Incidental Mutation 'R7186:Rfx5'
ID 559280
Institutional Source Beutler Lab
Gene Symbol Rfx5
Ensembl Gene ENSMUSG00000005774
Gene Name regulatory factor X, 5 (influences HLA class II expression)
Synonyms
MMRRC Submission 045271-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.242) question?
Stock # R7186 (G1)
Quality Score 225.009
Status Validated
Chromosome 3
Chromosomal Location 94861355-94868685 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 94865659 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Asparagine at position 319 (K319N)
Ref Sequence ENSEMBL: ENSMUSP00000029772 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029772] [ENSMUST00000107253] [ENSMUST00000107254] [ENSMUST00000107255] [ENSMUST00000107260] [ENSMUST00000132393] [ENSMUST00000137088] [ENSMUST00000140331] [ENSMUST00000142311] [ENSMUST00000144132] [ENSMUST00000145031] [ENSMUST00000145472] [ENSMUST00000147237] [ENSMUST00000152869]
AlphaFold Q9JL61
Predicted Effect probably benign
Transcript: ENSMUST00000029772
AA Change: K319N

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000029772
Gene: ENSMUSG00000005774
AA Change: K319N

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 84 169 7.2e-33 PFAM
RFX5_DNA_bdg 438 656 4.29e-130 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000107253
SMART Domains Protein: ENSMUSP00000102874
Gene: ENSMUSG00000005774

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 84 169 1.8e-33 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000107254
SMART Domains Protein: ENSMUSP00000102875
Gene: ENSMUSG00000005774

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 84 169 1.8e-33 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000107255
AA Change: K319N

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000102876
Gene: ENSMUSG00000005774
AA Change: K319N

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 84 169 7.2e-33 PFAM
RFX5_DNA_bdg 438 656 4.29e-130 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000107260
AA Change: K319N

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000102881
Gene: ENSMUSG00000005774
AA Change: K319N

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 88 167 5.3e-31 PFAM
RFX5_DNA_bdg 438 656 4.29e-130 SMART
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 benign
Transcript: ENSMUST00000137088
AA Change: K319N

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000117963
Gene: ENSMUSG00000005774
AA Change: K319N

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 84 169 7.2e-33 PFAM
RFX5_DNA_bdg 438 656 4.29e-130 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000140331
Predicted Effect probably benign
Transcript: ENSMUST00000142311
SMART Domains Protein: ENSMUSP00000119704
Gene: ENSMUSG00000005774

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 84 131 4.1e-10 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000144132
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: 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: ENSMUST00000152869
SMART Domains Protein: ENSMUSP00000121157
Gene: ENSMUSG00000005774

DomainStartEndE-ValueType
PDB:2KW3|B 23 89 7e-40 PDB
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (67/67)
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: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9930111J21Rik2 T A 11: 48,910,100 (GRCm39) I778F possibly damaging Het
Adam39 A T 8: 41,279,349 (GRCm39) N580I probably damaging Het
Adamts20 A G 15: 94,220,689 (GRCm39) S1415P possibly damaging Het
Adcy2 A G 13: 68,816,758 (GRCm39) Y743H probably damaging Het
Aldh1a3 A G 7: 66,055,831 (GRCm39) V320A probably damaging Het
Arid1a TGCCGCCGCCGCCGCCGCCGCCG TGCCGCCGCCGCCGCCGCCG 4: 133,480,544 (GRCm39) Het
Art5 G T 7: 101,746,536 (GRCm39) R268S probably benign Het
Bfar T C 16: 13,510,371 (GRCm39) V238A probably benign Het
Card6 TTGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGCGGATGAGAGGGCTTAGCATGGGAGGACTG TTGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGCGGATGAGAGGGCTTAGCATGGGAGGACTG 15: 5,128,173 (GRCm39) probably benign Het
Cdc23 G A 18: 34,770,175 (GRCm39) T408I probably damaging Het
Cdh24 G C 14: 54,870,949 (GRCm39) P522A probably benign Het
Clk4 T C 11: 51,159,607 (GRCm39) V61A probably benign Het
Clrn2 T C 5: 45,611,115 (GRCm39) probably benign Het
Cyp2j8 T C 4: 96,363,787 (GRCm39) D292G probably benign Het
Deaf1 T C 7: 140,907,383 (GRCm39) E34G probably benign Het
Elovl7 A G 13: 108,408,382 (GRCm39) E127G probably damaging Het
Flg A T 3: 93,187,252 (GRCm39) R235* probably null Het
Gbp3 G A 3: 142,269,923 (GRCm39) V77M probably damaging Het
Gda A T 19: 21,372,569 (GRCm39) F450I probably benign Het
Gipc1 A G 8: 84,390,762 (GRCm39) E289G possibly damaging Het
Gm4924 T C 10: 82,214,778 (GRCm39) Y859H unknown Het
Gpatch1 A T 7: 34,994,738 (GRCm39) D509E possibly damaging Het
Gpbp1 A G 13: 111,577,233 (GRCm39) V219A possibly damaging Het
Gpr107 A T 2: 31,042,371 (GRCm39) M1L possibly damaging Het
Heg1 T C 16: 33,552,034 (GRCm39) F1003L probably damaging Het
Hivep1 A G 13: 42,309,814 (GRCm39) T685A probably benign Het
Hpse T A 5: 100,843,395 (GRCm39) D259V probably damaging Het
Ido2 A T 8: 25,040,826 (GRCm39) probably null Het
Ighv14-1 T C 12: 113,895,649 (GRCm39) D92G probably damaging Het
Krt87 A T 15: 101,385,083 (GRCm39) probably null Het
Lsp1 T C 7: 142,044,089 (GRCm39) V278A probably damaging Het
Lurap1l C A 4: 80,829,747 (GRCm39) S52R possibly damaging Het
Luzp2 A G 7: 54,485,577 (GRCm39) probably benign Het
Micall1 A G 15: 79,009,575 (GRCm39) E399G unknown Het
Ncapd2 A G 6: 125,163,119 (GRCm39) S130P possibly damaging Het
Nrg2 A G 18: 36,178,973 (GRCm39) V321A probably benign Het
Nuf2 T C 1: 169,352,954 (GRCm39) H17R probably damaging Het
Numb A G 12: 83,842,920 (GRCm39) W419R probably damaging Het
Or4d2b G A 11: 87,780,591 (GRCm39) L44F possibly damaging Het
Or4f62 T A 2: 111,986,507 (GRCm39) D70E probably damaging Het
Or56a3b A G 7: 104,771,473 (GRCm39) R270G probably benign Het
Pde6a T A 18: 61,353,678 (GRCm39) M1K probably null Het
Pknox1 C T 17: 31,822,172 (GRCm39) A313V probably damaging Het
Ppp2ca T A 11: 52,010,080 (GRCm39) N229K possibly damaging Het
Ptgdr A T 14: 45,096,401 (GRCm39) C104S probably damaging Het
Ralgapa2 C A 2: 146,230,406 (GRCm39) probably null Het
Rnase10 A T 14: 51,247,242 (GRCm39) T207S probably damaging Het
Rreb1 A G 13: 38,125,608 (GRCm39) T1305A probably benign Het
Rrp12 C A 19: 41,859,744 (GRCm39) probably null Het
Rubcnl A C 14: 75,269,453 (GRCm39) D37A possibly damaging Het
Saxo5 T C 8: 3,529,049 (GRCm39) F208S probably damaging Het
Scn9a T C 2: 66,364,567 (GRCm39) Y802C probably damaging Het
Sec16a A T 2: 26,330,715 (GRCm39) Y433* probably null Het
Sgk3 T A 1: 9,956,227 (GRCm39) V331D probably benign Het
Sirt7 C T 11: 120,511,311 (GRCm39) R280H probably benign Het
Snx13 G C 12: 35,142,912 (GRCm39) R252S probably damaging Het
Stk32b G T 5: 37,624,125 (GRCm39) D207E probably damaging Het
Sult2a7 C T 7: 14,203,978 (GRCm39) V262I not run Het
Tcstv7b C T 13: 120,702,587 (GRCm39) L128F probably damaging Het
Tent5b T A 4: 133,213,518 (GRCm39) F130I probably damaging Het
Tmem33 G C 5: 67,421,130 (GRCm39) V35L possibly damaging Het
Uba1y A G Y: 825,537 (GRCm39) I300V probably benign Het
Usp32 A T 11: 84,942,060 (GRCm39) V344E probably benign Het
Usp50 C T 2: 126,625,218 (GRCm39) probably benign Het
Vmn1r238 A C 18: 3,122,661 (GRCm39) F251C probably damaging Het
Vmn2r74 A T 7: 85,601,150 (GRCm39) Y829* probably null Het
Wars1 A G 12: 108,846,982 (GRCm39) F141L probably damaging Het
Zfp879 A G 11: 50,724,621 (GRCm39) V145A probably benign Het
Zfp934 A T 13: 62,640,204 (GRCm39) V56D probably benign 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
R1972:Rfx5 UTSW 3 94,864,603 (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
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'- GGCAGTGACCCTTCTACATC -3'
(R):5'- CCCCTGACAAAGTAGGAACAGG -3'

Sequencing Primer
(F):5'- ATTGTAAGCCAGCTGCCATG -3'
(R):5'- ACAGGTGGTAAGATCATGTTGATG -3'
Posted On 2019-06-26