Incidental Mutation 'R0924:Rfx4'
ID 83097
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 039071-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0924 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 84591926-84742402 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 84704291 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 262 (V262E)
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: V405E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: V405E

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: V311E

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: V311E

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: V262E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
AA Change: V262E

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 0.6467 question?
Coding Region Coverage
  • 1x: 99.5%
  • 3x: 98.9%
  • 10x: 97.7%
  • 20x: 96.2%
Validation Efficiency 97% (69/71)
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
Adamts18 A T 8: 114,432,028 (GRCm39) probably null Het
Ahcyl2 A C 6: 29,870,627 (GRCm39) probably null Het
Ajap1 T A 4: 153,470,929 (GRCm39) I293F probably damaging Het
Akap10 T C 11: 61,795,689 (GRCm39) probably benign Het
Aldh3b2 T C 19: 4,029,350 (GRCm39) V241A probably benign Het
Anxa6 A T 11: 54,885,214 (GRCm39) probably null Het
Atpaf1 T A 4: 115,652,635 (GRCm39) V12D probably damaging Het
Aurkb C A 11: 68,936,822 (GRCm39) Y12* probably null Het
Bicdl1 A G 5: 115,799,587 (GRCm39) probably benign Het
Bnc1 A T 7: 81,628,156 (GRCm39) probably benign Het
Bpi A G 2: 158,103,346 (GRCm39) I114V possibly damaging Het
Cacna1c A T 6: 118,652,857 (GRCm39) I772N probably damaging Het
Cacna2d1 A G 5: 16,570,860 (GRCm39) N1045D possibly damaging Het
Ccrl2 A G 9: 110,885,036 (GRCm39) V154A probably benign Het
Celsr3 C A 9: 108,723,224 (GRCm39) Q2831K possibly damaging Het
Cplane1 T C 15: 8,280,554 (GRCm39) probably benign Het
Cul3 A T 1: 80,267,835 (GRCm39) M102K probably damaging Het
Cwf19l2 T C 9: 3,441,047 (GRCm39) probably benign Het
Dlg5 G A 14: 24,185,645 (GRCm39) P1920L probably damaging Het
Dnah2 T C 11: 69,312,134 (GRCm39) H4393R probably damaging Het
Eif2b3 T A 4: 116,938,775 (GRCm39) V408D possibly damaging Het
Eml3 T C 19: 8,910,675 (GRCm39) probably null Het
Enpp2 T C 15: 54,770,355 (GRCm39) probably benign Het
Fcgbpl1 A T 7: 27,839,555 (GRCm39) Y456F probably damaging Het
Gm14178 T A 11: 99,638,326 (GRCm39) T18S Het
H2bc12 G A 13: 22,220,210 (GRCm39) D52N probably damaging Het
H2-M11 A G 17: 36,860,106 (GRCm39) M324V probably benign Het
H2-T13 A T 17: 36,394,824 (GRCm39) V33E probably damaging Het
Hdac10 T C 15: 89,010,065 (GRCm39) T298A probably benign Het
Hepacam A C 9: 37,295,224 (GRCm39) probably benign Het
Hmx3 A T 7: 131,144,813 (GRCm39) H41L probably benign Het
Ifi27l2a A G 12: 103,408,639 (GRCm39) V68A probably damaging Het
Itga11 A G 9: 62,683,956 (GRCm39) E1079G probably benign Het
Krt6a T C 15: 101,599,235 (GRCm39) probably benign Het
L1td1 A G 4: 98,625,862 (GRCm39) N686D probably damaging Het
Lrrtm2 G A 18: 35,346,808 (GRCm39) R165C probably damaging Het
Macf1 G T 4: 123,279,271 (GRCm39) A3910E probably damaging Het
Muc5ac A T 7: 141,361,252 (GRCm39) Y1521F possibly damaging Het
Myo7a A T 7: 97,747,463 (GRCm39) I129N probably damaging Het
Ncam1 A T 9: 49,473,476 (GRCm39) probably benign Het
Nckap1 A T 2: 80,384,593 (GRCm39) C114S probably benign Het
Nf1 T G 11: 79,344,692 (GRCm39) W1260G probably damaging Het
Or3a1d T C 11: 74,237,624 (GRCm39) Y262C probably damaging Het
Or6b2b A G 1: 92,419,127 (GRCm39) S117P possibly damaging Het
Or6c76b A T 10: 129,692,515 (GRCm39) I43F probably damaging Het
Oxtr A T 6: 112,466,598 (GRCm39) probably null Het
Pabpc4 C T 4: 123,188,458 (GRCm39) R356C possibly damaging Het
Pcbp2 T A 15: 102,398,197 (GRCm39) D182E probably damaging Het
Pgm2 A T 5: 64,269,490 (GRCm39) I526F possibly damaging Het
Rab43 A T 6: 87,769,752 (GRCm39) Y151* probably null Het
Rbm19 A G 5: 120,264,269 (GRCm39) E343G probably benign Het
Rel A T 11: 23,692,439 (GRCm39) D531E probably benign Het
Rnf31 T C 14: 55,830,459 (GRCm39) probably benign Het
Robo3 T A 9: 37,340,778 (GRCm39) probably benign Het
Ryr3 A G 2: 112,672,178 (GRCm39) L1431P probably damaging Het
Sema3d A C 5: 12,513,183 (GRCm39) D51A possibly damaging Het
Sema6a A G 18: 47,381,559 (GRCm39) L996P probably damaging Het
Sh2d4a T A 8: 68,787,775 (GRCm39) F294I probably damaging Het
Sorl1 T A 9: 41,919,470 (GRCm39) probably benign Het
Sox1ot G T 8: 12,480,455 (GRCm39) noncoding transcript Het
Spsb3 A T 17: 25,110,358 (GRCm39) N395I probably damaging Het
Sptan1 A G 2: 29,906,040 (GRCm39) N1662S probably damaging Het
Srd5a2 G T 17: 74,331,516 (GRCm39) N160K probably damaging Het
Sting1 A G 18: 35,868,154 (GRCm39) probably null Het
Tmem132d G A 5: 128,061,503 (GRCm39) probably benign Het
Unc80 A T 1: 66,549,800 (GRCm39) Q686L possibly damaging Het
Vmn2r93 A G 17: 18,524,443 (GRCm39) T146A probably benign Het
Wdr19 A G 5: 65,413,782 (GRCm39) probably benign Het
Zfp646 C T 7: 127,482,982 (GRCm39) Q1500* probably null Het
Zfp683 T C 4: 133,783,138 (GRCm39) Y201H 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
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
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'- TCAGGAAGAGCTATGCAGTCCAGTC -3'
(R):5'- ACCTTCAAAGCCTGTGAAGCCG -3'

Sequencing Primer
(F):5'- GCAGTCCAGTCCTCTGTG -3'
(R):5'- GAGACTGAGAATCTTGTCTCTGCC -3'
Posted On 2013-11-08