Mutagenetix > Incidental Mutation

Incidental Mutation 'R0047:Ilf3'

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

Chromosomal Location

21367871-21405361 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 21388714 bp (GRCm38)

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] [ENSMUST00000214758] [ENSMUST00000214852] [ENSMUST00000216892]

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

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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

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

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

noncoding transcript
Transcript: ENSMUST00000217476

Predicted Effect

unknown
Transcript: ENSMUST00000217498
AA Change: M54K

Meta Mutation Damage Score

0.0842

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
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	A	G	3: 138,066,264	T405A	probably damaging	Het
4932438A13Rik	T	A	3: 36,908,192	L481M	possibly damaging	Het
Acer1	A	T	17: 56,955,624	D175E	possibly damaging	Het
Acsf2	T	C	11: 94,569,342	I395V	probably benign	Het
Adamts9	G	A	6: 92,905,306		probably benign	Het
Amigo3	T	C	9: 108,054,658	S427P	probably benign	Het
Ankrd35	A	G	3: 96,684,063	K555R	probably benign	Het
Arhgap35	A	T	7: 16,561,992	H1049Q	probably benign	Het
Arhgef5	G	A	6: 43,265,621		probably null	Het
Arid4a	T	G	12: 71,075,419	L858W	probably damaging	Het
Bbox1	A	G	2: 110,268,302	F310S	probably damaging	Het
Bhlhe22	T	C	3: 18,055,569	L261P	probably damaging	Het
Bmper	T	A	9: 23,406,686	C534S	probably damaging	Het
Cacna1d	T	G	14: 30,346,790		probably benign	Het
Camk2g	G	A	14: 20,771,068		probably benign	Het
Capn12	G	A	7: 28,890,387		probably null	Het
Cdkl4	T	G	17: 80,550,845	N115T	probably benign	Het
Chchd1	T	C	14: 20,704,163	S48P	possibly damaging	Het
Chia1	G	T	3: 106,115,257	C49F	probably damaging	Het
Cnot7	A	G	8: 40,495,921		probably benign	Het
Crh	T	C	3: 19,694,037	E147G	probably damaging	Het
Cux1	T	C	5: 136,363,253		probably benign	Het
Cyp2b19	T	A	7: 26,766,826	D351E	probably benign	Het
Dctn1	G	T	6: 83,182,632	G31*	probably null	Het
Duox1	T	A	2: 122,346,641		probably benign	Het
Egflam	T	G	15: 7,253,430	E382A	possibly damaging	Het
Ext1	T	C	15: 53,345,146	N73S	probably benign	Het
Ffar4	A	G	19: 38,114,004		probably benign	Het
Glg1	A	T	8: 111,165,582	M866K	probably damaging	Het
Golm1	T	A	13: 59,645,100	H197L	probably benign	Het
Gtse1	A	G	15: 85,862,378	K132E	probably damaging	Het
Gxylt2	A	T	6: 100,733,378		probably benign	Het
Hrc	T	A	7: 45,336,689	S421R	probably benign	Het
Ighg2c	T	A	12: 113,288,168		probably benign	Het
Ihh	A	G	1: 74,946,591	I245T	probably benign	Het
Insr	A	G	8: 3,202,947	V404A	probably damaging	Het
Irak2	G	A	6: 113,678,738	V367I	probably benign	Het
Irak2	G	T	6: 113,672,953		probably benign	Het
Kat7	A	C	11: 95,300,208	N119K	probably benign	Het
Kif9	A	G	9: 110,485,038	I33V	probably benign	Het
Klf17	A	G	4: 117,761,032	Y43H	probably benign	Het
Kng2	T	A	16: 22,987,563	T629S	possibly damaging	Het
Lama1	A	T	17: 67,795,186		probably benign	Het
Lamb1	T	C	12: 31,278,601	I188T	possibly damaging	Het
Lpp	T	A	16: 24,661,800		probably benign	Het
Lrp12	T	C	15: 39,878,239	E360G	probably damaging	Het
Mark2	A	C	19: 7,283,577		probably benign	Het
Mmp3	T	C	9: 7,451,910		probably benign	Het
Mthfd1l	T	A	10: 3,978,727		probably benign	Het
Mtr	A	T	13: 12,222,226	S569T	probably damaging	Het
Myh13	T	A	11: 67,367,237	S1752T	probably benign	Het
Myo5a	T	A	9: 75,156,207	L565H	probably damaging	Het
Nanos3	C	T	8: 84,176,134	R133Q	probably damaging	Het
Nfkb1	A	T	3: 135,595,053	L72*	probably null	Het
Numa1	A	G	7: 102,009,453	K296E	probably damaging	Het
Olfr1477	A	G	19: 13,502,589	E82G	probably benign	Het
Olfr186	T	A	16: 59,027,224	M228L	probably benign	Het
Olfr201	C	T	16: 59,269,211	G152D	probably damaging	Het
Olfr508	A	G	7: 108,630,552	I187V	probably benign	Het
Olfr613	A	T	7: 103,552,322	Y179F	probably damaging	Het
Pcdhb5	A	T	18: 37,321,268	I234F	possibly damaging	Het
Pgm5	T	A	19: 24,684,556	I545F	probably damaging	Het
Pla2g2c	T	C	4: 138,743,590		probably benign	Het
Pnpla7	A	T	2: 25,011,606	E548V	probably damaging	Het
Ppm1m	C	A	9: 106,196,696	E273*	probably null	Het
Ppp2r1b	C	T	9: 50,861,573	R117*	probably null	Het
Rabgap1l	G	A	1: 160,231,789		probably benign	Het
Rapgef6	T	A	11: 54,546,378	M49K	possibly damaging	Het
Rhox4f	A	C	X: 37,607,469	V15G	probably benign	Het
Rnf219	T	A	14: 104,503,344		probably null	Het
Rtel1	T	G	2: 181,323,405	I146M	probably damaging	Het
Sdr9c7	A	T	10: 127,903,672	M219L	probably benign	Het
Serpina3g	T	A	12: 104,240,284	S115T	possibly damaging	Het
Serpinb1a	A	T	13: 32,850,276	L44Q	probably damaging	Het
Slc13a4	A	G	6: 35,287,362	I190T	possibly damaging	Het
Slc46a2	A	G	4: 59,914,392	L177P	probably damaging	Het
Slc47a2	C	T	11: 61,336,242	V167M	possibly damaging	Het
Snrnp200	C	T	2: 127,234,954		probably benign	Het
Snx13	C	A	12: 35,101,124		probably benign	Het
Snx25	C	T	8: 46,041,365	A828T	probably damaging	Het
Spic	A	G	10: 88,675,941	L151P	probably damaging	Het
Ssu2	G	A	6: 112,374,820	H315Y	probably damaging	Het
Stk32a	T	C	18: 43,313,378		probably benign	Het
Tbx3	A	T	5: 119,680,446	E382V	probably damaging	Het
Tcaf2	A	G	6: 42,629,613	I469T	probably benign	Het
Tln2	A	G	9: 67,240,672		probably benign	Het
Top2a	T	A	11: 98,997,856	I1260L	probably benign	Het
Treml1	C	A	17: 48,364,980	S91*	probably null	Het
Trim26	T	C	17: 36,857,864		probably benign	Het
Trmt11	T	C	10: 30,535,243	N418S	probably benign	Het
Ttf1	A	G	2: 29,084,655	Y801C	probably damaging	Het
Usp34	C	T	11: 23,464,403	A2782V	probably benign	Het
Vmn2r77	T	C	7: 86,811,650	V728A	probably benign	Het
Vps4a	T	C	8: 107,036,701	L29P	probably damaging	Het
Wdfy3	A	G	5: 101,944,033	I480T	probably damaging	Het
Wdr41	A	G	13: 95,010,287	I197V	probably damaging	Het
Ywhag	A	T	5: 135,911,299	V147E	probably damaging	Het
Zan	A	G	5: 137,403,656	M4058T	unknown	Het
Zfp236	C	T	18: 82,680,692	C88Y	probably damaging	Het

Other mutations in Ilf3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00952:Ilf3	APN	9	21,396,051 (GRCm38)	missense	probably damaging	1.00
IGL01013:Ilf3	APN	9	21,399,691 (GRCm38)	missense	possibly damaging	0.91
IGL01352:Ilf3	APN	9	21,392,322 (GRCm38)	missense	possibly damaging	0.89
IGL01975:Ilf3	APN	9	21,392,379 (GRCm38)	missense	probably benign	0.03
IGL02826:Ilf3	APN	9	21,398,044 (GRCm38)	missense	probably benign	0.20
IGL03238:Ilf3	APN	9	21,392,350 (GRCm38)	missense	probably damaging	1.00
PIT4466001:Ilf3	UTSW	9	21,403,366 (GRCm38)	missense	unknown
R0047:Ilf3	UTSW	9	21,388,714 (GRCm38)	missense	possibly damaging	0.76
R0090:Ilf3	UTSW	9	21,395,414 (GRCm38)	missense	probably damaging	1.00
R0355:Ilf3	UTSW	9	21,397,970 (GRCm38)	missense	probably damaging	1.00
R1768:Ilf3	UTSW	9	21,403,142 (GRCm38)	unclassified	probably benign
R1889:Ilf3	UTSW	9	21,404,767 (GRCm38)	unclassified	probably benign
R1895:Ilf3	UTSW	9	21,404,767 (GRCm38)	unclassified	probably benign
R1918:Ilf3	UTSW	9	21,393,714 (GRCm38)	missense	probably damaging	1.00
R2930:Ilf3	UTSW	9	21,399,590 (GRCm38)	missense	possibly damaging	0.91
R3912:Ilf3	UTSW	9	21,398,126 (GRCm38)	missense	possibly damaging	0.77
R3913:Ilf3	UTSW	9	21,398,126 (GRCm38)	missense	possibly damaging	0.77
R4080:Ilf3	UTSW	9	21,403,134 (GRCm38)	critical splice acceptor site	probably null
R4412:Ilf3	UTSW	9	21,399,560 (GRCm38)	missense	possibly damaging	0.77
R4510:Ilf3	UTSW	9	21,399,215 (GRCm38)	missense	possibly damaging	0.95
R4511:Ilf3	UTSW	9	21,399,215 (GRCm38)	missense	possibly damaging	0.95
R5201:Ilf3	UTSW	9	21,389,383 (GRCm38)	missense	probably damaging	1.00
R5785:Ilf3	UTSW	9	21,394,872 (GRCm38)	missense	probably damaging	1.00
R6303:Ilf3	UTSW	9	21,403,136 (GRCm38)	unclassified	probably benign
R6406:Ilf3	UTSW	9	21,396,244 (GRCm38)	missense	probably damaging	0.99
R6434:Ilf3	UTSW	9	21,403,151 (GRCm38)	unclassified	probably benign
R7169:Ilf3	UTSW	9	21,395,426 (GRCm38)	missense	probably damaging	0.96
R7410:Ilf3	UTSW	9	21,399,804 (GRCm38)	missense	unknown
R7468:Ilf3	UTSW	9	21,403,411 (GRCm38)	missense	unknown
R7624:Ilf3	UTSW	9	21,398,044 (GRCm38)	missense	probably benign	0.20
R7720:Ilf3	UTSW	9	21,399,537 (GRCm38)	missense	possibly damaging	0.51
R8513:Ilf3	UTSW	9	21,388,636 (GRCm38)	missense	possibly damaging	0.92
R9056:Ilf3	UTSW	9	21,403,138 (GRCm38)	nonsense	probably null
R9317:Ilf3	UTSW	9	21,396,126 (GRCm38)	missense	probably damaging	1.00
R9522:Ilf3	UTSW	9	21,394,237 (GRCm38)	missense	probably benign	0.02
X0066:Ilf3	UTSW	9	21,392,406 (GRCm38)	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