Incidental Mutation 'R0449:Ints11'
ID 39508
Institutional Source Beutler Lab
Gene Symbol Ints11
Ensembl Gene ENSMUSG00000029034
Gene Name integrator complex subunit 11
Synonyms Cpsf3l, 2410006F12Rik
MMRRC Submission 038649-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0449 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 155954006-155973561 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 155972405 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Leucine at position 463 (R463L)
Ref Sequence ENSEMBL: ENSMUSP00000030901 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030901] [ENSMUST00000079031] [ENSMUST00000097737] [ENSMUST00000105584] [ENSMUST00000120794] [ENSMUST00000156460]
AlphaFold Q9CWS4
Predicted Effect probably benign
Transcript: ENSMUST00000030901
AA Change: R463L

PolyPhen 2 Score 0.173 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000030901
Gene: ENSMUSG00000029034
AA Change: R463L

DomainStartEndE-ValueType
Lactamase_B 16 233 3.38e-17 SMART
Beta-Casp 245 363 6.94e-37 SMART
Pfam:RMMBL 376 418 1.1e-16 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000079031
SMART Domains Protein: ENSMUSP00000078040
Gene: ENSMUSG00000029033

DomainStartEndE-ValueType
low complexity region 17 31 N/A INTRINSIC
PH 265 361 6.35e-16 SMART
low complexity region 377 391 N/A INTRINSIC
ArfGap 399 521 4.62e-56 SMART
low complexity region 554 566 N/A INTRINSIC
low complexity region 601 617 N/A INTRINSIC
low complexity region 628 650 N/A INTRINSIC
low complexity region 669 686 N/A INTRINSIC
ANK 696 725 3.91e-3 SMART
ANK 729 758 2.43e1 SMART
low complexity region 781 796 N/A INTRINSIC
low complexity region 797 809 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000097737
SMART Domains Protein: ENSMUSP00000095344
Gene: ENSMUSG00000051557

DomainStartEndE-ValueType
Pfam:PseudoU_synth_1 16 124 2.5e-12 PFAM
Pfam:PseudoU_synth_1 168 285 1.1e-17 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000105584
SMART Domains Protein: ENSMUSP00000101209
Gene: ENSMUSG00000029033

DomainStartEndE-ValueType
Pfam:BAR_3 3 236 4.1e-95 PFAM
PH 269 365 6.35e-16 SMART
low complexity region 381 395 N/A INTRINSIC
ArfGap 403 525 4.62e-56 SMART
low complexity region 558 570 N/A INTRINSIC
low complexity region 605 621 N/A INTRINSIC
low complexity region 632 654 N/A INTRINSIC
low complexity region 673 690 N/A INTRINSIC
ANK 700 729 3.91e-3 SMART
ANK 733 762 2.43e1 SMART
low complexity region 785 800 N/A INTRINSIC
low complexity region 801 813 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000120794
AA Change: R441L

PolyPhen 2 Score 0.095 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000112656
Gene: ENSMUSG00000029034
AA Change: R441L

DomainStartEndE-ValueType
Lactamase_B 16 211 6.42e-9 SMART
Beta-Casp 223 341 6.94e-37 SMART
Pfam:RMMBL 354 396 3.6e-16 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000123504
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137726
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130146
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132632
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134678
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135844
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131168
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126582
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142724
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142566
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150446
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129637
Predicted Effect probably benign
Transcript: ENSMUST00000156460
SMART Domains Protein: ENSMUSP00000118803
Gene: ENSMUSG00000029034

DomainStartEndE-ValueType
SCOP:d1smla_ 1 66 7e-7 SMART
PDB:2I7V|A 3 38 1e-9 PDB
Blast:Lactamase_B 16 66 4e-30 BLAST
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.7%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The Integrator complex contains at least 12 subunits and associates with the C-terminal domain of RNA polymerase II large subunit (POLR2A; MIM 180660) and mediates the 3-prime end processing of small nuclear RNAs U1 (RNU1; MIM 180680) and U2 (RNU2; MIM 180690). INTS11, or CPSF3L, is the catalytic subunit of the Integrator complex (Baillat et al., 2005 [PubMed 16239144]).[supplied by OMIM, Mar 2008]
Allele List at MGI
Other mutations in this stock
Total: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb4 A T 5: 8,989,885 (GRCm39) R813* probably null Het
Accsl T A 2: 93,696,419 (GRCm39) I60F probably benign Het
Adam29 C T 8: 56,325,716 (GRCm39) G246D probably benign Het
Ankrd13c A G 3: 157,697,351 (GRCm39) I319V probably benign Het
Bag6 T G 17: 35,360,442 (GRCm39) V327G probably damaging Het
Barhl1 C T 2: 28,805,304 (GRCm39) A130T probably benign Het
Bend4 T C 5: 67,555,583 (GRCm39) D541G probably damaging Het
Birc6 A C 17: 74,999,290 (GRCm39) T4673P probably damaging Het
Ccdc81 T C 7: 89,539,679 (GRCm39) R186G probably damaging Het
Cdyl2 A G 8: 117,309,931 (GRCm39) F342L probably damaging Het
Chd3 C A 11: 69,248,367 (GRCm39) V748L probably damaging Het
CN725425 G T 15: 91,123,147 (GRCm39) R72I possibly damaging Het
Col22a1 A G 15: 71,834,520 (GRCm39) probably null Het
Cops3 A G 11: 59,709,243 (GRCm39) probably null Het
Ctnnd1 G T 2: 84,433,606 (GRCm39) Q940K possibly damaging Het
Dtnb C T 12: 3,641,971 (GRCm39) Q45* probably null Het
Efr3a T A 15: 65,714,553 (GRCm39) I280K probably damaging Het
Eml6 A C 11: 29,843,213 (GRCm39) V167G probably benign Het
Fam83c T A 2: 155,672,215 (GRCm39) M407L probably benign Het
Fasn T C 11: 120,701,894 (GRCm39) T1862A probably benign Het
Fbxl6 A G 15: 76,420,155 (GRCm39) I486T probably damaging Het
Gpr182 A G 10: 127,586,565 (GRCm39) Y129H probably damaging Het
Gpr75 A G 11: 30,842,456 (GRCm39) S454G probably damaging Het
Hectd4 G A 5: 121,502,653 (GRCm39) probably null Het
Hsf4 A G 8: 106,002,222 (GRCm39) T411A probably benign Het
Hsh2d G A 8: 72,954,304 (GRCm39) D229N probably benign Het
Il4 A T 11: 53,509,432 (GRCm39) M1K probably null Het
Ints4 G A 7: 97,178,430 (GRCm39) E677K probably damaging Het
Klk1b11 G A 7: 43,647,216 (GRCm39) C50Y probably damaging Het
Krt14 C A 11: 100,098,221 (GRCm39) G21C unknown Het
Krt81 C A 15: 101,361,508 (GRCm39) R24L possibly damaging Het
L3mbtl2 C T 15: 81,552,942 (GRCm39) A125V probably damaging Het
Lama3 A G 18: 12,633,569 (GRCm39) probably null Het
Lrrk2 T C 15: 91,634,478 (GRCm39) L1414P probably damaging Het
Matn2 T C 15: 34,428,687 (GRCm39) S684P probably damaging Het
Mga T A 2: 119,771,862 (GRCm39) V1574D probably damaging Het
Mia2 T C 12: 59,219,380 (GRCm39) probably null Het
Mrpl21 T A 19: 3,342,459 (GRCm39) probably benign Het
Msh5 T A 17: 35,260,458 (GRCm39) Q266L probably benign Het
Mybpc1 C A 10: 88,376,822 (GRCm39) C758F probably damaging Het
Myo15a G A 11: 60,400,422 (GRCm39) A2932T possibly damaging Het
Nbas T A 12: 13,569,109 (GRCm39) I2021K probably benign Het
Neurl4 T C 11: 69,796,393 (GRCm39) S424P probably damaging Het
Or10j5 T A 1: 172,784,965 (GRCm39) V201E probably damaging Het
Or2w3 A C 11: 58,556,789 (GRCm39) I135L probably benign Het
Or6c6 A G 10: 129,187,103 (GRCm39) M224V probably benign Het
Or7g17 T C 9: 18,767,945 (GRCm39) M8T probably benign Het
Or7g32 T A 9: 19,389,388 (GRCm39) I53F possibly damaging Het
Phlpp1 C T 1: 106,278,308 (GRCm39) R907W probably damaging Het
Pigg T C 5: 108,484,277 (GRCm39) V508A probably benign Het
Pkhd1l1 T G 15: 44,364,915 (GRCm39) Y685D probably damaging Het
Polr3a A T 14: 24,534,534 (GRCm39) I34N probably damaging Het
Pramel17 T C 4: 101,694,158 (GRCm39) S242G probably benign Het
Prex1 A G 2: 166,411,297 (GRCm39) V1434A probably benign Het
Ptprh T A 7: 4,601,005 (GRCm39) D124V probably damaging Het
Rad54b T A 4: 11,606,131 (GRCm39) I513N probably benign Het
Rbm12b1 A G 4: 12,145,507 (GRCm39) N493S probably benign Het
Rfx7 A T 9: 72,517,586 (GRCm39) probably null Het
Serpini1 A G 3: 75,520,648 (GRCm39) K82E probably benign Het
Slc27a6 T G 18: 58,742,237 (GRCm39) probably null Het
Slc35f2 G T 9: 53,724,201 (GRCm39) L358F probably damaging Het
Slc45a1 A C 4: 150,727,762 (GRCm39) I158M probably damaging Het
Slurp2 G A 15: 74,614,955 (GRCm39) P62L probably damaging Het
Sspo C T 6: 48,443,674 (GRCm39) H1949Y probably damaging Het
Tiam1 A T 16: 89,634,715 (GRCm39) V865E possibly damaging Het
Tlr4 A C 4: 66,757,857 (GRCm39) I217L probably damaging Het
Top1 C T 2: 160,554,628 (GRCm39) R460* probably null Het
Trpm3 T A 19: 22,965,418 (GRCm39) S1638T probably benign Het
Tubgcp5 C T 7: 55,473,315 (GRCm39) R798C probably benign Het
Vars1 T G 17: 35,231,703 (GRCm39) probably null Het
Xylt2 A G 11: 94,557,159 (GRCm39) Y111H probably benign Het
Zbed5 G A 5: 129,930,567 (GRCm39) G172D probably damaging Het
Zfp53 C T 17: 21,729,095 (GRCm39) T376I probably benign Het
Zfp937 G T 2: 150,081,466 (GRCm39) V499L probably benign Het
Zyx T A 6: 42,328,247 (GRCm39) L152Q probably damaging Het
Other mutations in Ints11
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01145:Ints11 APN 4 155,969,583 (GRCm39) missense probably damaging 1.00
IGL01515:Ints11 APN 4 155,959,689 (GRCm39) missense probably damaging 1.00
IGL01613:Ints11 APN 4 155,969,655 (GRCm39) critical splice donor site probably null
IGL02024:Ints11 APN 4 155,972,972 (GRCm39) missense probably damaging 1.00
IGL02127:Ints11 APN 4 155,971,320 (GRCm39) missense probably damaging 1.00
IGL02850:Ints11 APN 4 155,959,761 (GRCm39) missense probably benign 0.03
IGL02926:Ints11 APN 4 155,972,568 (GRCm39) critical splice donor site probably null
IGL03296:Ints11 APN 4 155,969,780 (GRCm39) critical splice donor site probably null
IGL03357:Ints11 APN 4 155,956,581 (GRCm39) splice site probably benign
R0013:Ints11 UTSW 4 155,971,625 (GRCm39) missense probably damaging 1.00
R0013:Ints11 UTSW 4 155,971,625 (GRCm39) missense probably damaging 1.00
R0480:Ints11 UTSW 4 155,972,081 (GRCm39) missense probably damaging 1.00
R0589:Ints11 UTSW 4 155,971,343 (GRCm39) missense probably damaging 1.00
R0678:Ints11 UTSW 4 155,972,210 (GRCm39) missense probably damaging 1.00
R0865:Ints11 UTSW 4 155,971,564 (GRCm39) splice site probably null
R1135:Ints11 UTSW 4 155,972,384 (GRCm39) splice site probably null
R1466:Ints11 UTSW 4 155,972,567 (GRCm39) critical splice donor site probably null
R1466:Ints11 UTSW 4 155,972,567 (GRCm39) critical splice donor site probably null
R1658:Ints11 UTSW 4 155,972,185 (GRCm39) missense probably damaging 0.97
R1707:Ints11 UTSW 4 155,959,655 (GRCm39) missense probably benign 0.21
R2199:Ints11 UTSW 4 155,959,738 (GRCm39) missense probably benign 0.07
R2876:Ints11 UTSW 4 155,971,882 (GRCm39) unclassified probably benign
R4567:Ints11 UTSW 4 155,970,132 (GRCm39) missense probably damaging 1.00
R4900:Ints11 UTSW 4 155,972,887 (GRCm39) missense probably benign 0.01
R4964:Ints11 UTSW 4 155,971,385 (GRCm39) missense probably damaging 1.00
R4966:Ints11 UTSW 4 155,971,385 (GRCm39) missense probably damaging 1.00
R5306:Ints11 UTSW 4 155,959,665 (GRCm39) missense probably damaging 1.00
R5963:Ints11 UTSW 4 155,957,369 (GRCm39) nonsense probably null
R6246:Ints11 UTSW 4 155,972,546 (GRCm39) missense probably benign
R7285:Ints11 UTSW 4 155,970,568 (GRCm39) missense probably damaging 1.00
R7365:Ints11 UTSW 4 155,956,687 (GRCm39) splice site probably null
R7768:Ints11 UTSW 4 155,971,396 (GRCm39) missense probably damaging 0.97
R7774:Ints11 UTSW 4 155,970,140 (GRCm39) missense probably benign 0.00
R7999:Ints11 UTSW 4 155,971,413 (GRCm39) missense probably benign 0.12
R8103:Ints11 UTSW 4 155,972,687 (GRCm39) missense possibly damaging 0.93
R8785:Ints11 UTSW 4 155,954,165 (GRCm39) missense probably benign 0.17
R8825:Ints11 UTSW 4 155,969,587 (GRCm39) nonsense probably null
Z1088:Ints11 UTSW 4 155,971,427 (GRCm39) missense probably benign 0.41
Predicted Primers PCR Primer
(F):5'- ATTGGTGCATGGCGAAGCCAAG -3'
(R):5'- GCAATACCCACCCTACCACTGTTTG -3'

Sequencing Primer
(F):5'- TTCCTGAGGCAGAAGATTGAGC -3'
(R):5'- ACCACTGTTTGTACACTTACACTG -3'
Posted On 2013-05-23