Incidental Mutation 'R5156:Rfx4'
ID 470609
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 042738-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5156 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 84591926-84742402 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 84704218 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 238 (Y238H)
Ref Sequence ENSEMBL: ENSMUSP00000128690 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000060397] [ENSMUST00000095388] [ENSMUST00000166696]
AlphaFold Q7TNK1
Predicted Effect noncoding transcript
Transcript: ENSMUST00000020226
Predicted Effect probably damaging
Transcript: ENSMUST00000060397
AA Change: Y381H

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: Y381H

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 probably damaging
Transcript: ENSMUST00000095388
AA Change: Y287H

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: Y287H

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 damaging
Transcript: ENSMUST00000166696
AA Change: Y238H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
AA Change: Y238H

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
Meta Mutation Damage Score 0.0802 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 94.0%
Validation Efficiency 100% (52/52)
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: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921513D11Rik G T 17: 79,935,638 (GRCm39) probably benign Het
Apeh C T 9: 107,971,486 (GRCm39) A29T probably damaging Het
Arap2 A T 5: 62,826,524 (GRCm39) Y1013* probably null Het
Arhgef4 A G 1: 34,762,355 (GRCm39) E537G unknown Het
Asf1b T C 8: 84,682,540 (GRCm39) F28S probably damaging Het
Cd46 T A 1: 194,767,693 (GRCm39) I123L possibly damaging Het
Cdca7 A T 2: 72,309,370 (GRCm39) T48S probably damaging Het
Cfap53 T A 18: 74,492,838 (GRCm39) probably benign Het
Clca3a2 T A 3: 144,511,599 (GRCm39) T599S probably benign Het
Csf1 T A 3: 107,656,252 (GRCm39) T148S probably benign Het
Dmbt1 T C 7: 130,699,400 (GRCm39) probably null Het
Dmpk A G 7: 18,818,050 (GRCm39) D44G probably damaging Het
Dnajb12 T A 10: 59,728,782 (GRCm39) N223K probably damaging Het
Dync1h1 T A 12: 110,595,264 (GRCm39) M1392K probably benign Het
Edrf1 C T 7: 133,261,908 (GRCm39) A867V probably damaging Het
Efemp2 T A 19: 5,527,706 (GRCm39) C94S possibly damaging Het
Epha8 C T 4: 136,666,037 (GRCm39) S373N probably benign Het
Foxk1 A G 5: 142,434,588 (GRCm39) D284G possibly damaging Het
Fzd10 C A 5: 128,678,366 (GRCm39) R29S possibly damaging Het
Gm13991 T C 2: 116,358,665 (GRCm39) noncoding transcript Het
Gm6818 A T 7: 38,101,471 (GRCm39) noncoding transcript Het
Hydin T A 8: 111,336,333 (GRCm39) C5037S probably benign Het
Ikzf1 T A 11: 11,719,448 (GRCm39) M492K probably damaging Het
Krt20 G T 11: 99,320,879 (GRCm39) S394R possibly damaging Het
Lrrc71 T A 3: 87,653,094 (GRCm39) R107S probably benign Het
Mia2 A G 12: 59,219,323 (GRCm39) T436A possibly damaging Het
Muc19 T A 15: 91,784,614 (GRCm39) noncoding transcript Het
Neu4 T C 1: 93,952,177 (GRCm39) V182A probably damaging Het
Notch2 T G 3: 98,031,626 (GRCm39) F1167V possibly damaging Het
Nrap A G 19: 56,360,277 (GRCm39) M189T possibly damaging Het
Nt5m A T 11: 59,765,487 (GRCm39) I172F probably damaging Het
Or5b118 G T 19: 13,449,037 (GRCm39) K234N probably damaging Het
Or5w15 G A 2: 87,568,119 (GRCm39) P183L possibly damaging Het
Or8k41 A T 2: 86,313,362 (GRCm39) C241* probably null Het
Plekha5 C T 6: 140,372,254 (GRCm39) T68M probably damaging Het
Ppef2 A G 5: 92,392,461 (GRCm39) probably null Het
Ppp1r37 T C 7: 19,295,900 (GRCm39) probably benign Het
Sanbr A G 11: 23,543,424 (GRCm39) probably null Het
Sec13 G A 6: 113,707,837 (GRCm39) A161V probably benign Het
Serhl G A 15: 82,986,895 (GRCm39) probably benign Het
Slco4a1 T C 2: 180,114,572 (GRCm39) V588A probably benign Het
Slitrk3 T C 3: 72,956,592 (GRCm39) T727A probably benign Het
Sp100 T A 1: 85,601,404 (GRCm39) D241E probably damaging Het
Spata2 G T 2: 167,325,494 (GRCm39) H442N probably damaging Het
Speg T C 1: 75,404,731 (GRCm39) V2588A probably damaging Het
Tnfsf12 A G 11: 69,578,155 (GRCm39) S141P probably damaging Het
Trank1 A G 9: 111,219,762 (GRCm39) I2166M probably damaging Het
Trim10 T A 17: 37,187,948 (GRCm39) V388E probably damaging Het
Ttc23l G T 15: 10,551,636 (GRCm39) T30K possibly damaging Het
Vmn2r10 A G 5: 109,143,466 (GRCm39) V828A probably benign Het
Vmn2r75 T A 7: 85,813,436 (GRCm39) L455F possibly damaging Het
Vwa8 T A 14: 79,221,666 (GRCm39) S541T probably benign 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
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
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'- TGCTAGCCAGTGTTATTAATGAGG -3'
(R):5'- TAGCTCACCCTGGGATTCTG -3'

Sequencing Primer
(F):5'- TGGTAACATGCTATGAGAGATGTG -3'
(R):5'- GTGCTACTTAGGTGTCCATAGAGAC -3'
Posted On 2017-03-23