Incidental Mutation 'R1972:Rfx5'
ID 221043
Institutional Source Beutler Lab
Gene Symbol Rfx5
Ensembl Gene ENSMUSG00000005774
Gene Name regulatory factor X, 5 (influences HLA class II expression)
Synonyms
MMRRC Submission 039985-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.242) question?
Stock # R1972 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 94861355-94868685 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 94864603 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Phenylalanine at position 250 (L250F)
Ref Sequence ENSEMBL: ENSMUSP00000117963 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029772] [ENSMUST00000107253] [ENSMUST00000107254] [ENSMUST00000107255] [ENSMUST00000107260] [ENSMUST00000132393] [ENSMUST00000137088] [ENSMUST00000145472] [ENSMUST00000147237] [ENSMUST00000144132] [ENSMUST00000140331] [ENSMUST00000145031] [ENSMUST00000152869] [ENSMUST00000142311]
AlphaFold Q9JL61
Predicted Effect probably damaging
Transcript: ENSMUST00000029772
AA Change: L250F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000029772
Gene: ENSMUSG00000005774
AA Change: L250F

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 84 169 7.2e-33 PFAM
RFX5_DNA_bdg 438 656 4.29e-130 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000107253
AA Change: L250F

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000102874
Gene: ENSMUSG00000005774
AA Change: L250F

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 84 169 1.8e-33 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000107254
AA Change: L250F

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000102875
Gene: ENSMUSG00000005774
AA Change: L250F

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 84 169 1.8e-33 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000107255
AA Change: L250F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000102876
Gene: ENSMUSG00000005774
AA Change: L250F

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 84 169 7.2e-33 PFAM
RFX5_DNA_bdg 438 656 4.29e-130 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000107260
AA Change: L250F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000102881
Gene: ENSMUSG00000005774
AA Change: L250F

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 88 167 5.3e-31 PFAM
RFX5_DNA_bdg 438 656 4.29e-130 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125186
Predicted Effect probably benign
Transcript: ENSMUST00000132393
SMART Domains Protein: ENSMUSP00000117999
Gene: ENSMUSG00000005774

DomainStartEndE-ValueType
PDB:2KW3|B 23 89 9e-40 PDB
Predicted Effect probably damaging
Transcript: ENSMUST00000137088
AA Change: L250F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000117963
Gene: ENSMUSG00000005774
AA Change: L250F

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 84 169 7.2e-33 PFAM
RFX5_DNA_bdg 438 656 4.29e-130 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140294
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142708
Predicted Effect noncoding transcript
Transcript: ENSMUST00000148803
Predicted Effect probably benign
Transcript: ENSMUST00000145472
Predicted Effect probably benign
Transcript: ENSMUST00000147237
SMART Domains Protein: ENSMUSP00000118586
Gene: ENSMUSG00000005774

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 84 169 8.7e-34 PFAM
Pfam:Pox_D5 88 159 1e-7 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000144132
Predicted Effect probably benign
Transcript: ENSMUST00000140331
Predicted Effect probably benign
Transcript: ENSMUST00000145031
SMART Domains Protein: ENSMUSP00000118099
Gene: ENSMUSG00000005774

DomainStartEndE-ValueType
PDB:2KW3|B 23 89 9e-40 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000152869
SMART Domains Protein: ENSMUSP00000121157
Gene: ENSMUSG00000005774

DomainStartEndE-ValueType
PDB:2KW3|B 23 89 7e-40 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000142311
SMART Domains Protein: ENSMUSP00000119704
Gene: ENSMUSG00000005774

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 84 131 4.1e-10 PFAM
Meta Mutation Damage Score 0.0826 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 94.2%
Validation Efficiency 100% (77/77)
MGI Phenotype PHENOTYPE: Homozygous null mice have absent or decreased expression of MHC-II complexes on antigen presenting cells, which leads to reduced numbers of CD4+ thymocytes and T cells. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adat1 A G 8: 112,717,050 (GRCm39) probably benign Het
Bbs2 A G 8: 94,807,805 (GRCm39) probably benign Het
Bcl9 A C 3: 97,114,518 (GRCm39) D1035E probably damaging Het
Bmpr2 A G 1: 59,852,762 (GRCm39) E31G possibly damaging Het
Borcs5 A G 6: 134,687,137 (GRCm39) D164G probably damaging Het
Cap2 A G 13: 46,791,375 (GRCm39) R181G probably damaging Het
Ccdc113 A T 8: 96,264,874 (GRCm39) H128L probably benign Het
Cdh20 G A 1: 109,988,862 (GRCm39) V255I probably benign Het
Chat C T 14: 32,146,148 (GRCm39) V342I probably benign Het
Chrm4 C T 2: 91,757,838 (GRCm39) A82V probably benign Het
Cyp2d22 A T 15: 82,260,028 (GRCm39) M52K probably benign Het
Dennd2c T C 3: 103,039,014 (GRCm39) V54A probably benign Het
Dgka C T 10: 128,556,335 (GRCm39) G717D probably damaging Het
Dnah1 C T 14: 30,987,348 (GRCm39) W3550* probably null Het
Eif2ak1 A G 5: 143,821,532 (GRCm39) T283A probably benign Het
Entrep2 A T 7: 64,425,516 (GRCm39) I192N possibly damaging Het
Fcgbp A T 7: 27,793,617 (GRCm39) Y1173F probably benign Het
Flt1 G A 5: 147,591,903 (GRCm39) probably benign Het
Gpr149 T C 3: 62,438,216 (GRCm39) K647R probably benign Het
Gsdma2 T C 11: 98,541,744 (GRCm39) V157A probably benign Het
Heatr4 T A 12: 84,001,794 (GRCm39) I884F probably damaging Het
Ift56 C A 6: 38,387,738 (GRCm39) N396K probably benign Het
Il17ra A G 6: 120,459,177 (GRCm39) E776G probably benign Het
Inpp5d T C 1: 87,604,036 (GRCm39) S235P probably benign Het
Iqgap3 T A 3: 87,991,235 (GRCm39) probably null Het
Isoc2a T A 7: 4,895,086 (GRCm39) D171E probably damaging Het
Itga10 C T 3: 96,559,054 (GRCm39) probably benign Het
Kcnk12 T C 17: 88,104,560 (GRCm39) D108G possibly damaging Het
Klra9 A T 6: 130,159,345 (GRCm39) probably null Het
Lgmn A G 12: 102,362,080 (GRCm39) probably benign Het
Morf4l1 A T 9: 89,977,267 (GRCm39) probably benign Het
Mthfr T C 4: 148,136,384 (GRCm39) I380T probably damaging Het
Mybpc1 T C 10: 88,387,404 (GRCm39) I436V probably benign Het
Naip5 A G 13: 100,349,278 (GRCm39) V1350A probably damaging Het
Neil2 A T 14: 63,423,526 (GRCm39) C36S possibly damaging Het
Nlrx1 A G 9: 44,164,753 (GRCm39) V897A probably benign Het
Nod2 A T 8: 89,379,501 (GRCm39) M8L probably damaging Het
Nop2 A G 6: 125,111,602 (GRCm39) T112A probably benign Het
Nrap T A 19: 56,345,785 (GRCm39) T608S probably damaging Het
Nuak2 A T 1: 132,258,340 (GRCm39) H257L probably damaging Het
Or10x1 T C 1: 174,197,136 (GRCm39) F218L probably benign Het
Or2ag12 T C 7: 106,277,426 (GRCm39) D89G probably benign Het
Or4c113 A T 2: 88,884,891 (GRCm39) M293K probably benign Het
Or52e8 T C 7: 104,625,106 (GRCm39) I33V possibly damaging Het
Or5ac25 A T 16: 59,182,476 (GRCm39) V35D probably damaging Het
Or5b119 T C 19: 13,457,058 (GRCm39) N168S probably benign Het
Or8b40 T A 9: 38,027,863 (GRCm39) M257K possibly damaging Het
Pde1a T C 2: 79,696,065 (GRCm39) E358G probably damaging Het
Pdlim1 A T 19: 40,211,581 (GRCm39) S237R probably damaging Het
Pithd1 T C 4: 135,714,340 (GRCm39) D36G probably damaging Het
Ppp2r3d A G 9: 101,088,976 (GRCm39) F449S probably benign Het
Prr11 G A 11: 86,989,580 (GRCm39) R264C possibly damaging Het
Rbm43 A T 2: 51,815,548 (GRCm39) H224Q probably benign Het
Rgs22 T A 15: 36,103,982 (GRCm39) I160L probably benign Het
Rorb T A 19: 18,929,567 (GRCm39) Q393H probably damaging Het
Rpl13a T A 7: 44,775,419 (GRCm39) K368* probably null Het
Scaf8 T G 17: 3,219,646 (GRCm39) S276R unknown Het
Scube2 A T 7: 109,408,421 (GRCm39) N675K probably benign Het
Sec22c A T 9: 121,517,320 (GRCm39) M126K possibly damaging Het
Serpinb11 T C 1: 107,297,210 (GRCm39) F29L probably damaging Het
Sis A G 3: 72,828,337 (GRCm39) F1217S probably damaging Het
Slc18a2 A G 19: 59,263,085 (GRCm39) D294G possibly damaging Het
Slc9c1 A G 16: 45,413,835 (GRCm39) T988A possibly damaging Het
Smndc1 A C 19: 53,371,986 (GRCm39) probably null Het
Sned1 G A 1: 93,192,795 (GRCm39) G361S probably damaging Het
Spatc1 A T 15: 76,169,075 (GRCm39) probably null Het
Stab2 A T 10: 86,796,180 (GRCm39) C356S probably damaging Het
Stk4 C T 2: 163,942,448 (GRCm39) T360M probably benign Het
Tbc1d30 A T 10: 121,142,135 (GRCm39) probably null Het
Tenm3 T C 8: 48,681,626 (GRCm39) E2668G probably damaging Het
Tigar A G 6: 127,064,889 (GRCm39) V253A possibly damaging Het
Tmc2 T A 2: 130,056,584 (GRCm39) probably benign Het
Ugt1a10 A T 1: 87,983,769 (GRCm39) Y189F probably damaging Het
Vmn2r82 A G 10: 79,214,680 (GRCm39) D221G probably damaging Het
Xkr5 C T 8: 18,991,997 (GRCm39) V131M probably damaging Het
Other mutations in Rfx5
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01459:Rfx5 APN 3 94,865,086 (GRCm39) unclassified probably benign
IGL01478:Rfx5 APN 3 94,865,751 (GRCm39) missense possibly damaging 0.88
IGL02061:Rfx5 APN 3 94,865,792 (GRCm39) missense probably benign 0.03
IGL02152:Rfx5 APN 3 94,864,493 (GRCm39) missense probably damaging 1.00
IGL03395:Rfx5 APN 3 94,865,113 (GRCm39) nonsense probably null
chip UTSW 3 94,863,666 (GRCm39) missense probably damaging 1.00
nonplussed UTSW 3 94,866,272 (GRCm39) missense unknown
shrunken UTSW 3 94,862,454 (GRCm39) missense probably damaging 1.00
R0098:Rfx5 UTSW 3 94,865,679 (GRCm39) missense probably damaging 1.00
R0098:Rfx5 UTSW 3 94,865,679 (GRCm39) missense probably damaging 1.00
R0505:Rfx5 UTSW 3 94,863,666 (GRCm39) missense probably damaging 1.00
R0681:Rfx5 UTSW 3 94,863,666 (GRCm39) missense probably damaging 1.00
R1342:Rfx5 UTSW 3 94,865,723 (GRCm39) missense probably benign 0.09
R1460:Rfx5 UTSW 3 94,863,636 (GRCm39) missense probably damaging 1.00
R1466:Rfx5 UTSW 3 94,863,614 (GRCm39) missense probably damaging 1.00
R1466:Rfx5 UTSW 3 94,863,614 (GRCm39) missense probably damaging 1.00
R2173:Rfx5 UTSW 3 94,864,027 (GRCm39) splice site probably null
R4808:Rfx5 UTSW 3 94,865,591 (GRCm39) missense probably benign 0.03
R4993:Rfx5 UTSW 3 94,863,126 (GRCm39) missense probably benign 0.27
R4996:Rfx5 UTSW 3 94,863,126 (GRCm39) missense probably benign 0.27
R5104:Rfx5 UTSW 3 94,862,451 (GRCm39) missense probably benign 0.35
R5912:Rfx5 UTSW 3 94,866,029 (GRCm39) unclassified probably benign
R7097:Rfx5 UTSW 3 94,863,850 (GRCm39) missense probably damaging 1.00
R7186:Rfx5 UTSW 3 94,865,659 (GRCm39) missense probably benign 0.01
R7194:Rfx5 UTSW 3 94,862,454 (GRCm39) missense probably damaging 1.00
R7202:Rfx5 UTSW 3 94,866,272 (GRCm39) missense unknown
R7203:Rfx5 UTSW 3 94,866,187 (GRCm39) missense unknown
R7374:Rfx5 UTSW 3 94,866,053 (GRCm39) missense unknown
R7375:Rfx5 UTSW 3 94,866,053 (GRCm39) missense unknown
R8919:Rfx5 UTSW 3 94,864,475 (GRCm39) missense probably damaging 1.00
R9562:Rfx5 UTSW 3 94,866,639 (GRCm39) missense unknown
RF061:Rfx5 UTSW 3 94,863,070 (GRCm39) missense probably damaging 1.00
Z1176:Rfx5 UTSW 3 94,863,126 (GRCm39) missense probably benign 0.27
Predicted Primers PCR Primer
(F):5'- TCCGAATGAGCATGTTTCTCTC -3'
(R):5'- ATTCTGGAAGGCCTAGAGAGC -3'

Sequencing Primer
(F):5'- TCTCTACTCCAGCCAGAAATGGG -3'
(R):5'- GCCTAGAGAGCCGAGACG -3'
Posted On 2014-08-25