Incidental Mutation 'R2209:Prpf39'
ID 239273
Institutional Source Beutler Lab
Gene Symbol Prpf39
Ensembl Gene ENSMUSG00000035597
Gene Name pre-mRNA processing factor 39
Synonyms Srcs1
MMRRC Submission 040211-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.947) question?
Stock # R2209 (G1)
Quality Score 225
Status Not validated
Chromosome 12
Chromosomal Location 65083107-65110160 bp(+) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to C at 65104689 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000112953 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021332] [ENSMUST00000120580] [ENSMUST00000120580] [ENSMUST00000129956] [ENSMUST00000220730] [ENSMUST00000223315] [ENSMUST00000221166] [ENSMUST00000221913]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000021332
SMART Domains Protein: ENSMUSP00000021332
Gene: ENSMUSG00000020949

DomainStartEndE-ValueType
PDB:2KFV|A 1 73 2e-45 PDB
low complexity region 91 100 N/A INTRINSIC
Pfam:FKBP_C 121 221 3.9e-33 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000120580
SMART Domains Protein: ENSMUSP00000112953
Gene: ENSMUSG00000035597

DomainStartEndE-ValueType
HAT 107 139 3.71e-2 SMART
HAT 141 173 4.39e-4 SMART
HAT 181 216 2.07e0 SMART
HAT 218 251 1.36e2 SMART
low complexity region 277 290 N/A INTRINSIC
Blast:HAT 323 363 6e-18 BLAST
HAT 365 397 3.2e-6 SMART
HAT 398 431 3.21e1 SMART
HAT 505 537 3.63e1 SMART
low complexity region 645 664 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000120580
SMART Domains Protein: ENSMUSP00000112953
Gene: ENSMUSG00000035597

DomainStartEndE-ValueType
HAT 107 139 3.71e-2 SMART
HAT 141 173 4.39e-4 SMART
HAT 181 216 2.07e0 SMART
HAT 218 251 1.36e2 SMART
low complexity region 277 290 N/A INTRINSIC
Blast:HAT 323 363 6e-18 BLAST
HAT 365 397 3.2e-6 SMART
HAT 398 431 3.21e1 SMART
HAT 505 537 3.63e1 SMART
low complexity region 645 664 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000129956
SMART Domains Protein: ENSMUSP00000114713
Gene: ENSMUSG00000035597

DomainStartEndE-ValueType
Blast:HAT 107 139 7e-17 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000157165
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220462
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220729
Predicted Effect probably benign
Transcript: ENSMUST00000220730
Predicted Effect probably benign
Transcript: ENSMUST00000223315
Predicted Effect noncoding transcript
Transcript: ENSMUST00000223167
Predicted Effect probably benign
Transcript: ENSMUST00000221608
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220798
Predicted Effect noncoding transcript
Transcript: ENSMUST00000222154
Predicted Effect probably benign
Transcript: ENSMUST00000220983
Predicted Effect probably benign
Transcript: ENSMUST00000221166
Predicted Effect probably benign
Transcript: ENSMUST00000221913
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220957
Predicted Effect noncoding transcript
Transcript: ENSMUST00000222684
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.3%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
6430548M08Rik A G 8: 120,884,227 (GRCm39) E330G possibly damaging Het
Apob A C 12: 8,057,752 (GRCm39) D2078A probably benign Het
Arhgap21 T A 2: 20,854,331 (GRCm39) Q1681L probably damaging Het
Arsb A G 13: 93,998,609 (GRCm39) T306A probably benign Het
Brpf3 G A 17: 29,047,394 (GRCm39) D1053N probably damaging Het
Cenpf A T 1: 189,384,795 (GRCm39) I2495N probably benign Het
Col12a1 T C 9: 79,599,634 (GRCm39) K840E possibly damaging Het
Cry1 A G 10: 84,982,619 (GRCm39) L269P probably damaging Het
Cyp21a1 C A 17: 35,021,701 (GRCm39) E289* probably null Het
Dcp2 A T 18: 44,538,581 (GRCm39) K215* probably null Het
Dnaaf11 A G 15: 66,321,400 (GRCm39) I247T probably benign Het
Ecm2 A G 13: 49,683,632 (GRCm39) N537D probably damaging Het
Emid1 G A 11: 5,085,407 (GRCm39) T113M probably benign Het
Exoc8 C T 8: 125,622,918 (GRCm39) W483* probably null Het
Fes A T 7: 80,030,031 (GRCm39) N582K probably damaging Het
Flnb G T 14: 7,905,507 (GRCm38) E1086* probably null Het
Flnc T A 6: 29,455,844 (GRCm39) D2058E possibly damaging Het
Gatb G A 3: 85,561,112 (GRCm39) D543N probably benign Het
Gm14412 A G 2: 177,009,229 (GRCm39) V9A probably damaging Het
Gm4884 T C 7: 40,692,745 (GRCm39) V238A possibly damaging Het
Igfbp5 A G 1: 72,913,096 (GRCm39) V68A possibly damaging Het
Igflr1 T A 7: 30,267,222 (GRCm39) I330N probably damaging Het
Il1r2 A G 1: 40,154,298 (GRCm39) T222A probably benign Het
Krt87 T C 15: 101,330,989 (GRCm39) E419G probably benign Het
Lman2 A G 13: 55,499,315 (GRCm39) S187P probably damaging Het
Mrpl38 T C 11: 116,029,288 (GRCm39) E76G possibly damaging Het
Mtx3 A G 13: 92,984,112 (GRCm39) I130V probably benign Het
Naf1 T G 8: 67,313,188 (GRCm39) probably benign Het
Nkx2-1 T G 12: 56,580,293 (GRCm39) M216L probably benign Het
Notch1 C A 2: 26,350,019 (GRCm39) V2374L probably benign Het
Nrxn2 A G 19: 6,543,037 (GRCm39) D1087G probably benign Het
Nudt8 T C 19: 4,051,902 (GRCm39) F171S probably damaging Het
Or5an1 T G 19: 12,261,224 (GRCm39) F271V probably benign Het
Pds5a A T 5: 65,785,357 (GRCm39) C916* probably null Het
Phyhip A T 14: 70,699,334 (GRCm39) N46Y probably damaging Het
Pomt1 A G 2: 32,140,874 (GRCm39) Y502C possibly damaging Het
Prkcg A C 7: 3,352,097 (GRCm39) probably benign Het
Prl8a6 C T 13: 27,619,369 (GRCm39) E118K probably benign Het
Ptprb A G 10: 116,205,262 (GRCm39) H2159R probably damaging Het
Ripor2 A T 13: 24,885,595 (GRCm39) D571V probably damaging Het
Rps19 C T 7: 24,584,552 (GRCm39) L34F probably benign Het
Rusc1 A G 3: 88,996,128 (GRCm39) S145P probably damaging Het
Scn4a T A 11: 106,230,051 (GRCm39) T586S probably damaging Het
Slc7a12 A G 3: 14,546,124 (GRCm39) S90G possibly damaging Het
Specc1l A G 10: 75,082,410 (GRCm39) D619G probably damaging Het
Src A G 2: 157,304,710 (GRCm39) D143G probably benign Het
Sst T C 16: 23,708,558 (GRCm39) N91S probably benign Het
Stxbp5l T A 16: 37,036,398 (GRCm39) I406F probably damaging Het
Thsd1 T A 8: 22,748,887 (GRCm39) I525N probably damaging Het
Ticam2 A T 18: 46,693,467 (GRCm39) F207I probably damaging Het
Tsc22d1 C A 14: 76,656,180 (GRCm39) N31K probably damaging Het
Tspan10 T C 11: 120,336,989 (GRCm39) V253A probably benign Het
Ttc33 A G 15: 5,237,924 (GRCm39) K99R possibly damaging Het
Vmn1r63 T A 7: 5,806,212 (GRCm39) N140I probably damaging Het
Yju2b C T 8: 84,990,498 (GRCm39) V45I probably benign Het
Zbtb25 A G 12: 76,395,903 (GRCm39) *440Q probably null Het
Zfhx4 T A 3: 5,461,978 (GRCm39) C1218S probably damaging Het
Zfp84 T A 7: 29,476,607 (GRCm39) I433N probably damaging Het
Other mutations in Prpf39
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00834:Prpf39 APN 12 65,090,037 (GRCm39) missense probably damaging 0.99
IGL01025:Prpf39 APN 12 65,089,255 (GRCm39) unclassified probably benign
IGL01323:Prpf39 APN 12 65,089,498 (GRCm39) missense possibly damaging 0.70
IGL02346:Prpf39 APN 12 65,104,510 (GRCm39) missense probably benign 0.02
IGL02966:Prpf39 APN 12 65,089,553 (GRCm39) missense probably benign 0.45
IGL03189:Prpf39 APN 12 65,090,076 (GRCm39) nonsense probably null
IGL03357:Prpf39 APN 12 65,108,211 (GRCm39) unclassified probably benign
R0103:Prpf39 UTSW 12 65,102,057 (GRCm39) missense possibly damaging 0.56
R0103:Prpf39 UTSW 12 65,102,057 (GRCm39) missense possibly damaging 0.56
R0328:Prpf39 UTSW 12 65,090,145 (GRCm39) splice site probably benign
R0549:Prpf39 UTSW 12 65,103,030 (GRCm39) missense probably benign 0.05
R0840:Prpf39 UTSW 12 65,094,980 (GRCm39) missense probably benign 0.21
R1248:Prpf39 UTSW 12 65,100,740 (GRCm39) splice site probably benign
R1322:Prpf39 UTSW 12 65,089,436 (GRCm39) missense possibly damaging 0.48
R1481:Prpf39 UTSW 12 65,100,088 (GRCm39) missense probably damaging 1.00
R2232:Prpf39 UTSW 12 65,090,786 (GRCm39) nonsense probably null
R2507:Prpf39 UTSW 12 65,104,589 (GRCm39) missense probably benign 0.36
R2508:Prpf39 UTSW 12 65,104,589 (GRCm39) missense probably benign 0.36
R2959:Prpf39 UTSW 12 65,089,297 (GRCm39) missense probably damaging 1.00
R3117:Prpf39 UTSW 12 65,104,651 (GRCm39) missense possibly damaging 0.79
R3118:Prpf39 UTSW 12 65,104,651 (GRCm39) missense possibly damaging 0.79
R3980:Prpf39 UTSW 12 65,108,231 (GRCm39) unclassified probably benign
R4407:Prpf39 UTSW 12 65,103,040 (GRCm39) missense probably damaging 1.00
R4620:Prpf39 UTSW 12 65,089,337 (GRCm39) missense probably benign
R4926:Prpf39 UTSW 12 65,090,830 (GRCm39) missense possibly damaging 0.90
R5154:Prpf39 UTSW 12 65,095,051 (GRCm39) missense probably benign 0.29
R6248:Prpf39 UTSW 12 65,089,528 (GRCm39) missense probably damaging 1.00
R6334:Prpf39 UTSW 12 65,089,587 (GRCm39) splice site probably null
R6614:Prpf39 UTSW 12 65,089,337 (GRCm39) missense probably benign
R6749:Prpf39 UTSW 12 65,103,048 (GRCm39) missense possibly damaging 0.94
R6944:Prpf39 UTSW 12 65,089,454 (GRCm39) missense probably benign 0.03
R7023:Prpf39 UTSW 12 65,100,074 (GRCm39) missense possibly damaging 0.94
R7503:Prpf39 UTSW 12 65,100,167 (GRCm39) missense probably benign 0.04
R7532:Prpf39 UTSW 12 65,100,145 (GRCm39) missense probably benign 0.00
R7608:Prpf39 UTSW 12 65,100,220 (GRCm39) missense probably benign 0.41
R8286:Prpf39 UTSW 12 65,103,132 (GRCm39) missense probably benign
R8439:Prpf39 UTSW 12 65,102,036 (GRCm39) missense possibly damaging 0.95
R8787:Prpf39 UTSW 12 65,089,555 (GRCm39) missense possibly damaging 0.95
R9101:Prpf39 UTSW 12 65,090,078 (GRCm39) missense probably damaging 1.00
R9153:Prpf39 UTSW 12 65,106,671 (GRCm39) missense probably damaging 0.99
R9448:Prpf39 UTSW 12 65,108,034 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- TCAGGAGAACACAAAGTTATACCTC -3'
(R):5'- ACCTTCACGTGTATCTCATAGC -3'

Sequencing Primer
(F):5'- CAGTTGTGACCTCAAGCAA -3'
(R):5'- ACATGAGTAAGCCTGGTTACCTGC -3'
Posted On 2014-10-15