Incidental Mutation 'R5066:Nfx1'
ID 388314
Institutional Source Beutler Lab
Gene Symbol Nfx1
Ensembl Gene ENSMUSG00000028423
Gene Name nuclear transcription factor, X-box binding 1
Synonyms Tex42, 3000003M19Rik, 1300017N15Rik, TEG-42
MMRRC Submission 042656-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.602) question?
Stock # R5066 (G1)
Quality Score 225
Status Validated
Chromosome 4
Chromosomal Location 40970906-41025992 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 40991868 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 519 (I519V)
Ref Sequence ENSEMBL: ENSMUSP00000095747 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030133] [ENSMUST00000091614] [ENSMUST00000098143]
AlphaFold B1AY10
Predicted Effect probably benign
Transcript: ENSMUST00000030133
AA Change: I519V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000030133
Gene: ENSMUSG00000028423
AA Change: I519V

DomainStartEndE-ValueType
RING 352 402 3.91e-2 SMART
ZnF_NFX 447 465 1.23e-3 SMART
ZnF_NFX 500 519 6.16e-4 SMART
ZnF_NFX 561 580 2e-3 SMART
ZnF_NFX 626 649 5.45e-5 SMART
ZnF_NFX 688 707 5.25e0 SMART
ZnF_NFX 715 734 2.92e-5 SMART
ZnF_NFX 772 791 5.25e0 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000091614
AA Change: I519V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000089203
Gene: ENSMUSG00000028423
AA Change: I519V

DomainStartEndE-ValueType
RING 352 402 3.91e-2 SMART
ZnF_NFX 447 465 1.23e-3 SMART
ZnF_NFX 500 519 6.16e-4 SMART
ZnF_NFX 561 580 2e-3 SMART
ZnF_NFX 626 649 5.45e-5 SMART
ZnF_NFX 688 707 5.25e0 SMART
ZnF_NFX 715 734 2.92e-5 SMART
ZnF_NFX 772 791 5.25e0 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000098143
AA Change: I519V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000095747
Gene: ENSMUSG00000028423
AA Change: I519V

DomainStartEndE-ValueType
RING 352 402 3.91e-2 SMART
ZnF_NFX 447 465 1.23e-3 SMART
ZnF_NFX 500 519 6.16e-4 SMART
ZnF_NFX 561 580 2e-3 SMART
ZnF_NFX 626 649 5.45e-5 SMART
ZnF_NFX 688 707 5.25e0 SMART
ZnF_NFX 715 734 2.92e-5 SMART
ZnF_NFX 772 791 5.25e0 SMART
ZnF_NFX 826 848 7.7e-5 SMART
ZnF_NFX 857 878 4.23e-2 SMART
coiled coil region 930 956 N/A INTRINSIC
R3H 977 1055 1.38e-22 SMART
low complexity region 1070 1088 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000175121
Meta Mutation Damage Score 0.0594 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.4%
Validation Efficiency 100% (45/45)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] MHC class II gene expression is controlled primarily at the transcriptional level by transcription factors that bind to the X and Y boxes, two highly conserved elements in the proximal promoter of MHC class II genes. The protein encoded by this gene is a transcriptional repressor capable of binding to the conserved X box motif of HLA-DRA and other MHC class II genes in vitro. The protein may play a role in regulating the duration of an inflammatory response by limiting the period in which class II MHC molecules are induced by IFN-gamma. Three alternative splice variants, each of which encodes a different isoform, have been identified. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930544D05Rik A T 11: 70,507,417 (GRCm39) Y154F probably benign Het
Abca5 A T 11: 110,200,176 (GRCm39) probably benign Het
Agtpbp1 T A 13: 59,622,364 (GRCm39) D11V probably damaging Het
Aldh1a2 G A 9: 71,188,982 (GRCm39) A299T possibly damaging Het
Apc T A 18: 34,449,158 (GRCm39) V1984D probably damaging Het
Asxl3 C G 18: 22,658,356 (GRCm39) A2122G possibly damaging Het
Atp13a2 G A 4: 140,732,449 (GRCm39) V905M probably damaging Het
Atp1a1 C T 3: 101,489,420 (GRCm39) G731R probably damaging Het
Atrn T C 2: 130,836,113 (GRCm39) V1131A possibly damaging Het
Bcl2l13 T A 6: 120,863,982 (GRCm39) V312E possibly damaging Het
Chic2 A G 5: 75,187,817 (GRCm39) V81A possibly damaging Het
Drg1 A T 11: 3,209,353 (GRCm39) I122N possibly damaging Het
Efcab3 A G 11: 104,611,490 (GRCm39) D444G probably benign Het
Flt4 A G 11: 49,524,990 (GRCm39) N612S possibly damaging Het
Hadhb T C 5: 30,369,094 (GRCm39) probably benign Het
Heg1 G T 16: 33,559,041 (GRCm39) R856S probably benign Het
Ice2 A C 9: 69,315,573 (GRCm39) N143T probably benign Het
Igkv8-21 G A 6: 70,292,427 (GRCm39) Q4* probably null Het
Lrfn2 T C 17: 49,403,448 (GRCm39) S524P probably damaging Het
Mndal C A 1: 173,703,229 (GRCm39) A59S probably damaging Het
Mpp7 T C 18: 7,513,002 (GRCm39) E33G possibly damaging Het
Msantd5l A G 11: 51,145,251 (GRCm39) F112S probably damaging Het
Nedd4 T A 9: 72,617,801 (GRCm39) D187E probably damaging Het
Or10p22 G A 10: 128,826,660 (GRCm39) R293Q probably damaging Het
Or6c204 T C 10: 129,022,433 (GRCm39) I286V possibly damaging Het
Padi1 T C 4: 140,556,748 (GRCm39) N153S probably damaging Het
Parp10 A G 15: 76,125,146 (GRCm39) probably benign Het
Setbp1 A T 18: 78,900,514 (GRCm39) M1051K probably damaging Het
Slc2a7 T A 4: 150,244,573 (GRCm39) M347K probably damaging Het
Slc45a2 C A 15: 11,012,693 (GRCm39) T232K probably benign Het
Snd1 C A 6: 28,888,239 (GRCm39) N891K probably damaging Het
Spata13 T C 14: 60,987,538 (GRCm39) Y899H possibly damaging Het
Sult1c2 T A 17: 54,281,026 (GRCm39) I26F probably damaging Het
Sybu A G 15: 44,541,040 (GRCm39) C341R probably damaging Het
Syk T A 13: 52,796,018 (GRCm39) S538T possibly damaging Het
Syne2 A G 12: 76,013,325 (GRCm39) T2840A probably benign Het
Thsd4 A G 9: 59,883,615 (GRCm39) C924R probably damaging Het
Tle1 A G 4: 72,076,504 (GRCm39) S175P probably benign Het
Tmbim4 C T 10: 120,053,537 (GRCm39) T112M probably benign Het
Tmprss11a A G 5: 86,567,859 (GRCm39) probably null Het
Tnc C A 4: 63,893,466 (GRCm39) D1698Y probably damaging Het
Ypel1 A G 16: 16,927,539 (GRCm39) Y18H probably benign Het
Other mutations in Nfx1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01377:Nfx1 APN 4 40,977,241 (GRCm39) missense probably benign 0.00
IGL01998:Nfx1 APN 4 41,004,353 (GRCm39) missense probably damaging 1.00
IGL02072:Nfx1 APN 4 41,016,119 (GRCm39) missense probably benign
IGL02170:Nfx1 APN 4 41,018,019 (GRCm39) missense probably damaging 1.00
IGL02188:Nfx1 APN 4 40,993,827 (GRCm39) missense probably damaging 1.00
IGL02502:Nfx1 APN 4 40,976,345 (GRCm39) splice site probably benign
IGL02674:Nfx1 APN 4 40,999,717 (GRCm39) critical splice donor site probably null
IGL03007:Nfx1 APN 4 40,984,962 (GRCm39) missense probably benign 0.02
IGL03092:Nfx1 APN 4 41,024,851 (GRCm39) missense probably damaging 1.00
IGL03303:Nfx1 APN 4 41,004,323 (GRCm39) splice site probably benign
K7371:Nfx1 UTSW 4 40,976,803 (GRCm39) missense probably damaging 1.00
PIT4498001:Nfx1 UTSW 4 40,977,244 (GRCm39) missense probably benign
R0032:Nfx1 UTSW 4 41,015,321 (GRCm39) missense probably benign 0.00
R0032:Nfx1 UTSW 4 41,015,321 (GRCm39) missense probably benign 0.00
R0069:Nfx1 UTSW 4 40,986,688 (GRCm39) splice site probably benign
R1056:Nfx1 UTSW 4 41,003,057 (GRCm39) missense probably damaging 0.97
R1449:Nfx1 UTSW 4 40,976,803 (GRCm39) missense probably damaging 1.00
R1635:Nfx1 UTSW 4 40,977,004 (GRCm39) missense probably benign
R1636:Nfx1 UTSW 4 41,016,072 (GRCm39) splice site probably null
R1882:Nfx1 UTSW 4 41,009,240 (GRCm39) missense possibly damaging 0.55
R2089:Nfx1 UTSW 4 40,977,004 (GRCm39) missense probably benign
R2091:Nfx1 UTSW 4 40,977,004 (GRCm39) missense probably benign
R2091:Nfx1 UTSW 4 40,977,004 (GRCm39) missense probably benign
R3792:Nfx1 UTSW 4 41,004,357 (GRCm39) nonsense probably null
R3793:Nfx1 UTSW 4 41,004,357 (GRCm39) nonsense probably null
R4668:Nfx1 UTSW 4 40,976,367 (GRCm39) missense possibly damaging 0.50
R4678:Nfx1 UTSW 4 41,012,070 (GRCm39) missense probably benign 0.01
R4894:Nfx1 UTSW 4 40,996,877 (GRCm39) missense probably damaging 1.00
R4972:Nfx1 UTSW 4 40,976,375 (GRCm39) missense probably benign 0.36
R5389:Nfx1 UTSW 4 40,985,000 (GRCm39) missense probably damaging 1.00
R5429:Nfx1 UTSW 4 41,004,343 (GRCm39) missense probably damaging 1.00
R5643:Nfx1 UTSW 4 40,984,973 (GRCm39) missense probably null 1.00
R5644:Nfx1 UTSW 4 40,984,973 (GRCm39) missense probably null 1.00
R5915:Nfx1 UTSW 4 40,977,285 (GRCm39) missense probably benign 0.02
R6286:Nfx1 UTSW 4 40,986,728 (GRCm39) missense probably damaging 1.00
R6393:Nfx1 UTSW 4 40,976,851 (GRCm39) missense possibly damaging 0.92
R7409:Nfx1 UTSW 4 41,021,830 (GRCm39) missense possibly damaging 0.64
R7523:Nfx1 UTSW 4 41,016,119 (GRCm39) missense probably benign
R7916:Nfx1 UTSW 4 40,977,142 (GRCm39) missense probably benign 0.11
R8497:Nfx1 UTSW 4 40,976,968 (GRCm39) missense possibly damaging 0.67
R8799:Nfx1 UTSW 4 41,023,727 (GRCm39) missense probably damaging 1.00
R9154:Nfx1 UTSW 4 40,990,845 (GRCm39) missense probably damaging 1.00
R9364:Nfx1 UTSW 4 41,023,756 (GRCm39) missense probably benign 0.31
R9497:Nfx1 UTSW 4 40,994,104 (GRCm39) missense probably benign 0.00
X0025:Nfx1 UTSW 4 40,976,422 (GRCm39) missense possibly damaging 0.83
Predicted Primers PCR Primer
(F):5'- CAGTCTGTGTAGTGGGAACTTC -3'
(R):5'- CTATTCTGAGGCAGGGTCTG -3'

Sequencing Primer
(F):5'- AACTTCGGAGTGATGCATTTG -3'
(R):5'- GTCTGGCTGGATCATGACATACAC -3'
Posted On 2016-06-06