Incidental Mutation 'R4300:Rfx4'
ID 322385
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 041657-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4300 (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 84740966 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 601 (Y601H)
Ref Sequence ENSEMBL: ENSMUSP00000093035 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000060397] [ENSMUST00000095388] [ENSMUST00000166696]
AlphaFold Q7TNK1
Predicted Effect possibly damaging
Transcript: ENSMUST00000060397
AA Change: Y695H

PolyPhen 2 Score 0.841 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: Y695H

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: Y601H

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: Y601H

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: Y552H

PolyPhen 2 Score 0.841 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
AA Change: Y552H

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 0.1987 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.6%
Validation Efficiency 100% (40/40)
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: 33 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930503B20Rik T A 3: 146,356,675 (GRCm39) R78* probably null Het
A2m G A 6: 121,650,434 (GRCm39) V1181I probably benign Het
Cacna1b T C 2: 24,525,251 (GRCm39) S1639G probably damaging Het
Ccs T C 19: 4,884,285 (GRCm39) T56A probably benign Het
Cd177 T C 7: 24,449,845 (GRCm39) I547V possibly damaging Het
Ckmt2 C A 13: 92,011,457 (GRCm39) probably null Het
Cyth1 A G 11: 118,074,720 (GRCm39) F180L probably damaging Het
Dip2c A G 13: 9,660,747 (GRCm39) I840M probably damaging Het
Gm37150 G A 9: 72,292,758 (GRCm39) noncoding transcript Het
Herc1 A G 9: 66,396,688 (GRCm39) D4255G probably damaging Het
Kcnd3 C T 3: 105,566,082 (GRCm39) A421V probably damaging Het
Kcnn4 G T 7: 24,077,029 (GRCm39) V193L probably benign Het
Lrrc8d G A 5: 105,961,606 (GRCm39) R672Q probably damaging Het
Mboat2 A G 12: 25,009,082 (GRCm39) N463D probably benign Het
Mtfr1 T A 3: 19,269,621 (GRCm39) probably null Het
Or10g6 A C 9: 39,934,435 (GRCm39) I249L probably benign Het
Or5h24 T C 16: 58,918,641 (GRCm39) Y238C unknown Het
Pcnt G C 10: 76,203,225 (GRCm39) R2626G probably benign Het
Pik3cg A G 12: 32,226,671 (GRCm39) I1072T probably damaging Het
Prc1 G A 7: 79,960,964 (GRCm39) probably benign Het
Psph G T 5: 129,864,529 (GRCm39) probably null Het
Rmc1 A G 18: 12,321,919 (GRCm39) N513D probably benign Het
Setd5 T G 6: 113,127,123 (GRCm39) V1249G probably damaging Het
Sirpb1b A T 3: 15,613,821 (GRCm39) I87K probably damaging Het
Slc14a2 G A 18: 78,250,283 (GRCm39) R62C probably damaging Het
Spata31 A T 13: 65,067,575 (GRCm39) H79L probably benign Het
Srbd1 C A 17: 86,292,632 (GRCm39) R979L probably damaging Het
Stox2 A T 8: 47,647,027 (GRCm39) Y208* probably null Het
Sun1 A T 5: 139,213,349 (GRCm39) probably benign Het
Tfap4 T C 16: 4,369,224 (GRCm39) D132G probably damaging Het
Top2b T G 14: 16,409,189 (GRCm38) I777M probably damaging Het
Tubgcp3 G T 8: 12,707,600 (GRCm39) P130T probably damaging Het
Txlnb A G 10: 17,703,673 (GRCm39) E277G 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
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'- GGGTGCACATAACTTCAAGC -3'
(R):5'- GTCAGCCCGCAAGTTATGATG -3'

Sequencing Primer
(F):5'- TTCAAGCTAACTTTAATTTTGTGGAC -3'
(R):5'- CAGCCCGCAAGTTATGATGTATTG -3'
Posted On 2015-06-20