Incidental Mutation 'R5377:Rfx4'
ID 425628
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 042845-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5377 (G1)
Quality Score 225
Status Not validated
Chromosome 10
Chromosomal Location 84591926-84742402 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 84696406 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Aspartic acid at position 233 (N233D)
Ref Sequence ENSEMBL: ENSMUSP00000093035 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000060397] [ENSMUST00000095388] [ENSMUST00000166696]
AlphaFold Q7TNK1
Predicted Effect noncoding transcript
Transcript: ENSMUST00000020226
Predicted Effect possibly damaging
Transcript: ENSMUST00000060397
AA Change: N327D

PolyPhen 2 Score 0.712 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: N327D

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: N233D

PolyPhen 2 Score 0.810 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: N233D

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 possibly damaging
Transcript: ENSMUST00000166696
AA Change: N184D

PolyPhen 2 Score 0.712 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
AA Change: N184D

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: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.5%
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: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A2m G T 6: 121,622,212 (GRCm39) V372F probably benign Het
Adcy10 G A 1: 165,347,464 (GRCm39) C393Y probably damaging Het
Adgrg7 A C 16: 56,550,669 (GRCm39) I681S possibly damaging Het
Akap8l T C 17: 32,540,485 (GRCm39) probably benign Het
Akr1a1 A T 4: 116,497,092 (GRCm39) V156E probably damaging Het
Alk T G 17: 72,202,734 (GRCm39) D1167A probably damaging Het
Ankrd11 T C 8: 123,620,453 (GRCm39) probably null Het
Aspm T A 1: 139,385,221 (GRCm39) N288K probably damaging Het
Aspm A G 1: 139,398,133 (GRCm39) probably null Het
Asxl2 G A 12: 3,524,618 (GRCm39) probably null Het
Atp6v0a1 A G 11: 100,946,413 (GRCm39) H802R probably damaging Het
B4galnt1 A G 10: 127,007,691 (GRCm39) T531A possibly damaging Het
Cecr2 A G 6: 120,733,530 (GRCm39) N506D possibly damaging Het
Crebrf T C 17: 26,978,839 (GRCm39) V509A probably damaging Het
Cyp4f40 A T 17: 32,894,590 (GRCm39) I413F probably null Het
Defb12 C A 8: 19,164,342 (GRCm39) probably null Het
Dnah2 T C 11: 69,312,674 (GRCm39) E4297G probably damaging Het
Dpysl5 A T 5: 30,948,857 (GRCm39) N371Y probably damaging Het
Eef1d G T 15: 75,775,038 (GRCm39) T207N probably benign Het
Esrrb C T 12: 86,565,783 (GRCm39) Q416* probably null Het
Exd2 T C 12: 80,536,222 (GRCm39) L284P probably damaging Het
Fat3 T A 9: 16,287,739 (GRCm39) I595F probably benign Het
Gm9920 A G 15: 54,972,371 (GRCm39) probably benign Het
Hephl1 T C 9: 14,981,084 (GRCm39) K783E probably damaging Het
Irs2 A G 8: 11,055,277 (GRCm39) S1052P probably benign Het
Kctd18 T C 1: 58,002,252 (GRCm39) I192V probably benign Het
Lama3 A G 18: 12,586,803 (GRCm39) D722G probably damaging Het
Lepr T C 4: 101,672,216 (GRCm39) V1080A possibly damaging Het
Lpin1 C T 12: 16,613,656 (GRCm39) G504S probably damaging Het
Lrit2 A C 14: 36,791,140 (GRCm39) Q273P possibly damaging Het
Mlkl T A 8: 112,054,569 (GRCm39) E189D probably benign Het
Mttp C T 3: 137,810,790 (GRCm39) R608H probably benign Het
Nav2 T C 7: 49,238,908 (GRCm39) V2011A probably benign Het
Nos2 A T 11: 78,848,317 (GRCm39) I1075F probably benign Het
Npat A G 9: 53,461,336 (GRCm39) probably null Het
Nucks1 T C 1: 131,846,771 (GRCm39) F16L probably damaging Het
Nus1 T C 10: 52,305,309 (GRCm39) S150P possibly damaging Het
Odad1 C T 7: 45,591,506 (GRCm39) R257* probably null Het
Oga A T 19: 45,746,461 (GRCm39) Y779* probably null Het
Or4c123 G T 2: 89,127,506 (GRCm39) T36K probably damaging Het
Or8b35 A T 9: 37,903,908 (GRCm39) Y40F probably benign Het
Pclo A G 5: 14,731,367 (GRCm39) T3290A unknown Het
Pign A T 1: 105,585,537 (GRCm39) F4Y probably benign Het
Rpgrip1 A T 14: 52,397,652 (GRCm39) M1325L possibly damaging Het
Rufy4 T C 1: 74,186,822 (GRCm39) C537R probably damaging Het
Scaf11 T A 15: 96,315,001 (GRCm39) H1227L possibly damaging Het
Sec31b G T 19: 44,507,076 (GRCm39) P840T probably damaging Het
Slc16a9 T A 10: 70,118,958 (GRCm39) L426I probably damaging Het
Slc22a30 G A 19: 8,321,757 (GRCm39) Q436* probably null Het
Slc34a1 T C 13: 23,996,575 (GRCm39) S27P probably damaging Het
Tacc1 A G 8: 25,672,299 (GRCm39) S310P possibly damaging Het
Tmem245 G A 4: 56,947,084 (GRCm39) R110C probably damaging Het
Trip12 T C 1: 84,735,152 (GRCm39) Y953C probably damaging Het
Trpm7 C A 2: 126,684,775 (GRCm39) probably null Het
Ush2a G A 1: 188,644,320 (GRCm39) V4561I probably benign Het
Vmn1r192 C T 13: 22,371,801 (GRCm39) V140I probably benign Het
Vmn2r66 A T 7: 84,656,026 (GRCm39) I330N probably damaging Het
Vmn2r99 T C 17: 19,599,531 (GRCm39) V405A probably damaging Het
Wdhd1 A C 14: 47,509,678 (GRCm39) V172G probably benign Het
Zfhx3 C T 8: 109,677,817 (GRCm39) R2956C possibly damaging Het
Zfp446 T C 7: 12,716,178 (GRCm39) L283P possibly damaging Het
Zfp82 T C 7: 29,756,591 (GRCm39) K164E 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
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'- GCAGGAGTTAGCCAGTAAGTC -3'
(R):5'- TTTGAGGCCCCAGATCATGTC -3'

Sequencing Primer
(F):5'- GTTAGCCAGTAAGTCCCTAAAACAG -3'
(R):5'- TCATGTCTGAAAGGTACAGGGGC -3'
Posted On 2016-08-04