Incidental Mutation 'R2163:Rpap3'
ID 235317
Institutional Source Beutler Lab
Gene Symbol Rpap3
Ensembl Gene ENSMUSG00000022466
Gene Name RNA polymerase II associated protein 3
Synonyms D15Ertd682e, 2310042P20Rik
MMRRC Submission 040166-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2163 (G1)
Quality Score 176
Status Validated
Chromosome 15
Chromosomal Location 97572978-97603706 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 97578229 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Phenylalanine at position 562 (Y562F)
Ref Sequence ENSEMBL: ENSMUSP00000023104 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023104]
AlphaFold Q9D706
Predicted Effect possibly damaging
Transcript: ENSMUST00000023104
AA Change: Y562F

PolyPhen 2 Score 0.707 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000023104
Gene: ENSMUSG00000022466
AA Change: Y562F

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229008
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229109
Meta Mutation Damage Score 0.0795 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.6%
  • 20x: 95.9%
Validation Efficiency 97% (76/78)
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: 77 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930578I07Rik C A 14: 67,175,997 (GRCm39) T64K unknown Het
Ablim2 T C 5: 35,959,697 (GRCm39) probably benign Het
Acp4 T C 7: 43,905,400 (GRCm39) D107G probably damaging Het
Adamts2 T A 11: 50,679,632 (GRCm39) C871S probably benign Het
Adamts3 A G 5: 89,856,577 (GRCm39) V332A probably damaging Het
Alkal1 C T 1: 6,459,736 (GRCm39) T104M probably benign Het
Astn1 A G 1: 158,329,720 (GRCm39) S192G probably damaging Het
Axdnd1 A C 1: 156,219,573 (GRCm39) V337G probably damaging Het
Baiap2l2 T C 15: 79,143,395 (GRCm39) D481G possibly damaging Het
Cacna2d1 C T 5: 16,567,317 (GRCm39) T964I probably damaging Het
Carf T C 1: 60,186,645 (GRCm39) probably benign Het
Catsper2 T C 2: 121,230,656 (GRCm39) D295G probably damaging Het
Cdh1 A G 8: 107,375,713 (GRCm39) T84A probably benign Het
Chd8 T A 14: 52,436,275 (GRCm39) H2508L possibly damaging Het
Chl1 A T 6: 103,688,192 (GRCm39) T284S probably damaging Het
Chtop A T 3: 90,409,518 (GRCm39) M125K probably benign Het
Col14a1 T A 15: 55,308,041 (GRCm39) probably benign Het
Cplane1 T A 15: 8,232,735 (GRCm39) probably null Het
Cyp2b10 A T 7: 25,624,810 (GRCm39) probably benign Het
Cyp2c70 G A 19: 40,149,163 (GRCm39) H328Y possibly damaging Het
Dcbld1 A G 10: 52,162,452 (GRCm39) T77A probably damaging Het
Dnah6 A T 6: 73,066,729 (GRCm39) probably null Het
Efhd1 A T 1: 87,217,195 (GRCm39) D104V probably damaging Het
Eif5b A T 1: 38,087,875 (GRCm39) D957V probably benign Het
Eps15 T A 4: 109,227,866 (GRCm39) S549R probably damaging Het
Fbxo3 C A 2: 103,885,330 (GRCm39) H400N probably benign Het
Fcer1a A G 1: 173,050,264 (GRCm39) V86A probably damaging Het
Fh1 A G 1: 175,442,406 (GRCm39) M148T possibly damaging Het
Foxc1 C A 13: 31,992,586 (GRCm39) H466N unknown Het
Gadl1 T A 9: 115,778,626 (GRCm39) I180N possibly damaging Het
Gm10801 G C 2: 98,494,352 (GRCm39) R143T possibly damaging Het
Gm21718 T C 14: 51,555,223 (GRCm39) noncoding transcript Het
Hivep2 T A 10: 14,003,970 (GRCm39) Y189* probably null Het
Hoxd13 T A 2: 74,499,413 (GRCm39) S254T possibly damaging Het
Hspd1 A G 1: 55,117,697 (GRCm39) probably benign Het
Il1r1 A G 1: 40,334,023 (GRCm39) M198V probably benign Het
Katnal1 T A 5: 148,825,746 (GRCm39) I362F probably damaging Het
Muc2 CGTG CGTGTG 7: 141,699,185 (GRCm38) probably null Het
Mybpc1 T C 10: 88,376,804 (GRCm39) probably benign Het
Mycbp2 A G 14: 103,407,291 (GRCm39) probably null Het
Nell2 G T 15: 95,327,859 (GRCm39) N301K probably damaging Het
Nenf T A 1: 191,042,132 (GRCm39) D108V probably damaging Het
Nfkbiz T C 16: 55,638,581 (GRCm39) N293S probably benign Het
Nipbl T C 15: 8,366,403 (GRCm39) K1229E probably damaging Het
Nlrp4a T C 7: 26,152,822 (GRCm39) F631L probably benign Het
Nrp1 T A 8: 129,224,352 (GRCm39) V705E probably damaging Het
Nsf G C 11: 103,754,159 (GRCm39) A459G possibly damaging Het
Or1af1 A G 2: 37,110,089 (GRCm39) E196G probably damaging Het
Or5w10 A G 2: 87,375,238 (GRCm39) S217P probably damaging Het
Pdia4 C T 6: 47,775,341 (GRCm39) D490N possibly damaging Het
Pinlyp T A 7: 24,241,226 (GRCm39) Y192F probably benign Het
Pkd2 T C 5: 104,603,543 (GRCm39) probably benign Het
Ppara A G 15: 85,685,247 (GRCm39) K399E probably benign Het
Ppp4r2 C A 6: 100,842,047 (GRCm39) N169K probably damaging Het
Prom1 T A 5: 44,171,505 (GRCm39) E632V possibly damaging Het
Rsph14 T A 10: 74,793,611 (GRCm39) K263N probably damaging Het
Sanbr T C 11: 23,526,826 (GRCm39) probably benign Het
Scn11a T G 9: 119,584,091 (GRCm39) D1508A probably damaging Het
Scn7a T C 2: 66,506,300 (GRCm39) T1530A probably damaging Het
Sec14l1 T A 11: 117,034,108 (GRCm39) probably null Het
Slc4a4 A G 5: 89,362,435 (GRCm39) I840V probably damaging Het
Slco1a8 G A 6: 141,926,664 (GRCm39) T554I possibly damaging Het
Slco1c1 T A 6: 141,505,478 (GRCm39) V419D probably benign Het
Sltm T A 9: 70,498,964 (GRCm39) F1013I probably damaging Het
Spam1 A G 6: 24,796,846 (GRCm39) K266E probably benign Het
Syt15 A G 14: 33,948,073 (GRCm39) E306G probably benign Het
Tap1 A T 17: 34,408,447 (GRCm39) probably null Het
Tbc1d16 G C 11: 119,045,904 (GRCm39) probably benign Het
Tex47 T C 5: 7,355,022 (GRCm39) Y68H probably damaging Het
Ttn T C 2: 76,642,845 (GRCm39) T13264A probably damaging Het
Ttn A T 2: 76,641,587 (GRCm39) L5176Q possibly damaging Het
Ubxn2a A T 12: 4,935,757 (GRCm39) F131Y probably damaging Het
Usp40 T C 1: 87,923,580 (GRCm39) probably benign Het
Vmn1r170 T C 7: 23,306,462 (GRCm39) L288P probably damaging Het
Vmn1r175 A G 7: 23,508,352 (GRCm39) Y92H probably benign Het
Wdpcp G T 11: 21,835,015 (GRCm39) E673* probably null Het
Zfr T A 15: 12,162,309 (GRCm39) L820I probably damaging 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
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
YA93:Rpap3 UTSW 15 97,591,114 (GRCm39) missense possibly damaging 0.86
Predicted Primers PCR Primer
(F):5'- ACAGCTCACTTCCCGGATAG -3'
(R):5'- CCGATGTTAGGATTCCCCTTGC -3'

Sequencing Primer
(F):5'- TTCCCGGATAGAAAACCAGGATTC -3'
(R):5'- TGGCTAATGCTCGGAAATCC -3'
Posted On 2014-10-01