Incidental Mutation 'R0503:Rfx4'
ID 47267
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 038698-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0503 (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 84730196 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Lysine at position 495 (I495K)
Ref Sequence ENSEMBL: ENSMUSP00000093035 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000060397] [ENSMUST00000095388] [ENSMUST00000166696]
AlphaFold Q7TNK1
Predicted Effect probably benign
Transcript: ENSMUST00000060397
AA Change: I589K

PolyPhen 2 Score 0.103 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: I589K

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: I495K

PolyPhen 2 Score 0.563 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: I495K

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: I446K

PolyPhen 2 Score 0.103 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
AA Change: I446K

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 0.1115 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.7%
Validation Efficiency 98% (57/58)
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: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9930111J21Rik1 T C 11: 48,838,322 (GRCm39) H755R possibly damaging Het
Atp2c2 A G 8: 120,461,316 (GRCm39) E279G probably null Het
Ccdc65 G T 15: 98,607,041 (GRCm39) D83Y probably damaging Het
Cd200r2 T A 16: 44,698,325 (GRCm39) M1K probably null Het
Clca4c-ps A T 3: 144,585,583 (GRCm39) noncoding transcript Het
Col6a6 A T 9: 105,644,550 (GRCm39) M1246K probably benign Het
Comp A T 8: 70,828,384 (GRCm39) N130I possibly damaging Het
Crot A G 5: 9,026,075 (GRCm39) V304A possibly damaging Het
Dapk1 T A 13: 60,878,662 (GRCm39) probably null Het
Dspp A T 5: 104,325,122 (GRCm39) D495V unknown Het
Erich2 A T 2: 70,340,043 (GRCm39) R169S probably damaging Het
Erich2 C A 2: 70,371,119 (GRCm39) S426R unknown Het
Gab1 C T 8: 81,526,771 (GRCm39) R109H probably damaging Het
Ggcx GTCTAT GTCTATCTAT 6: 72,406,140 (GRCm39) probably null Het
Gria1 T G 11: 57,080,542 (GRCm39) V175G probably damaging Het
Hmcn1 C T 1: 150,735,003 (GRCm39) V170M probably damaging Het
Irx4 T A 13: 73,414,703 (GRCm39) probably null Het
Katnb1 A G 8: 95,821,802 (GRCm39) T212A probably damaging Het
Kirrel1 A G 3: 87,005,109 (GRCm39) S80P probably benign Het
Lrrc75b T C 10: 75,389,488 (GRCm39) T81A possibly damaging Het
Macf1 A G 4: 123,363,608 (GRCm39) S1775P probably damaging Het
Mmp10 A T 9: 7,507,340 (GRCm39) I387F probably damaging Het
Mphosph10 A T 7: 64,039,641 (GRCm39) C110S probably benign Het
Mpig6b A G 17: 35,283,424 (GRCm39) probably benign Het
Mrps27 G T 13: 99,546,303 (GRCm39) probably benign Het
Muc6 G T 7: 141,218,685 (GRCm39) T1996N possibly damaging Het
Mybpc2 A G 7: 44,161,994 (GRCm39) probably benign Het
Nbea C T 3: 55,550,257 (GRCm39) G2724S possibly damaging Het
Nck2 A G 1: 43,572,728 (GRCm39) M1V probably null Het
Nefl T A 14: 68,321,432 (GRCm39) D7E probably benign Het
Nktr T A 9: 121,579,806 (GRCm39) probably benign Het
Nlrp12 C T 7: 3,298,007 (GRCm39) E55K probably damaging Het
Nsun7 T A 5: 66,440,924 (GRCm39) probably benign Het
Or10d4c A G 9: 39,558,772 (GRCm39) Y250C probably damaging Het
Or4c109 C T 2: 88,818,322 (GRCm39) V75I probably benign Het
Or4k5 T A 14: 50,385,935 (GRCm39) Y132F probably damaging Het
Or51a5 A T 7: 102,771,643 (GRCm39) M112K possibly damaging Het
Or6c2b T C 10: 128,947,671 (GRCm39) T208A probably damaging Het
Or6f2 T C 7: 139,756,354 (GRCm39) V113A possibly damaging Het
Pcdh15 A G 10: 74,046,217 (GRCm39) T165A probably damaging Het
Pikfyve A T 1: 65,259,058 (GRCm39) H410L probably damaging Het
Polr3c A T 3: 96,620,952 (GRCm39) probably null Het
Ptdss2 T A 7: 140,731,710 (GRCm39) probably benign Het
Ptprg A G 14: 12,237,138 (GRCm38) M1386V possibly damaging Het
Ptpru T C 4: 131,520,954 (GRCm39) N784S probably benign Het
Serpina12 C A 12: 103,997,418 (GRCm39) A368S probably damaging Het
Tmem39b A C 4: 129,580,779 (GRCm39) Y238D possibly damaging Het
Tspan11 T C 6: 127,916,075 (GRCm39) W124R probably benign Het
Ttll10 T C 4: 156,132,005 (GRCm39) probably benign Het
Tyro3 T C 2: 119,633,711 (GRCm39) probably benign Het
Unc79 A G 12: 103,045,127 (GRCm39) M644V probably benign Het
Vmn1r196 G A 13: 22,477,557 (GRCm39) M65I probably benign Het
Vmn2r85 T C 10: 130,258,609 (GRCm39) Y482C probably damaging Het
Zfp940 A G 7: 29,545,445 (GRCm39) probably benign Het
Zfyve9 A T 4: 108,576,961 (GRCm39) L40* probably null Het
Zkscan1 T A 5: 138,091,588 (GRCm39) I107N 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
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
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'- CTGTGCTGCCAGAGATTGTGATACC -3'
(R):5'- AGCTACAGGCCATTCAGCCTTTC -3'

Sequencing Primer
(F):5'- GATTCTATGACTCTACCAGGAGCTG -3'
(R):5'- GCCATTCAGCCTTTCTTCCATC -3'
Posted On 2013-06-12