Incidental Mutation 'R0549:Prpf39'
ID 45037
Institutional Source Beutler Lab
Gene Symbol Prpf39
Ensembl Gene ENSMUSG00000035597
Gene Name pre-mRNA processing factor 39
Synonyms Srcs1
MMRRC Submission 038741-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.947) question?
Stock # R0549 (G1)
Quality Score 225
Status Validated
Chromosome 12
Chromosomal Location 65083107-65110160 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 65103030 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 435 (I435F)
Ref Sequence ENSEMBL: ENSMUSP00000112953 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000120580] [ENSMUST00000129956] [ENSMUST00000223315]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000120580
AA Change: I435F

PolyPhen 2 Score 0.047 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000112953
Gene: ENSMUSG00000035597
AA Change: I435F

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 noncoding transcript
Transcript: ENSMUST00000220798
Predicted Effect probably benign
Transcript: ENSMUST00000223315
Predicted Effect noncoding transcript
Transcript: ENSMUST00000222154
Meta Mutation Damage Score 0.0845 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 96.9%
  • 20x: 94.3%
Validation Efficiency 96% (48/50)
Allele List at MGI
Other mutations in this stock
Total: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc10 A G 17: 46,633,216 (GRCm39) F498L probably damaging Het
Adamts6 A T 13: 104,433,763 (GRCm39) D64V possibly damaging Het
Agbl2 T C 2: 90,620,187 (GRCm39) probably benign Het
Angptl3 A G 4: 98,919,692 (GRCm39) S151G probably benign Het
Arhgap39 C T 15: 76,619,086 (GRCm39) D833N probably damaging Het
C4b G T 17: 34,954,389 (GRCm39) L927I probably damaging Het
Ccl3 T C 11: 83,539,162 (GRCm39) T66A probably damaging Het
Cdh20 T C 1: 110,036,674 (GRCm39) L618P probably damaging Het
Cfap65 T C 1: 74,957,603 (GRCm39) T989A probably benign Het
Cfhr4 A T 1: 139,667,226 (GRCm39) D377E probably damaging Het
Cnpy4 T C 5: 138,185,899 (GRCm39) F18S possibly damaging Het
Col6a5 A G 9: 105,781,778 (GRCm39) probably benign Het
Dppa2 G A 16: 48,139,034 (GRCm39) R289H probably benign Het
Evx2 T C 2: 74,489,478 (GRCm39) T96A probably benign Het
Frmd4a A G 2: 4,608,778 (GRCm39) E577G possibly damaging Het
Gcgr G A 11: 120,427,387 (GRCm39) G166S probably benign Het
Gm5316 T C 6: 122,877,150 (GRCm39) noncoding transcript Het
Gria1 G A 11: 57,119,799 (GRCm39) R292Q probably damaging Het
Hars2 T A 18: 36,919,261 (GRCm39) probably null Het
Hkdc1 T A 10: 62,236,019 (GRCm39) T508S probably benign Het
Kif2b A T 11: 91,467,410 (GRCm39) I291N probably damaging Het
Lmbrd1 A T 1: 24,784,001 (GRCm39) T377S probably benign Het
Lrrc28 A G 7: 67,278,090 (GRCm39) probably benign Het
Mmp3 A T 9: 7,455,638 (GRCm39) N463I probably benign Het
Myh6 A G 14: 55,196,065 (GRCm39) F578S probably damaging Het
Ncbp1 T A 4: 46,168,476 (GRCm39) M608K possibly damaging Het
Nf1 T C 11: 79,359,597 (GRCm39) F1412L probably damaging Het
Nlrp5 T A 7: 23,141,227 (GRCm39) W1083R probably damaging Het
Nrsn1 T C 13: 25,446,241 (GRCm39) Y45C probably benign Het
Or3a1b T G 11: 74,012,301 (GRCm39) M62R probably damaging Het
Osbpl7 G T 11: 96,958,368 (GRCm39) R881L probably damaging Het
Papss1 A G 3: 131,324,974 (GRCm39) E456G possibly damaging Het
Pbxip1 T A 3: 89,350,899 (GRCm39) probably benign Het
Pcca A G 14: 122,875,789 (GRCm39) probably benign Het
Pde1a T A 2: 79,695,414 (GRCm39) N511I probably damaging Het
Rnf213 C T 11: 119,355,908 (GRCm39) T4117M probably damaging Het
Sel1l2 A T 2: 140,107,802 (GRCm39) M216K probably damaging Het
Sidt2 A G 9: 45,864,417 (GRCm39) probably null Het
Sirt3 A T 7: 140,449,400 (GRCm39) probably null Het
Smpd4 T C 16: 17,457,176 (GRCm39) V378A probably benign Het
Svil T A 18: 5,064,566 (GRCm39) S642T possibly damaging Het
Tcp10a A G 17: 7,593,950 (GRCm39) K92E probably benign Het
Tmem144 T C 3: 79,730,051 (GRCm39) D233G probably damaging Het
Tnfrsf21 C T 17: 43,349,104 (GRCm39) H239Y probably benign Het
Tnik T C 3: 28,625,069 (GRCm39) S335P possibly damaging Het
Ush2a T C 1: 188,679,150 (GRCm39) L4786P probably damaging Het
Utp11 A T 4: 124,579,872 (GRCm39) probably benign Het
Vmn1r67 A G 7: 10,181,641 (GRCm39) N241D probably damaging Het
Vmn2r11 A T 5: 109,199,963 (GRCm39) C497S possibly 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
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
R2209:Prpf39 UTSW 12 65,104,689 (GRCm39) critical splice donor site probably null
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'- TTTAGCACAGGGTGGAGTTACAGGA -3'
(R):5'- AGACCAAATCTTTCATCACAGTTGCCA -3'

Sequencing Primer
(F):5'- ATTGTTTCCTTGCCATATCCTAAGAG -3'
(R):5'- CTTTCATCACAGTTGCCAAAGGG -3'
Posted On 2013-06-11