Incidental Mutation 'R5431:Rfx1'
ID 428053
Institutional Source Beutler Lab
Gene Symbol Rfx1
Ensembl Gene ENSMUSG00000031706
Gene Name regulatory factor X, 1 (influences HLA class II expression)
MMRRC Submission 042847-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5431 (G1)
Quality Score 190
Status Not validated
Chromosome 8
Chromosomal Location 84066834-84096992 bp(+) (GRCm38)
Type of Mutation nonsense
DNA Base Change (assembly) C to T at 84082720 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Glutamine to Stop codon at position 225 (Q225*)
Ref Sequence ENSEMBL: ENSMUSP00000147677 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005600] [ENSMUST00000211046]
AlphaFold P48377
Predicted Effect probably null
Transcript: ENSMUST00000005600
AA Change: Q225*
SMART Domains Protein: ENSMUSP00000005600
Gene: ENSMUSG00000031706
AA Change: Q225*

low complexity region 11 47 N/A INTRINSIC
low complexity region 53 67 N/A INTRINSIC
low complexity region 73 92 N/A INTRINSIC
Pfam:RFX1_trans_act 106 176 9.6e-9 PFAM
Pfam:RFX1_trans_act 211 366 1.8e-59 PFAM
Pfam:RFX_DNA_binding 420 498 2.5e-35 PFAM
Blast:HisKA 705 768 3e-28 BLAST
low complexity region 908 920 N/A INTRINSIC
low complexity region 932 948 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000102190
Predicted Effect noncoding transcript
Transcript: ENSMUST00000209362
Predicted Effect noncoding transcript
Transcript: ENSMUST00000210660
Predicted Effect probably null
Transcript: ENSMUST00000211046
AA Change: Q225*
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.1%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the regulatory factor X (RFX) family of transcription factors, which are characterized by a winged-helix DNA-binding domain. The encoded transcription factor contains an N-terminal activation domain and a C-terminal repression domain, and may activate or repress target gene expression depending on cellular context. This transcription factor has been shown to regulate a wide variety of genes involved in immunity and cancer, including the MHC class II genes and genes that may be involved in cancer progression. This gene exhibits altered expression in glioblastoma and the autoimmune disease systemic lupus erythematosis (SLE). [provided by RefSeq, Jul 2016]
PHENOTYPE: Mice homozygous for a gene trap allele die prior to implantation. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310061N02Rik T C 16: 88,707,538 (GRCm38) S124G possibly damaging Het
4921539E11Rik T C 4: 103,270,848 (GRCm38) T27A probably benign Het
Aspg T A 12: 112,123,412 (GRCm38) N461K probably benign Het
B4galnt3 T A 6: 120,218,967 (GRCm38) T300S probably damaging Het
BC035044 A G 6: 128,885,007 (GRCm38) probably benign Het
Bmp5 C T 9: 75,893,709 (GRCm38) P374S probably damaging Het
C330018D20Rik A T 18: 56,957,856 (GRCm38) F78L probably benign Het
Cds2 T A 2: 132,302,170 (GRCm38) S289T probably benign Het
Cerkl C T 2: 79,341,335 (GRCm38) C393Y probably damaging Het
Cibar2 C A 8: 120,167,303 (GRCm38) probably null Het
Ciita C T 16: 10,523,792 (GRCm38) R1020C probably damaging Het
Dcaf13 C A 15: 39,123,224 (GRCm38) D130E probably benign Het
Dnal4 C T 15: 79,762,447 (GRCm38) G50R probably damaging Het
Elfn1 A G 5: 139,971,568 (GRCm38) N109S probably damaging Het
Ep400 A G 5: 110,676,554 (GRCm38) V2435A unknown Het
Fam178b T C 1: 36,632,485 (GRCm38) E185G probably damaging Het
Fam227b C A 2: 126,126,931 (GRCm38) L74F probably benign Het
Fgfr4 G A 13: 55,156,651 (GRCm38) V138I probably benign Het
Flnc A G 6: 29,456,384 (GRCm38) I2161V possibly damaging Het
Frmd5 T C 2: 121,562,909 (GRCm38) N235S probably damaging Het
Gad1-ps G A 10: 99,445,147 (GRCm38) noncoding transcript Het
Ggt6 A G 11: 72,437,738 (GRCm38) T355A possibly damaging Het
Gm14393 G A 2: 175,063,876 (GRCm38) T41I probably damaging Het
Gpr151 A C 18: 42,578,867 (GRCm38) S249A probably damaging Het
Gpr152 T A 19: 4,143,747 (GRCm38) V429D probably benign Het
Grm7 G A 6: 111,358,426 (GRCm38) M599I probably benign Het
Hdac4 T A 1: 91,972,790 (GRCm38) R54* probably null Het
Ice1 A G 13: 70,592,650 (GRCm38) L2146S probably damaging Het
Igfbpl1 C T 4: 45,815,588 (GRCm38) V183I probably benign Het
Kel G A 6: 41,698,420 (GRCm38) S299F probably benign Het
Kif14 T C 1: 136,496,695 (GRCm38) I1016T possibly damaging Het
Lhx3 T C 2: 26,201,118 (GRCm38) D395G probably damaging Het
Micu1 T C 10: 59,750,521 (GRCm38) Y140H possibly damaging Het
Myt1l G A 12: 29,832,332 (GRCm38) G509R unknown Het
Nbn C T 4: 15,986,593 (GRCm38) H665Y probably benign Het
Pkhd1 G T 1: 20,117,836 (GRCm38) T3416K probably benign Het
Plxnb1 T C 9: 109,100,772 (GRCm38) F232S probably damaging Het
Pus7l T C 15: 94,529,486 (GRCm38) N472D probably damaging Het
Rnase2a T C 14: 51,255,563 (GRCm38) Y115C possibly damaging Het
Ryr1 T A 7: 29,109,812 (GRCm38) D386V probably benign Het
Sfi1 A ATCTTCCCAAAGCCAGTGC 11: 3,153,384 (GRCm38) probably benign Homo
Sgcz T A 8: 37,639,984 (GRCm38) T125S probably damaging Het
Sntb1 C G 15: 55,642,795 (GRCm38) G461R probably damaging Het
Syt2 A G 1: 134,740,957 (GRCm38) S36G probably benign Het
Tcaf3 A G 6: 42,597,185 (GRCm38) L31P probably damaging Het
Tenm3 C A 8: 48,367,377 (GRCm38) E142* probably null Het
Tgfbr2 G T 9: 116,131,601 (GRCm38) S94R probably damaging Het
Tut4 T A 4: 108,491,412 (GRCm38) I297N probably damaging Het
Vmn2r12 A G 5: 109,091,818 (GRCm38) I293T probably damaging Het
Wrap73 G A 4: 154,145,274 (GRCm38) R34Q probably damaging Het
Zc3h14 A G 12: 98,780,065 (GRCm38) D511G possibly damaging Het
Other mutations in Rfx1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01612:Rfx1 APN 8 84,092,972 (GRCm38) critical splice acceptor site probably null
IGL01779:Rfx1 APN 8 84,092,662 (GRCm38) splice site probably benign
IGL02505:Rfx1 APN 8 84,095,809 (GRCm38) missense possibly damaging 0.79
IGL02741:Rfx1 APN 8 84,095,842 (GRCm38) missense possibly damaging 0.94
R1565:Rfx1 UTSW 8 84,073,946 (GRCm38) missense probably benign
R1793:Rfx1 UTSW 8 84,066,421 (GRCm38) unclassified probably benign
R1808:Rfx1 UTSW 8 84,095,048 (GRCm38) missense probably damaging 1.00
R1971:Rfx1 UTSW 8 84,095,497 (GRCm38) missense probably damaging 1.00
R4542:Rfx1 UTSW 8 84,090,237 (GRCm38) missense probably damaging 1.00
R4690:Rfx1 UTSW 8 84,082,745 (GRCm38) missense possibly damaging 0.50
R4995:Rfx1 UTSW 8 84,080,114 (GRCm38) splice site probably null
R5163:Rfx1 UTSW 8 84,093,211 (GRCm38) missense probably damaging 0.98
R5212:Rfx1 UTSW 8 84,066,592 (GRCm38) unclassified probably benign
R5227:Rfx1 UTSW 8 84,074,058 (GRCm38) missense probably damaging 0.99
R5401:Rfx1 UTSW 8 84,066,376 (GRCm38) splice site probably null
R5584:Rfx1 UTSW 8 84,088,077 (GRCm38) splice site probably null
R5693:Rfx1 UTSW 8 84,073,904 (GRCm38) missense unknown
R6210:Rfx1 UTSW 8 84,093,018 (GRCm38) missense probably damaging 1.00
R6715:Rfx1 UTSW 8 84,095,815 (GRCm38) missense possibly damaging 0.49
R6920:Rfx1 UTSW 8 84,095,488 (GRCm38) missense probably damaging 1.00
R7131:Rfx1 UTSW 8 84,095,079 (GRCm38) missense probably damaging 0.96
R7155:Rfx1 UTSW 8 84,094,826 (GRCm38) missense probably damaging 0.99
R7336:Rfx1 UTSW 8 84,073,756 (GRCm38) start gained probably benign
R7467:Rfx1 UTSW 8 84,073,913 (GRCm38) missense possibly damaging 0.86
R8105:Rfx1 UTSW 8 84,087,876 (GRCm38) missense possibly damaging 0.92
R8145:Rfx1 UTSW 8 84,074,028 (GRCm38) missense probably benign 0.06
R8261:Rfx1 UTSW 8 84,092,850 (GRCm38) missense probably benign 0.00
R8263:Rfx1 UTSW 8 84,094,854 (GRCm38) missense probably damaging 1.00
R8443:Rfx1 UTSW 8 84,079,886 (GRCm38) missense probably benign 0.00
R8680:Rfx1 UTSW 8 84,091,455 (GRCm38) missense possibly damaging 0.82
R9302:Rfx1 UTSW 8 84,091,033 (GRCm38) missense possibly damaging 0.50
R9473:Rfx1 UTSW 8 84,093,274 (GRCm38) missense probably damaging 0.96
R9766:Rfx1 UTSW 8 84,087,747 (GRCm38) missense probably damaging 1.00
Z1177:Rfx1 UTSW 8 84,090,277 (GRCm38) missense probably damaging 1.00
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2016-09-01