Incidental Mutation 'R1808:Rfx1'
ID 203607
Institutional Source Beutler Lab
Gene Symbol Rfx1
Ensembl Gene ENSMUSG00000031706
Gene Name regulatory factor X, 1 (influences HLA class II expression)
Synonyms
MMRRC Submission 039837-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1808 (G1)
Quality Score 155
Status Not validated
Chromosome 8
Chromosomal Location 84793463-84823621 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 84821677 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Histidine at position 804 (Q804H)
Ref Sequence ENSEMBL: ENSMUSP00000005600 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005600] [ENSMUST00000041367] [ENSMUST00000210279] [ENSMUST00000211046]
AlphaFold P48377
Predicted Effect probably damaging
Transcript: ENSMUST00000005600
AA Change: Q804H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000005600
Gene: ENSMUSG00000031706
AA Change: Q804H

DomainStartEndE-ValueType
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 probably benign
Transcript: ENSMUST00000041367
SMART Domains Protein: ENSMUSP00000038568
Gene: ENSMUSG00000037103

DomainStartEndE-ValueType
low complexity region 12 33 N/A INTRINSIC
Pfam:DCAF15_WD40 48 259 1.1e-84 PFAM
low complexity region 275 294 N/A INTRINSIC
low complexity region 343 359 N/A INTRINSIC
low complexity region 374 384 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000210279
Predicted Effect probably damaging
Transcript: ENSMUST00000211046
AA Change: Q804H

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 96.9%
  • 10x: 95.1%
  • 20x: 91.9%
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: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700001J03Rik G T 5: 146,121,691 (GRCm39) Y69* probably null Het
2310011J03Rik A G 10: 80,156,015 (GRCm39) probably null Het
A2ml1 A C 6: 128,520,262 (GRCm39) D1367E probably damaging Het
Adam6a C G 12: 113,508,334 (GRCm39) L236V probably benign Het
Arf3 T C 15: 98,638,954 (GRCm39) N101S probably benign Het
Arhgap42 T C 9: 9,180,051 (GRCm39) E76G probably damaging Het
Atp2a1 A G 7: 126,052,573 (GRCm39) F382S probably damaging Het
Bud13 T A 9: 46,199,705 (GRCm39) F355L probably benign Het
C2 G A 17: 35,083,508 (GRCm39) P349S probably damaging Het
Cbl C A 9: 44,075,526 (GRCm39) G373V probably damaging Het
Ccdc3 T A 2: 5,142,896 (GRCm39) L51Q probably damaging Het
Ccdc34 T A 2: 109,874,601 (GRCm39) M320K probably benign Het
Cntln A G 4: 85,015,000 (GRCm39) E1097G probably damaging Het
Ctsc A C 7: 87,948,750 (GRCm39) K195Q possibly damaging Het
Ctsf C T 19: 4,906,562 (GRCm39) P163L probably benign Het
Dcxr A T 11: 120,616,438 (GRCm39) probably null Het
Dgki T C 6: 37,126,509 (GRCm39) E157G possibly damaging Het
Dnah8 T C 17: 30,903,160 (GRCm39) L933P probably damaging Het
Dtna T C 18: 23,702,697 (GRCm39) L76P probably damaging Het
Fcgbp T A 7: 27,784,515 (GRCm39) C192S probably benign Het
Galnt5 T A 2: 57,916,137 (GRCm39) D683E probably benign Het
Greb1l G A 18: 10,542,143 (GRCm39) A1297T probably benign Het
Grik4 T C 9: 42,540,322 (GRCm39) N286S probably benign Het
Hrc A T 7: 44,986,202 (GRCm39) E451V probably damaging Het
Hrh3 G A 2: 179,741,577 (GRCm39) probably benign Het
Ints13 A G 6: 146,455,695 (GRCm39) I152T probably damaging Het
Irgm1 A T 11: 48,757,259 (GRCm39) V184D probably damaging Het
Itga5 C T 15: 103,258,826 (GRCm39) A791T probably damaging Het
Kcp T C 6: 29,505,654 (GRCm39) T73A probably benign Het
Kidins220 A G 12: 25,053,008 (GRCm39) T433A probably benign Het
Kirrel1 C T 3: 86,996,458 (GRCm39) M380I probably null Het
Kmt2d T C 15: 98,764,567 (GRCm39) D12G probably damaging Het
Mms19 A G 19: 41,954,698 (GRCm39) S74P probably damaging Het
Myh1 G T 11: 67,102,300 (GRCm39) E864* probably null Het
Nek1 A G 8: 61,469,264 (GRCm39) D107G probably damaging Het
Npc1 T C 18: 12,327,149 (GRCm39) N1149D probably damaging Het
Or14j6 T A 17: 38,214,661 (GRCm39) S75T probably damaging Het
Or3a1b C A 11: 74,012,257 (GRCm39) S47R probably damaging Het
Or4k36 T C 2: 111,146,343 (GRCm39) V173A probably benign Het
Or5p79 A C 7: 108,221,817 (GRCm39) K266T possibly damaging Het
Osbp T C 19: 11,948,142 (GRCm39) S150P probably damaging Het
Paf1 T C 7: 28,096,247 (GRCm39) Y287H probably damaging Het
Pdgfrb T C 18: 61,201,174 (GRCm39) V420A probably benign Het
Pdss1 G T 2: 22,796,846 (GRCm39) E120* probably null Het
Pink1 A T 4: 138,044,630 (GRCm39) V339E probably damaging Het
Pkn3 C T 2: 29,969,663 (GRCm39) R58C probably damaging Het
Pm20d1 G A 1: 131,730,165 (GRCm39) V235I probably benign Het
Ppp2r2a A G 14: 67,276,412 (GRCm39) I31T probably damaging Het
Rbms3 T C 9: 116,651,894 (GRCm39) E152G probably damaging Het
Rpe G T 1: 66,754,356 (GRCm39) V143L probably benign Het
Sap30l G T 11: 57,700,771 (GRCm39) V142L probably benign Het
Sh3tc1 T C 5: 35,863,268 (GRCm39) Q973R probably benign Het
Slc10a2 T C 8: 5,154,856 (GRCm39) T110A probably damaging Het
Snrnp200 A T 2: 127,060,947 (GRCm39) probably null Het
Snrnp200 G A 2: 127,060,948 (GRCm39) probably null Het
Spaca3 T A 11: 80,758,511 (GRCm39) V158E probably damaging Het
Sprtn C A 8: 125,629,770 (GRCm39) N354K probably benign Het
Stab1 T A 14: 30,863,101 (GRCm39) Y2166F possibly damaging Het
Tmem106c G A 15: 97,866,548 (GRCm39) probably null Het
Tnc A G 4: 63,918,168 (GRCm39) S1248P probably damaging Het
Tshr T C 12: 91,504,090 (GRCm39) F343L probably benign Het
Ttn C A 2: 76,555,698 (GRCm39) A30436S probably damaging Het
Ubxn2a A T 12: 4,935,839 (GRCm39) M68K probably benign Het
Ucp2 T C 7: 100,148,021 (GRCm39) V238A probably damaging Het
Urgcp C A 11: 5,667,242 (GRCm39) L365F probably damaging Het
Vezt A T 10: 93,826,026 (GRCm39) D328E probably damaging Het
Vmn1r168 G T 7: 23,240,184 (GRCm39) V14L probably benign Het
Vps13b T C 15: 35,792,205 (GRCm39) F2158L probably benign Het
Other mutations in Rfx1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01612:Rfx1 APN 8 84,819,601 (GRCm39) critical splice acceptor site probably null
IGL01779:Rfx1 APN 8 84,819,291 (GRCm39) splice site probably benign
IGL02505:Rfx1 APN 8 84,822,438 (GRCm39) missense possibly damaging 0.79
IGL02741:Rfx1 APN 8 84,822,471 (GRCm39) missense possibly damaging 0.94
R1565:Rfx1 UTSW 8 84,800,575 (GRCm39) missense probably benign
R1793:Rfx1 UTSW 8 84,793,050 (GRCm39) unclassified probably benign
R1971:Rfx1 UTSW 8 84,822,126 (GRCm39) missense probably damaging 1.00
R4542:Rfx1 UTSW 8 84,816,866 (GRCm39) missense probably damaging 1.00
R4690:Rfx1 UTSW 8 84,809,374 (GRCm39) missense possibly damaging 0.50
R4995:Rfx1 UTSW 8 84,806,743 (GRCm39) splice site probably null
R5163:Rfx1 UTSW 8 84,819,840 (GRCm39) missense probably damaging 0.98
R5212:Rfx1 UTSW 8 84,793,221 (GRCm39) unclassified probably benign
R5227:Rfx1 UTSW 8 84,800,687 (GRCm39) missense probably damaging 0.99
R5401:Rfx1 UTSW 8 84,793,005 (GRCm39) splice site probably null
R5431:Rfx1 UTSW 8 84,809,349 (GRCm39) nonsense probably null
R5584:Rfx1 UTSW 8 84,814,706 (GRCm39) splice site probably null
R5693:Rfx1 UTSW 8 84,800,533 (GRCm39) missense unknown
R6210:Rfx1 UTSW 8 84,819,647 (GRCm39) missense probably damaging 1.00
R6715:Rfx1 UTSW 8 84,822,444 (GRCm39) missense possibly damaging 0.49
R6920:Rfx1 UTSW 8 84,822,117 (GRCm39) missense probably damaging 1.00
R7131:Rfx1 UTSW 8 84,821,708 (GRCm39) missense probably damaging 0.96
R7155:Rfx1 UTSW 8 84,821,455 (GRCm39) missense probably damaging 0.99
R7336:Rfx1 UTSW 8 84,800,385 (GRCm39) start gained probably benign
R7467:Rfx1 UTSW 8 84,800,542 (GRCm39) missense possibly damaging 0.86
R8105:Rfx1 UTSW 8 84,814,505 (GRCm39) missense possibly damaging 0.92
R8145:Rfx1 UTSW 8 84,800,657 (GRCm39) missense probably benign 0.06
R8261:Rfx1 UTSW 8 84,819,479 (GRCm39) missense probably benign 0.00
R8263:Rfx1 UTSW 8 84,821,483 (GRCm39) missense probably damaging 1.00
R8443:Rfx1 UTSW 8 84,806,515 (GRCm39) missense probably benign 0.00
R8680:Rfx1 UTSW 8 84,818,084 (GRCm39) missense possibly damaging 0.82
R9302:Rfx1 UTSW 8 84,817,662 (GRCm39) missense possibly damaging 0.50
R9473:Rfx1 UTSW 8 84,819,903 (GRCm39) missense probably damaging 0.96
R9766:Rfx1 UTSW 8 84,814,376 (GRCm39) missense probably damaging 1.00
Z1177:Rfx1 UTSW 8 84,816,906 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TCAACCAGATGCTAAGCGAC -3'
(R):5'- TTCTCTAACACACTGGGTTGC -3'

Sequencing Primer
(F):5'- GATGCTAAGCGACCTCAATCGG -3'
(R):5'- GGTTGCCCCTGGTCTCATC -3'
Posted On 2014-06-23