Incidental Mutation 'R4517:Pcf11'
ID 332949
Institutional Source Beutler Lab
Gene Symbol Pcf11
Ensembl Gene ENSMUSG00000041328
Gene Name PCF11 cleavage and polyadenylation factor subunit
Synonyms 5730417B17Rik, 2500001H09Rik
MMRRC Submission 041761-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.961) question?
Stock # R4517 (G1)
Quality Score 225
Status Validated
Chromosome 7
Chromosomal Location 92292751-92319142 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 92295696 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 1451 (Y1451C)
Ref Sequence ENSEMBL: ENSMUSP00000113717 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000119954]
AlphaFold G3X9Z4
Predicted Effect probably damaging
Transcript: ENSMUST00000119954
AA Change: Y1451C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000113717
Gene: ENSMUSG00000041328
AA Change: Y1451C

DomainStartEndE-ValueType
RPR 17 139 6.74e-43 SMART
low complexity region 173 194 N/A INTRINSIC
coiled coil region 202 243 N/A INTRINSIC
low complexity region 355 380 N/A INTRINSIC
low complexity region 421 434 N/A INTRINSIC
low complexity region 471 513 N/A INTRINSIC
low complexity region 793 819 N/A INTRINSIC
low complexity region 833 853 N/A INTRINSIC
internal_repeat_1 854 931 1.77e-14 PROSPERO
low complexity region 932 948 N/A INTRINSIC
internal_repeat_1 969 1105 1.77e-14 PROSPERO
low complexity region 1159 1178 N/A INTRINSIC
low complexity region 1294 1315 N/A INTRINSIC
low complexity region 1445 1458 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000148539
Predicted Effect unknown
Transcript: ENSMUST00000151177
AA Change: Y1373C
SMART Domains Protein: ENSMUSP00000115278
Gene: ENSMUSG00000041328
AA Change: Y1373C

DomainStartEndE-ValueType
coiled coil region 1 34 N/A INTRINSIC
low complexity region 147 172 N/A INTRINSIC
low complexity region 213 226 N/A INTRINSIC
low complexity region 263 305 N/A INTRINSIC
low complexity region 716 742 N/A INTRINSIC
low complexity region 756 776 N/A INTRINSIC
internal_repeat_1 777 854 3.34e-13 PROSPERO
low complexity region 855 871 N/A INTRINSIC
internal_repeat_1 892 1028 3.34e-13 PROSPERO
low complexity region 1082 1101 N/A INTRINSIC
low complexity region 1217 1238 N/A INTRINSIC
low complexity region 1368 1381 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000182265
Predicted Effect noncoding transcript
Transcript: ENSMUST00000192772
Meta Mutation Damage Score 0.2960 question?
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.5%
  • 10x: 96.7%
  • 20x: 93.6%
Validation Efficiency 95% (39/41)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene binds to CLP1 to form pre-mRNA cleavage factor IIm. The encoded protein is necessary for efficient Pol II transcription termination and may be involved in degradation of the 3' product of polyA site cleavage. [provided by RefSeq, Oct 2016]
Allele List at MGI

All alleles(13) : Targeted, other(2) Gene trapped(11)

Other mutations in this stock
Total: 32 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ank A G 15: 27,562,835 (GRCm39) H181R possibly damaging Het
B4galnt4 A G 7: 140,647,635 (GRCm39) K408E probably damaging Het
Cd209a T A 8: 3,795,525 (GRCm39) D123V probably damaging Het
Cyp4f37 A G 17: 32,850,566 (GRCm39) I340V probably benign Het
Echs1 A G 7: 139,692,409 (GRCm39) S113P possibly damaging Het
Fap T C 2: 62,361,059 (GRCm39) I391V probably benign Het
Glb1l C T 1: 75,185,347 (GRCm39) C121Y probably damaging Het
Glod4 T A 11: 76,134,397 (GRCm39) D25V probably damaging Het
Gpc5 T A 14: 115,789,651 (GRCm39) N508K possibly damaging Het
H2-M10.3 C T 17: 36,678,722 (GRCm39) probably null Het
Ibsp C A 5: 104,453,863 (GRCm39) S67* probably null Het
Ifit1bl2 C T 19: 34,607,164 (GRCm39) probably benign Het
Iqgap2 A G 13: 95,800,569 (GRCm39) probably null Het
Kcnma1 A G 14: 23,387,097 (GRCm39) S982P probably damaging Het
Kif5b T C 18: 6,213,272 (GRCm39) S707G probably benign Het
Lrrk2 A G 15: 91,589,323 (GRCm39) I437V probably benign Het
Mapkbp1 T C 2: 119,855,545 (GRCm39) probably benign Het
Mcu T C 10: 59,303,456 (GRCm39) Y127C probably damaging Het
Mlst8 T C 17: 24,695,031 (GRCm39) Y284C probably damaging Het
Nr2f2 T G 7: 70,007,870 (GRCm39) N204T probably benign Het
Or13a26 A G 7: 140,285,004 (GRCm39) Y280C probably damaging Het
Or7a42 T A 10: 78,791,877 (GRCm39) Y279* probably null Het
Pabir3 G A X: 52,382,376 (GRCm39) R94H possibly damaging Het
Plekhn1 T C 4: 156,309,988 (GRCm39) S109G probably damaging Het
Rttn T C 18: 89,047,097 (GRCm39) S920P probably damaging Het
Rufy4 T C 1: 74,186,822 (GRCm39) C537R probably damaging Het
Tas2r135 A T 6: 42,383,013 (GRCm39) H184L probably benign Het
Tmem38a C T 8: 73,326,005 (GRCm39) P20S possibly damaging Het
Ubqlnl C T 7: 103,798,925 (GRCm39) V191M probably benign Het
Vmn2r102 A G 17: 19,901,475 (GRCm39) Y534C probably damaging Het
Wdr62 A G 7: 29,969,683 (GRCm39) V259A probably damaging Het
Whrn A G 4: 63,379,517 (GRCm39) probably null Het
Other mutations in Pcf11
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01160:Pcf11 APN 7 92,310,894 (GRCm39) missense possibly damaging 0.51
IGL02439:Pcf11 APN 7 92,311,049 (GRCm39) missense possibly damaging 0.93
IGL02658:Pcf11 APN 7 92,296,254 (GRCm39) missense probably damaging 1.00
IGL02702:Pcf11 APN 7 92,310,826 (GRCm39) missense possibly damaging 0.76
3-1:Pcf11 UTSW 7 92,307,726 (GRCm39) missense probably damaging 1.00
R0015:Pcf11 UTSW 7 92,307,525 (GRCm39) missense probably benign 0.28
R0015:Pcf11 UTSW 7 92,307,525 (GRCm39) missense probably benign 0.28
R0078:Pcf11 UTSW 7 92,318,767 (GRCm39) missense possibly damaging 0.90
R0110:Pcf11 UTSW 7 92,307,039 (GRCm39) missense probably damaging 1.00
R0373:Pcf11 UTSW 7 92,310,423 (GRCm39) missense probably benign
R0450:Pcf11 UTSW 7 92,307,039 (GRCm39) missense probably damaging 1.00
R1717:Pcf11 UTSW 7 92,312,793 (GRCm39) missense probably benign 0.00
R1952:Pcf11 UTSW 7 92,310,546 (GRCm39) missense probably damaging 1.00
R1965:Pcf11 UTSW 7 92,310,809 (GRCm39) missense probably benign
R2045:Pcf11 UTSW 7 92,311,087 (GRCm39) missense probably damaging 1.00
R2245:Pcf11 UTSW 7 92,315,080 (GRCm39) unclassified probably benign
R3824:Pcf11 UTSW 7 92,308,828 (GRCm39) intron probably benign
R4439:Pcf11 UTSW 7 92,307,225 (GRCm39) missense probably damaging 0.99
R4671:Pcf11 UTSW 7 92,306,737 (GRCm39) missense possibly damaging 0.62
R4674:Pcf11 UTSW 7 92,308,985 (GRCm39) intron probably benign
R4675:Pcf11 UTSW 7 92,308,985 (GRCm39) intron probably benign
R4732:Pcf11 UTSW 7 92,308,041 (GRCm39) missense probably benign 0.33
R4733:Pcf11 UTSW 7 92,308,041 (GRCm39) missense probably benign 0.33
R4758:Pcf11 UTSW 7 92,310,383 (GRCm39) missense probably damaging 0.97
R4985:Pcf11 UTSW 7 92,311,110 (GRCm39) missense probably benign 0.01
R5041:Pcf11 UTSW 7 92,307,613 (GRCm39) missense probably benign 0.00
R5248:Pcf11 UTSW 7 92,310,699 (GRCm39) missense probably damaging 1.00
R5688:Pcf11 UTSW 7 92,308,016 (GRCm39) missense possibly damaging 0.92
R5814:Pcf11 UTSW 7 92,306,922 (GRCm39) missense probably benign 0.00
R6240:Pcf11 UTSW 7 92,295,710 (GRCm39) missense probably damaging 1.00
R6327:Pcf11 UTSW 7 92,308,817 (GRCm39) intron probably benign
R6615:Pcf11 UTSW 7 92,307,090 (GRCm39) missense probably damaging 0.96
R6795:Pcf11 UTSW 7 92,306,786 (GRCm39) missense probably benign 0.04
R6896:Pcf11 UTSW 7 92,298,759 (GRCm39) missense probably damaging 0.99
R6902:Pcf11 UTSW 7 92,307,507 (GRCm39) missense probably damaging 0.99
R7030:Pcf11 UTSW 7 92,306,886 (GRCm39) missense probably benign 0.21
R7135:Pcf11 UTSW 7 92,306,524 (GRCm39) missense probably benign 0.05
R7162:Pcf11 UTSW 7 92,313,221 (GRCm39) missense probably damaging 0.97
R7210:Pcf11 UTSW 7 92,312,684 (GRCm39) missense probably benign
R7243:Pcf11 UTSW 7 92,309,268 (GRCm39) missense probably damaging 1.00
R7362:Pcf11 UTSW 7 92,302,453 (GRCm39) missense possibly damaging 0.83
R7876:Pcf11 UTSW 7 92,310,534 (GRCm39) missense probably damaging 1.00
R8208:Pcf11 UTSW 7 92,298,731 (GRCm39) missense probably damaging 1.00
R8212:Pcf11 UTSW 7 92,308,706 (GRCm39) missense probably damaging 0.97
R8515:Pcf11 UTSW 7 92,307,998 (GRCm39) missense possibly damaging 0.92
R8534:Pcf11 UTSW 7 92,302,432 (GRCm39) missense probably benign 0.00
R8907:Pcf11 UTSW 7 92,302,451 (GRCm39) missense probably benign 0.00
R9307:Pcf11 UTSW 7 92,306,534 (GRCm39) missense possibly damaging 0.81
R9585:Pcf11 UTSW 7 92,311,006 (GRCm39) missense probably benign 0.01
R9648:Pcf11 UTSW 7 92,307,318 (GRCm39) missense probably damaging 0.99
R9780:Pcf11 UTSW 7 92,313,313 (GRCm39) missense possibly damaging 0.63
R9781:Pcf11 UTSW 7 92,297,228 (GRCm39) missense possibly damaging 0.50
Predicted Primers PCR Primer
(F):5'- ATGGTTGCTAGAATCCCTCCAAAG -3'
(R):5'- GGTTGGATGCCATCAGTGAC -3'

Sequencing Primer
(F):5'- GTTGCTAGAATCCCTCCAAAGGAAAC -3'
(R):5'- GGATGCCATCAGTGACTAATATAGTG -3'
Posted On 2015-08-18