIC
low complexity region 114 125 N/A INTRINSIC
TPR 134 167 1.12e-7 SMART
TPR 168 201 2.07e1 SMART
TPR 202 235 2.36e-6 SMART
low complexity region 252 273 N/A INTRINSIC
TPR 284 317 6.58e-5 SMART
TPR 318 351 4.45e-2 SMART
TPR 352 385 3.87e-2 SMART
Pfam:RPAP3_C 540 631 3.8e-26 PFAM
Meta Mutation Damage Score 0.2403 question?
Coding Region Coverage
  • 1x: 90.4%
  • 3x: 81.3%
Validation Efficiency 88% (101/115)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an RNA polymerase II-associated protein. The encoded protein may function in transcriptional regulation and may also regulate apoptosis. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]
Allele List at MGI

All alleles(10) : Targeted, other(1) Gene trapped(9)

Other mutations in this stock
Total: 15 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Arhgef4 C T 1: 34,771,298 (GRCm39) R1202W probably benign Het
B4galnt4 T A 7: 140,647,324 (GRCm39) I358K possibly damaging Homo
Ccdc168 A G 1: 44,104,245 (GRCm39) probably benign Het
Chodl A G 16: 78,738,170 (GRCm39) H46R probably benign Homo
Cubn C A 2: 13,388,803 (GRCm39) R1468L probably benign Het
Dlg5 G A 14: 24,205,201 (GRCm39) probably benign Het
Dntt A C 19: 41,041,626 (GRCm39) M437L probably benign Het
Grsf1 G A 5: 88,821,594 (GRCm39) P157S probably damaging Het
Lct C T 1: 128,229,057 (GRCm39) G812D probably damaging Het
Osbpl5 T A 7: 143,247,607 (GRCm39) I720F probably benign Homo
Pbld2 T A 10: 62,890,224 (GRCm39) Y211N possibly damaging Het
Peg3 T A 7: 6,714,646 (GRCm39) E192V probably damaging Het
Ptbp3 T C 4: 59,524,413 (GRCm39) T38A possibly damaging Het
Scara3 C A 14: 66,168,398 (GRCm39) M406I probably damaging Het
Serpinf2 C A 11: 75,323,510 (GRCm39) V399L probably benign Het
Other mutations in Rpap3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01835:Rpap3 APN 15 97,601,120 (GRCm39) missense possibly damaging 0.85
IGL02714:Rpap3 APN 15 97,594,458 (GRCm39) missense possibly damaging 0.93
IGL03409:Rpap3 APN 15 97,579,620 (GRCm39) missense possibly damaging 0.46
R0095:Rpap3 UTSW 15 97,578,417 (GRCm39) splice site probably benign
R0847:Rpap3 UTSW 15 97,601,082 (GRCm39) critical splice donor site probably null
R1496:Rpap3 UTSW 15 97,584,364 (GRCm39) missense possibly damaging 0.86
R1562:Rpap3 UTSW 15 97,592,098 (GRCm39) missense possibly damaging 0.86
R1603:Rpap3 UTSW 15 97,599,002 (GRCm39) missense possibly damaging 0.53
R1801:Rpap3 UTSW 15 97,592,090 (GRCm39) missense possibly damaging 0.73
R2163:Rpap3 UTSW 15 97,578,229 (GRCm39) missense possibly damaging 0.71
R4969:Rpap3 UTSW 15 97,584,407 (GRCm39) missense probably benign
R5226:Rpap3 UTSW 15 97,601,104 (GRCm39) missense possibly damaging 0.53
R6610:Rpap3 UTSW 15 97,586,049 (GRCm39) missense probably benign 0.24
R6613:Rpap3 UTSW 15 97,579,722 (GRCm39) critical splice acceptor site probably null
R7040:Rpap3 UTSW 15 97,576,993 (GRCm39) missense possibly damaging 0.51
R7429:Rpap3 UTSW 15 97,586,031 (GRCm39) missense possibly damaging 0.96
R7430:Rpap3 UTSW 15 97,586,031 (GRCm39) missense possibly damaging 0.96
R7829:Rpap3 UTSW 15 97,579,589 (GRCm39) missense probably benign 0.02
R7853:Rpap3 UTSW 15 97,576,299 (GRCm39) missense possibly damaging 0.92
R8223:Rpap3 UTSW 15 97,589,185 (GRCm39) missense probably benign 0.02
R8366:Rpap3 UTSW 15 97,579,548 (GRCm39) missense probably benign 0.18
R8897:Rpap3 UTSW 15 97,585,998 (GRCm39) missense probably benign 0.02
R9043:Rpap3 UTSW 15 97,584,443 (GRCm39) missense possibly damaging 0.86
R9144:Rpap3 UTSW 15 97,589,184 (GRCm39) missense possibly damaging 0.68
R9453:Rpap3 UTSW 15 97,579,641 (GRCm39) missense
R9530:Rpap3 UTSW 15 97,579,655 (GRCm39) missense probably benign
Nature of Mutation

DNA sequencing using the SOLiD technique identified an A to T transversion at position 810 of the Rpap3 transcript in exon 7 of 17 total exons.  The mutated nucleotide causes a glutamic acid to valine substitution at amino acid 241 of the encoded protein. The mutation has been confirmed by DNA sequencing using the Sanger method (Figure 1).

Protein Function and Prediction
The Rpap3 gene encodes a 660 amino acid protein that belongs to the RPAP3 (RNA polymerase II-associated protein) family. RPAP3 forms an interface between the RNA polymerase II enzyme and chaperone/scaffolding protein, suggesting that it is required to connect RNA polymerase II to regulators of protein complex formation. The protein contains seven TPRs (tetratrico peptide repeats) at amino acids 8-41, 134-167, 169-201, 202, 235, 284-317, 319-351, and 352-385. These repeats mediate protein-protein interactions and the assembly of multiprotein complexes (Uniprot Q9D706). 
 
The E241V change is predicted to be probably damaging by the PolyPhen program.
Posted On 2010-03-02