Incidental Mutation 'R7428:Rfx4'
ID 576261
Institutional Source Beutler Lab
Gene Symbol Rfx4
Ensembl Gene ENSMUSG00000020037
Gene Name regulatory factor X, 4 (influences HLA class II expression)
Synonyms 4933412G19Rik
MMRRC Submission 045506-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7428 (G1)
Quality Score 225.009
Status Validated
Chromosome 10
Chromosomal Location 84591926-84742402 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 84731876 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Lysine at position 618 (Q618K)
Ref Sequence ENSEMBL: ENSMUSP00000051107 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000060397] [ENSMUST00000095388] [ENSMUST00000166696]
AlphaFold Q7TNK1
Predicted Effect probably benign
Transcript: ENSMUST00000060397
AA Change: Q618K

PolyPhen 2 Score 0.285 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: Q618K

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 58 136 7.9e-37 PFAM
Blast:HisKA 293 356 5e-7 BLAST
low complexity region 503 515 N/A INTRINSIC
low complexity region 521 537 N/A INTRINSIC
low complexity region 599 611 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000095388
AA Change: Q524K

PolyPhen 2 Score 0.487 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: Q524K

DomainStartEndE-ValueType
SCOP:d1kwha_ 11 201 6e-3 SMART
Blast:HisKA 199 262 4e-7 BLAST
low complexity region 409 421 N/A INTRINSIC
low complexity region 427 443 N/A INTRINSIC
low complexity region 505 517 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000166696
AA Change: Q475K

PolyPhen 2 Score 0.285 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
AA Change: Q475K

DomainStartEndE-ValueType
Blast:HisKA 150 213 6e-7 BLAST
low complexity region 360 372 N/A INTRINSIC
low complexity region 378 394 N/A INTRINSIC
low complexity region 456 468 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.2%
Validation Efficiency 100% (71/71)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X2, X3, and X5. It has been shown to interact with itself as well as with regulatory factors X2 and X3, but it does not interact with regulatory factor X1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]
PHENOTYPE: Inactivating null allele or homozygous point mutation alleles exhibit missing dorsal midline structure of the cortex including the subcommissural organ and neonatal lethality. Heterozygous null mice have congenital hydrocephalus. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Anxa10 T A 8: 62,545,543 (GRCm39) Y63F probably benign Het
Atl2 T C 17: 80,183,227 (GRCm39) probably null Het
B3gnt4 A G 5: 123,648,794 (GRCm39) N53S probably damaging Het
Bpifb5 G A 2: 154,067,042 (GRCm39) M98I probably benign Het
Cacna2d3 A G 14: 28,786,232 (GRCm39) M585T probably damaging Het
Cbarp T C 10: 79,967,138 (GRCm39) D701G probably damaging Het
Cep295 A G 9: 15,244,794 (GRCm39) S1221P possibly damaging Het
Cep350 T C 1: 155,770,365 (GRCm39) S1842G probably benign Het
Cntrl T A 2: 35,060,546 (GRCm39) W1913R probably benign Het
Creb5 C A 6: 53,658,143 (GRCm39) Q158K unknown Het
Crtam G C 9: 40,892,478 (GRCm39) A266G probably benign Het
Cry2 T C 2: 92,243,392 (GRCm39) D483G possibly damaging Het
Csmd1 A G 8: 16,073,864 (GRCm39) F2044L possibly damaging Het
Cxcr6 A T 9: 123,639,305 (GRCm39) Y109F probably benign Het
Cyb5b A G 8: 107,897,048 (GRCm39) D106G probably benign Het
D630036H23Rik T C 12: 36,431,537 (GRCm39) R154G unknown Het
Ddit4l A G 3: 137,331,931 (GRCm39) E99G probably damaging Het
Dmbt1 A T 7: 130,710,192 (GRCm39) T1495S possibly damaging Het
Gm21886 A T 18: 80,132,867 (GRCm39) L97Q probably damaging Het
Hlcs A G 16: 94,068,758 (GRCm39) V154A probably benign Het
Hpdl A T 4: 116,678,062 (GRCm39) L133Q probably damaging Het
Inpp5f A G 7: 128,281,529 (GRCm39) D510G probably damaging Het
Ism2 G T 12: 87,333,769 (GRCm39) T92K possibly damaging Het
Kif13b T C 14: 65,025,909 (GRCm39) I1422T probably benign Het
Leng8 C T 7: 4,146,572 (GRCm39) R395W probably damaging Het
Mocs2 A G 13: 114,957,400 (GRCm39) I6V probably benign Het
Mthfr A G 4: 148,136,060 (GRCm39) M378V probably benign Het
Myh13 A G 11: 67,223,390 (GRCm39) T237A probably damaging Het
Nr1h4 T C 10: 89,334,267 (GRCm39) E41G probably benign Het
Nup205 T A 6: 35,204,494 (GRCm39) I1460N probably damaging Het
Nup98 A T 7: 101,784,208 (GRCm39) probably null Het
Nxpe5 A C 5: 138,238,022 (GRCm39) Y194S probably damaging Het
Or12e9 G T 2: 87,202,034 (GRCm39) V53L probably benign Het
Or52m1 A G 7: 102,289,533 (GRCm39) I27V probably benign Het
Or5m12 T A 2: 85,734,475 (GRCm39) R308* probably null Het
Or5m3 A T 2: 85,838,563 (GRCm39) I148L probably benign Het
Or9s18 A G 13: 65,300,866 (GRCm39) Y276C probably damaging Het
Otof G T 5: 30,547,169 (GRCm39) D383E probably damaging Het
Pcdh9 G T 14: 94,124,547 (GRCm39) T541K probably damaging Het
Pclo A T 5: 14,800,531 (GRCm39) I1179F Het
Pde6c T C 19: 38,145,984 (GRCm39) probably null Het
Pdia6 T C 12: 17,328,546 (GRCm39) V167A probably damaging Het
Phf7 C T 14: 30,962,370 (GRCm39) R145Q possibly damaging Het
Plxnb1 T C 9: 108,937,236 (GRCm39) V1139A probably benign Het
Prkg1 T C 19: 30,556,235 (GRCm39) I585M probably damaging Het
Prom2 A G 2: 127,381,731 (GRCm39) L195P probably damaging Het
Ptprd G A 4: 76,004,705 (GRCm39) P17S probably benign Het
Rhobtb1 T A 10: 69,084,654 (GRCm39) I15N probably damaging Het
Sap30 C T 8: 57,940,546 (GRCm39) V19M possibly damaging Het
Scrib G A 15: 75,933,047 (GRCm39) T721M probably damaging Het
Slc12a1 C A 2: 125,056,052 (GRCm39) T861N probably benign Het
Slc35f1 T A 10: 52,965,510 (GRCm39) S308R probably damaging Het
Slc35f4 T A 14: 49,536,355 (GRCm39) I427F probably damaging Het
Slco4c1 T C 1: 96,765,245 (GRCm39) T402A possibly damaging Het
Sprr2f G A 3: 92,273,251 (GRCm39) V17M unknown Het
Stab1 T C 14: 30,881,216 (GRCm39) T605A probably benign Het
Taar8c A C 10: 23,977,446 (GRCm39) L122R probably damaging Het
Tbc1d2 G A 4: 46,649,965 (GRCm39) P24S probably benign Het
Tex36 T C 7: 133,196,866 (GRCm39) probably null Het
Tmem145 T C 7: 25,006,590 (GRCm39) probably null Het
Ttn T G 2: 76,550,698 (GRCm39) D31528A probably damaging Het
Vars2 A T 17: 35,977,578 (GRCm39) V118E probably benign Het
Vmn1r195 T C 13: 22,463,022 (GRCm39) V164A probably benign Het
Vmn2r69 T C 7: 85,060,467 (GRCm39) I372M probably benign Het
Vmn2r93 A T 17: 18,546,672 (GRCm39) H848L probably benign Het
Wnt9b T C 11: 103,621,643 (GRCm39) Q338R probably benign Het
Zfp128 A G 7: 12,624,289 (GRCm39) D219G probably benign Het
Zfp541 A T 7: 15,826,793 (GRCm39) R1181W probably damaging Het
Zfp867 C T 11: 59,354,760 (GRCm39) G190S probably benign Het
Zfp971 T A 2: 177,674,967 (GRCm39) C189S probably damaging Het
Other mutations in Rfx4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00094:Rfx4 APN 10 84,676,063 (GRCm39) missense probably damaging 1.00
IGL00334:Rfx4 APN 10 84,615,917 (GRCm39) missense possibly damaging 0.91
IGL00928:Rfx4 APN 10 84,675,978 (GRCm39) missense probably benign 0.04
IGL01063:Rfx4 APN 10 84,704,246 (GRCm39) missense possibly damaging 0.90
IGL01490:Rfx4 APN 10 84,676,715 (GRCm39) missense possibly damaging 0.85
IGL02390:Rfx4 APN 10 84,676,014 (GRCm39) missense probably damaging 1.00
IGL02454:Rfx4 APN 10 84,675,970 (GRCm39) missense possibly damaging 0.83
R0099:Rfx4 UTSW 10 84,730,168 (GRCm39) missense probably benign
R0503:Rfx4 UTSW 10 84,730,196 (GRCm39) missense possibly damaging 0.56
R0924:Rfx4 UTSW 10 84,704,291 (GRCm39) missense probably damaging 1.00
R0930:Rfx4 UTSW 10 84,704,291 (GRCm39) missense probably damaging 1.00
R1386:Rfx4 UTSW 10 84,699,149 (GRCm39) missense probably damaging 1.00
R1715:Rfx4 UTSW 10 84,680,144 (GRCm39) missense probably damaging 1.00
R1738:Rfx4 UTSW 10 84,716,839 (GRCm39) critical splice donor site probably null
R1987:Rfx4 UTSW 10 84,731,952 (GRCm39) missense possibly damaging 0.87
R3717:Rfx4 UTSW 10 84,716,088 (GRCm39) missense probably damaging 1.00
R4231:Rfx4 UTSW 10 84,650,558 (GRCm39) missense probably benign 0.03
R4300:Rfx4 UTSW 10 84,740,966 (GRCm39) missense probably damaging 0.98
R4581:Rfx4 UTSW 10 84,680,164 (GRCm39) missense possibly damaging 0.93
R4582:Rfx4 UTSW 10 84,680,164 (GRCm39) missense possibly damaging 0.93
R4618:Rfx4 UTSW 10 84,716,760 (GRCm39) missense probably benign 0.01
R5156:Rfx4 UTSW 10 84,704,218 (GRCm39) missense probably damaging 1.00
R5185:Rfx4 UTSW 10 84,699,114 (GRCm39) missense probably damaging 1.00
R5377:Rfx4 UTSW 10 84,696,406 (GRCm39) missense possibly damaging 0.81
R5601:Rfx4 UTSW 10 84,634,442 (GRCm39) missense probably damaging 1.00
R5879:Rfx4 UTSW 10 84,650,625 (GRCm39) critical splice donor site probably null
R5996:Rfx4 UTSW 10 84,675,881 (GRCm39) nonsense probably null
R6358:Rfx4 UTSW 10 84,680,099 (GRCm39) missense probably damaging 1.00
R6805:Rfx4 UTSW 10 84,676,092 (GRCm39) missense possibly damaging 0.86
R7248:Rfx4 UTSW 10 84,740,919 (GRCm39) missense probably benign 0.05
R7427:Rfx4 UTSW 10 84,731,876 (GRCm39) missense probably benign 0.28
R7514:Rfx4 UTSW 10 84,716,090 (GRCm39) missense probably damaging 1.00
R7576:Rfx4 UTSW 10 84,699,213 (GRCm39) missense probably damaging 0.98
R8002:Rfx4 UTSW 10 84,676,721 (GRCm39) missense probably damaging 0.97
R8838:Rfx4 UTSW 10 84,676,758 (GRCm39) missense probably damaging 1.00
R8938:Rfx4 UTSW 10 84,675,936 (GRCm39) missense probably damaging 1.00
R9359:Rfx4 UTSW 10 84,740,921 (GRCm39) missense probably benign 0.00
R9513:Rfx4 UTSW 10 84,674,050 (GRCm39) start codon destroyed probably null 0.01
RF010:Rfx4 UTSW 10 84,694,351 (GRCm39) critical splice acceptor site probably benign
RF014:Rfx4 UTSW 10 84,694,353 (GRCm39) critical splice acceptor site probably benign
RF015:Rfx4 UTSW 10 84,694,353 (GRCm39) critical splice acceptor site probably benign
RF023:Rfx4 UTSW 10 84,694,349 (GRCm39) critical splice acceptor site probably benign
RF030:Rfx4 UTSW 10 84,694,344 (GRCm39) critical splice acceptor site probably benign
RF035:Rfx4 UTSW 10 84,694,344 (GRCm39) critical splice acceptor site probably benign
RF046:Rfx4 UTSW 10 84,694,345 (GRCm39) critical splice acceptor site probably benign
RF060:Rfx4 UTSW 10 84,694,358 (GRCm39) critical splice acceptor site probably benign
RF062:Rfx4 UTSW 10 84,694,345 (GRCm39) critical splice acceptor site probably benign
X0024:Rfx4 UTSW 10 84,615,938 (GRCm39) missense possibly damaging 0.82
Z1177:Rfx4 UTSW 10 84,731,955 (GRCm39) missense probably benign 0.30
Z1177:Rfx4 UTSW 10 84,650,548 (GRCm39) missense possibly damaging 0.85
Predicted Primers PCR Primer
(F):5'- GGGTTTTAAAGCTCACCACAGC -3'
(R):5'- ACAGCGGACTTATTAACTGTGGG -3'

Sequencing Primer
(F):5'- TTTTAAAGCTCACCACAGCAAGGC -3'
(R):5'- ACTTATTAACTGTGGGTAGTTGGC -3'
Posted On 2019-10-07