Incidental Mutation 'R5879:Rfx4'
ID 455724
Institutional Source Beutler Lab
Gene Symbol Rfx4
Ensembl Gene ENSMUSG00000020037
Gene Name regulatory factor X, 4 (influences HLA class II expression)
Synonyms 4933412G19Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5879 (G1)
Quality Score 225
Status Not validated
Chromosome 10
Chromosomal Location 84591926-84742402 bp(+) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to G at 84650625 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000051107 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000060397]
AlphaFold Q7TNK1
Predicted Effect probably null
Transcript: ENSMUST00000060397
SMART Domains Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037

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 noncoding transcript
Transcript: ENSMUST00000158826
Predicted Effect noncoding transcript
Transcript: ENSMUST00000165868
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173479
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.9%
  • 20x: 93.7%
Validation Efficiency
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: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aldh16a1 C T 7: 44,796,930 (GRCm39) W66* probably null Het
Arhgap39 T C 15: 76,636,007 (GRCm39) D76G probably damaging Het
Arhgef2 G A 3: 88,550,924 (GRCm39) probably null Het
C1qtnf2 T C 11: 43,376,835 (GRCm39) M99T probably damaging Het
Cyren A G 6: 34,851,593 (GRCm39) L87P probably damaging Het
Eml3 G A 19: 8,912,379 (GRCm39) C392Y possibly damaging Het
Ephb4 C A 5: 137,358,678 (GRCm39) P287Q probably benign Het
Fat4 G T 3: 38,941,485 (GRCm39) R126L probably benign Het
Flt3 T C 5: 147,271,719 (GRCm39) M858V probably damaging Het
Gprin3 A C 6: 59,331,698 (GRCm39) I203R probably benign Het
Insr G T 8: 3,248,173 (GRCm39) Y457* probably null Het
Ipo13 G A 4: 117,760,400 (GRCm39) T649I possibly damaging Het
Krba1 A G 6: 48,392,678 (GRCm39) D818G possibly damaging Het
Llgl1 G A 11: 60,603,806 (GRCm39) G1016R probably benign Het
Loxl4 A G 19: 42,596,066 (GRCm39) V142A probably benign Het
Mthfd1 A G 12: 76,340,992 (GRCm39) I464V probably benign Het
Mycs C A X: 5,380,131 (GRCm39) K316N probably damaging Het
Ncor2 A G 5: 125,103,839 (GRCm39) probably benign Het
Nlrc3 A G 16: 3,781,909 (GRCm39) F516S probably damaging Het
Oacyl A G 18: 65,882,743 (GRCm39) S540G probably damaging Het
Olfml2a A T 2: 38,850,242 (GRCm39) T653S probably damaging Het
Or8s16 C T 15: 98,211,369 (GRCm39) V21I probably benign Het
Pcnx2 A T 8: 126,500,685 (GRCm39) N1468K probably damaging Het
Plbd1 A G 6: 136,611,503 (GRCm39) I258T probably damaging Het
Ppargc1b C G 18: 61,442,164 (GRCm39) D591H probably damaging Het
Pramel21 A T 4: 143,344,161 (GRCm39) Y487F possibly damaging Het
Prop1 C T 11: 50,844,153 (GRCm39) V27M probably damaging Het
Rgs11 C T 17: 26,422,437 (GRCm39) probably benign Het
Slc6a5 T A 7: 49,595,260 (GRCm39) F541I probably damaging Het
Srgap3 A T 6: 112,699,807 (GRCm39) V1057E possibly damaging Het
Synpo2 A T 3: 122,907,946 (GRCm39) W457R probably damaging Het
Tet2 T A 3: 133,193,721 (GRCm39) N238Y possibly damaging Het
Tiam2 T A 17: 3,487,540 (GRCm39) M687K probably damaging Het
Ticrr A G 7: 79,346,438 (GRCm39) E1866G probably benign Het
Tspan8 T C 10: 115,669,156 (GRCm39) S64P possibly damaging Het
Ugt2b37 C T 5: 87,402,265 (GRCm39) G122D probably benign Het
Uqcrc2 A G 7: 120,237,111 (GRCm39) E53G probably damaging Het
Vcan T C 13: 89,852,071 (GRCm39) D963G probably damaging Het
Vmn2r24 T A 6: 123,764,226 (GRCm39) Y368N possibly damaging Het
Wdr5 A G 2: 27,418,323 (GRCm39) T208A probably benign Het
Zbtb18 A G 1: 177,275,936 (GRCm39) Y423C probably damaging Het
Zc3h6 A G 2: 128,839,696 (GRCm39) probably null 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
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
R7428: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'- GCTTGCAATCCCATCAACAATG -3'
(R):5'- GAGGGTTGTGGCAGCAAAAT -3'

Sequencing Primer
(F):5'- CAACAATGGAGGAGTGATTTTCTC -3'
(R):5'- AACTCAGACCTTCAGGCTTGGTG -3'
Posted On 2017-02-10