Incidental Mutation 'R0047:Ilf3'
ID 32965
Institutional Source Beutler Lab
Gene Symbol Ilf3
Ensembl Gene ENSMUSG00000032178
Gene Name interleukin enhancer binding factor 3
Synonyms NF90
MMRRC Submission 038341-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0047 (G1)
Quality Score 225
Status Validated (trace)
Chromosome 9
Chromosomal Location 21279167-21316657 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 21300010 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 65 (M65K)
Ref Sequence ENSEMBL: ENSMUSP00000065770 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000067646] [ENSMUST00000115414] [ENSMUST00000213518] [ENSMUST00000213603] [ENSMUST00000214474] [ENSMUST00000214852] [ENSMUST00000216892] [ENSMUST00000214758]
AlphaFold Q9Z1X4
PDB Structure Crystal structure of the NF90-NF45 dimerisation domain complex [X-RAY DIFFRACTION]
Crystal structure of the NF90-NF45 dimerisation domain complex with ATP [X-RAY DIFFRACTION]
Crystal structure of the NF90-NF45 dimerisation domain complex with UTP [X-RAY DIFFRACTION]
Crystal structure of the NF90-NF45 dimerisation domain complex with CTP [X-RAY DIFFRACTION]
Predicted Effect possibly damaging
Transcript: ENSMUST00000067646
AA Change: M65K

PolyPhen 2 Score 0.757 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000065770
Gene: ENSMUSG00000032178
AA Change: M65K

DomainStartEndE-ValueType
DZF 88 342 3.87e-166 SMART
low complexity region 375 396 N/A INTRINSIC
DSRM 402 466 2.2e-16 SMART
low complexity region 490 508 N/A INTRINSIC
DSRM 525 589 2.73e-21 SMART
low complexity region 638 688 N/A INTRINSIC
low complexity region 691 725 N/A INTRINSIC
low complexity region 745 769 N/A INTRINSIC
low complexity region 777 807 N/A INTRINSIC
low complexity region 810 886 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000115414
AA Change: M65K

PolyPhen 2 Score 0.039 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000111074
Gene: ENSMUSG00000032178
AA Change: M65K

DomainStartEndE-ValueType
DZF 88 342 3.87e-166 SMART
low complexity region 375 396 N/A INTRINSIC
DSRM 402 466 2.2e-16 SMART
low complexity region 490 508 N/A INTRINSIC
DSRM 525 589 2.73e-21 SMART
low complexity region 638 688 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000213518
AA Change: M78K

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
Predicted Effect probably benign
Transcript: ENSMUST00000213603
AA Change: M78K

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000214217
Predicted Effect probably benign
Transcript: ENSMUST00000214474
AA Change: M70K

PolyPhen 2 Score 0.283 (Sensitivity: 0.91; Specificity: 0.88)
Predicted Effect unknown
Transcript: ENSMUST00000217498
AA Change: M54K
Predicted Effect probably benign
Transcript: ENSMUST00000214852
AA Change: M70K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Predicted Effect probably benign
Transcript: ENSMUST00000216892
AA Change: M78K

PolyPhen 2 Score 0.250 (Sensitivity: 0.91; Specificity: 0.88)
Predicted Effect probably benign
Transcript: ENSMUST00000214758
AA Change: M78K

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
Predicted Effect probably benign
Transcript: ENSMUST00000214821
Predicted Effect noncoding transcript
Transcript: ENSMUST00000217476
Meta Mutation Damage Score 0.0842 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.8%
Validation Efficiency 100% (98/98)
MGI Phenotype FUNCTION: The protein encoded by this gene contains two double-stranded RNA binding domains and functions in the post-transcriptional regulation of gene expression. It is a component of an RNA-protein complex that may be involved in mediating the export of messenger RNAs. Alternative splicing results in multiple transcript variants encoding distinct isoforms. These isoforms are grouped into two categories, NFAR-1 or NFAR-2, based on variation at the C-terminus. [provided by RefSeq, Mar 2013]
PHENOTYPE: Mice homozygous for a knock-out allele are born small and weak, show tachypnea and multi-organ apoptosis, and die neonatally due to neuromuscular respiratory failure. The diaphragm and other skeletal muscles show disorganization and paucity of myofibers,myocyte degeneration and elevated apoptosis. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 99 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik A G 3: 137,772,025 (GRCm39) T405A probably damaging Het
Acer1 A T 17: 57,262,624 (GRCm39) D175E possibly damaging Het
Acsf2 T C 11: 94,460,168 (GRCm39) I395V probably benign Het
Adamts9 G A 6: 92,882,287 (GRCm39) probably benign Het
Amigo3 T C 9: 107,931,857 (GRCm39) S427P probably benign Het
Ankrd35 A G 3: 96,591,379 (GRCm39) K555R probably benign Het
Arhgap35 A T 7: 16,295,917 (GRCm39) H1049Q probably benign Het
Arhgef5 G A 6: 43,242,555 (GRCm39) probably null Het
Arid4a T G 12: 71,122,193 (GRCm39) L858W probably damaging Het
Bbox1 A G 2: 110,098,647 (GRCm39) F310S probably damaging Het
Bhlhe22 T C 3: 18,109,733 (GRCm39) L261P probably damaging Het
Bltp1 T A 3: 36,962,341 (GRCm39) L481M possibly damaging Het
Bmper T A 9: 23,317,982 (GRCm39) C534S probably damaging Het
Cacna1d T G 14: 30,068,747 (GRCm39) probably benign Het
Camk2g G A 14: 20,821,136 (GRCm39) probably benign Het
Capn12 G A 7: 28,589,812 (GRCm39) probably null Het
Cdkl4 T G 17: 80,858,274 (GRCm39) N115T probably benign Het
Chchd1 T C 14: 20,754,231 (GRCm39) S48P possibly damaging Het
Chia1 G T 3: 106,022,573 (GRCm39) C49F probably damaging Het
Cnot7 A G 8: 40,948,962 (GRCm39) probably benign Het
Crh T C 3: 19,748,201 (GRCm39) E147G probably damaging Het
Cux1 T C 5: 136,392,107 (GRCm39) probably benign Het
Cyp2b19 T A 7: 26,466,251 (GRCm39) D351E probably benign Het
Dctn1 G T 6: 83,159,614 (GRCm39) G31* probably null Het
Duox1 T A 2: 122,177,122 (GRCm39) probably benign Het
Egflam T G 15: 7,282,911 (GRCm39) E382A possibly damaging Het
Ext1 T C 15: 53,208,542 (GRCm39) N73S probably benign Het
Ffar4 A G 19: 38,102,452 (GRCm39) probably benign Het
Glg1 A T 8: 111,892,214 (GRCm39) M866K probably damaging Het
Golm1 T A 13: 59,792,914 (GRCm39) H197L probably benign Het
Gtse1 A G 15: 85,746,579 (GRCm39) K132E probably damaging Het
Gxylt2 A T 6: 100,710,339 (GRCm39) probably benign Het
Hrc T A 7: 44,986,113 (GRCm39) S421R probably benign Het
Ighg2c T A 12: 113,251,788 (GRCm39) probably benign Het
Ihh A G 1: 74,985,750 (GRCm39) I245T probably benign Het
Insr A G 8: 3,252,947 (GRCm39) V404A probably damaging Het
Irak2 G T 6: 113,649,914 (GRCm39) probably benign Het
Irak2 G A 6: 113,655,699 (GRCm39) V367I probably benign Het
Kat7 A C 11: 95,191,034 (GRCm39) N119K probably benign Het
Kif9 A G 9: 110,314,106 (GRCm39) I33V probably benign Het
Klf17 A G 4: 117,618,229 (GRCm39) Y43H probably benign Het
Kng2 T A 16: 22,806,313 (GRCm39) T629S possibly damaging Het
Lama1 A T 17: 68,102,181 (GRCm39) probably benign Het
Lamb1 T C 12: 31,328,600 (GRCm39) I188T possibly damaging Het
Lpp T A 16: 24,480,550 (GRCm39) probably benign Het
Lrp12 T C 15: 39,741,635 (GRCm39) E360G probably damaging Het
Mark2 A C 19: 7,260,942 (GRCm39) probably benign Het
Mmp3 T C 9: 7,451,910 (GRCm39) probably benign Het
Mthfd1l T A 10: 3,928,727 (GRCm39) probably benign Het
Mtr A T 13: 12,237,112 (GRCm39) S569T probably damaging Het
Myh13 T A 11: 67,258,063 (GRCm39) S1752T probably benign Het
Myo5a T A 9: 75,063,489 (GRCm39) L565H probably damaging Het
Nanos3 C T 8: 84,902,763 (GRCm39) R133Q probably damaging Het
Nfkb1 A T 3: 135,300,814 (GRCm39) L72* probably null Het
Numa1 A G 7: 101,658,660 (GRCm39) K296E probably damaging Het
Obi1 T A 14: 104,740,780 (GRCm39) probably null Het
Or51ab3 A T 7: 103,201,529 (GRCm39) Y179F probably damaging Het
Or5ac19 C T 16: 59,089,574 (GRCm39) G152D probably damaging Het
Or5b120 A G 19: 13,479,953 (GRCm39) E82G probably benign Het
Or5h18 T A 16: 58,847,587 (GRCm39) M228L probably benign Het
Or5p80 A G 7: 108,229,759 (GRCm39) I187V probably benign Het
Pcdhb5 A T 18: 37,454,321 (GRCm39) I234F possibly damaging Het
Pgm5 T A 19: 24,661,920 (GRCm39) I545F probably damaging Het
Pla2g2c T C 4: 138,470,901 (GRCm39) probably benign Het
Pnpla7 A T 2: 24,901,618 (GRCm39) E548V probably damaging Het
Ppm1m C A 9: 106,073,895 (GRCm39) E273* probably null Het
Ppp2r1b C T 9: 50,772,873 (GRCm39) R117* probably null Het
Rabgap1l G A 1: 160,059,359 (GRCm39) probably benign Het
Rapgef6 T A 11: 54,437,204 (GRCm39) M49K possibly damaging Het
Rhox4f A C X: 36,789,122 (GRCm39) V15G probably benign Het
Rtel1 T G 2: 180,965,198 (GRCm39) I146M probably damaging Het
Sdr9c7 A T 10: 127,739,541 (GRCm39) M219L probably benign Het
Serpina3g T A 12: 104,206,543 (GRCm39) S115T possibly damaging Het
Serpinb1a A T 13: 33,034,259 (GRCm39) L44Q probably damaging Het
Slc13a4 A G 6: 35,264,297 (GRCm39) I190T possibly damaging Het
Slc46a2 A G 4: 59,914,392 (GRCm39) L177P probably damaging Het
Slc47a2 C T 11: 61,227,068 (GRCm39) V167M possibly damaging Het
Snrnp200 C T 2: 127,076,874 (GRCm39) probably benign Het
Snx13 C A 12: 35,151,123 (GRCm39) probably benign Het
Snx25 C T 8: 46,494,402 (GRCm39) A828T probably damaging Het
Spic A G 10: 88,511,803 (GRCm39) L151P probably damaging Het
Ssu2 G A 6: 112,351,781 (GRCm39) H315Y probably damaging Het
Stk32a T C 18: 43,446,443 (GRCm39) probably benign Het
Tbx3 A T 5: 119,818,511 (GRCm39) E382V probably damaging Het
Tcaf2 A G 6: 42,606,547 (GRCm39) I469T probably benign Het
Tln2 A G 9: 67,147,954 (GRCm39) probably benign Het
Top2a T A 11: 98,888,682 (GRCm39) I1260L probably benign Het
Treml1 C A 17: 48,672,008 (GRCm39) S91* probably null Het
Trim26 T C 17: 37,168,756 (GRCm39) probably benign Het
Trmt11 T C 10: 30,411,239 (GRCm39) N418S probably benign Het
Ttf1 A G 2: 28,974,667 (GRCm39) Y801C probably damaging Het
Usp34 C T 11: 23,414,403 (GRCm39) A2782V probably benign Het
Vmn2r77 T C 7: 86,460,858 (GRCm39) V728A probably benign Het
Vps4a T C 8: 107,763,333 (GRCm39) L29P probably damaging Het
Wdfy3 A G 5: 102,091,899 (GRCm39) I480T probably damaging Het
Wdr41 A G 13: 95,146,795 (GRCm39) I197V probably damaging Het
Ywhag A T 5: 135,940,153 (GRCm39) V147E probably damaging Het
Zan A G 5: 137,401,918 (GRCm39) M4058T unknown Het
Zfp236 C T 18: 82,698,817 (GRCm39) C88Y probably damaging Het
Other mutations in Ilf3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00952:Ilf3 APN 9 21,307,347 (GRCm39) missense probably damaging 1.00
IGL01013:Ilf3 APN 9 21,310,987 (GRCm39) missense possibly damaging 0.91
IGL01352:Ilf3 APN 9 21,303,618 (GRCm39) missense possibly damaging 0.89
IGL01975:Ilf3 APN 9 21,303,675 (GRCm39) missense probably benign 0.03
IGL02826:Ilf3 APN 9 21,309,340 (GRCm39) missense probably benign 0.20
IGL03238:Ilf3 APN 9 21,303,646 (GRCm39) missense probably damaging 1.00
PIT4466001:Ilf3 UTSW 9 21,314,662 (GRCm39) missense unknown
R0047:Ilf3 UTSW 9 21,300,010 (GRCm39) missense possibly damaging 0.76
R0090:Ilf3 UTSW 9 21,306,710 (GRCm39) missense probably damaging 1.00
R0355:Ilf3 UTSW 9 21,309,266 (GRCm39) missense probably damaging 1.00
R1768:Ilf3 UTSW 9 21,314,438 (GRCm39) unclassified probably benign
R1889:Ilf3 UTSW 9 21,316,063 (GRCm39) unclassified probably benign
R1895:Ilf3 UTSW 9 21,316,063 (GRCm39) unclassified probably benign
R1918:Ilf3 UTSW 9 21,305,010 (GRCm39) missense probably damaging 1.00
R2930:Ilf3 UTSW 9 21,310,886 (GRCm39) missense possibly damaging 0.91
R3912:Ilf3 UTSW 9 21,309,422 (GRCm39) missense possibly damaging 0.77
R3913:Ilf3 UTSW 9 21,309,422 (GRCm39) missense possibly damaging 0.77
R4080:Ilf3 UTSW 9 21,314,430 (GRCm39) critical splice acceptor site probably null
R4412:Ilf3 UTSW 9 21,310,856 (GRCm39) missense possibly damaging 0.77
R4510:Ilf3 UTSW 9 21,310,511 (GRCm39) missense possibly damaging 0.95
R4511:Ilf3 UTSW 9 21,310,511 (GRCm39) missense possibly damaging 0.95
R5201:Ilf3 UTSW 9 21,300,679 (GRCm39) missense probably damaging 1.00
R5785:Ilf3 UTSW 9 21,306,168 (GRCm39) missense probably damaging 1.00
R6303:Ilf3 UTSW 9 21,314,432 (GRCm39) unclassified probably benign
R6406:Ilf3 UTSW 9 21,307,540 (GRCm39) missense probably damaging 0.99
R6434:Ilf3 UTSW 9 21,314,447 (GRCm39) unclassified probably benign
R7169:Ilf3 UTSW 9 21,306,722 (GRCm39) missense probably damaging 0.96
R7410:Ilf3 UTSW 9 21,311,100 (GRCm39) missense unknown
R7468:Ilf3 UTSW 9 21,314,707 (GRCm39) missense unknown
R7624:Ilf3 UTSW 9 21,309,340 (GRCm39) missense probably benign 0.20
R7720:Ilf3 UTSW 9 21,310,833 (GRCm39) missense possibly damaging 0.51
R8513:Ilf3 UTSW 9 21,299,932 (GRCm39) missense possibly damaging 0.92
R9056:Ilf3 UTSW 9 21,314,434 (GRCm39) nonsense probably null
R9317:Ilf3 UTSW 9 21,307,422 (GRCm39) missense probably damaging 1.00
R9522:Ilf3 UTSW 9 21,305,533 (GRCm39) missense probably benign 0.02
X0066:Ilf3 UTSW 9 21,303,702 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CGTGATGGCAAAGCATTCTTCAGTG -3'
(R):5'- AAGTCGGGCTCAATGGGAAACC -3'

Sequencing Primer
(F):5'- GCAAAGCATTCTTCAGTGTACCC -3'
(R):5'- gtgacacagacctgtaatccc -3'
Posted On 2013-05-09