Incidental Mutation 'R0099:Rfx4'
ID 33157
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 038385-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0099 (G1)
Quality Score 225
Status Validated (trace)
Chromosome 10
Chromosomal Location 84591926-84742402 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 84730168 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Leucine at position 437 (M437L)
Ref Sequence ENSEMBL: ENSMUSP00000128690 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000060397] [ENSMUST00000095388] [ENSMUST00000166696]
AlphaFold Q7TNK1
Predicted Effect probably benign
Transcript: ENSMUST00000060397
AA Change: M580L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: M580L

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 benign
Transcript: ENSMUST00000095388
AA Change: M486L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: M486L

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: M437L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
AA Change: M437L

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 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 94.3%
Validation Efficiency 100% (65/65)
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
A930018M24Rik C T 14: 51,134,179 (GRCm39) probably benign Het
Aadacl2fm1 A C 3: 59,843,856 (GRCm39) K183N probably benign Het
Acad10 A C 5: 121,759,353 (GRCm39) D1043E probably damaging Het
Adamtsl4 C T 3: 95,591,449 (GRCm39) G173R probably benign Het
Astn1 G T 1: 158,329,721 (GRCm39) S192I probably damaging Het
Atg2a T A 19: 6,302,819 (GRCm39) V1010E probably damaging Het
Col11a2 A G 17: 34,268,648 (GRCm39) E311G probably damaging Het
Col4a3 A C 1: 82,695,714 (GRCm39) E1638A probably benign Het
Cstf2t A G 19: 31,061,231 (GRCm39) R256G probably benign Het
Cyp4a12a T C 4: 115,183,869 (GRCm39) L225P probably damaging Het
Dnah5 G A 15: 28,240,080 (GRCm39) R479H probably damaging Het
Dsg3 A G 18: 20,673,079 (GRCm39) I917V probably benign Het
Fam76a G T 4: 132,638,098 (GRCm39) probably benign Het
Fras1 T A 5: 96,762,776 (GRCm39) probably null Het
Gli1 A G 10: 127,171,875 (GRCm39) V293A probably damaging Het
Gm10782 T A 13: 56,510,956 (GRCm39) noncoding transcript Het
Greb1l A G 18: 10,509,158 (GRCm39) E490G probably damaging Het
Hydin G A 8: 111,316,193 (GRCm39) G4362R probably damaging Het
Ica1 A T 6: 8,749,778 (GRCm39) probably benign Het
Ikzf4 T A 10: 128,470,066 (GRCm39) I485F probably damaging Het
Irf5 A G 6: 29,533,966 (GRCm39) T34A probably damaging Het
Krt81 A T 15: 101,361,402 (GRCm39) C59* probably null Het
Kynu T A 2: 43,519,065 (GRCm39) probably null Het
Ly6g6c T C 17: 35,287,891 (GRCm39) V61A probably damaging Het
Manea A C 4: 26,328,104 (GRCm39) I312M probably damaging Het
Micall1 G T 15: 79,016,101 (GRCm39) probably benign Het
Mthfs A T 9: 89,108,216 (GRCm39) probably benign Het
Myh4 A G 11: 67,150,173 (GRCm39) T1877A probably benign Het
Myo3a T C 2: 22,250,409 (GRCm39) I92T probably benign Het
Nepn A G 10: 52,277,181 (GRCm39) S306G probably damaging Het
Nol8 T C 13: 49,826,165 (GRCm39) V995A probably benign Het
Or5b101 A G 19: 13,005,165 (GRCm39) F176S probably damaging Het
Or5b105 T A 19: 13,080,504 (GRCm39) T49S probably benign Het
Or8a1b A T 9: 37,622,750 (GRCm39) V275E probably damaging Het
Or8g4 A G 9: 39,661,957 (GRCm39) I92V possibly damaging Het
Pde1a T A 2: 79,698,657 (GRCm39) probably null Het
Phf14 A G 6: 11,987,696 (GRCm39) probably benign Het
Plekhh2 C T 17: 84,899,100 (GRCm39) Q1026* probably null Het
Polr2b T A 5: 77,468,797 (GRCm39) probably benign Het
Ppp1r36 G T 12: 76,483,056 (GRCm39) probably null Het
Prdm14 A T 1: 13,189,169 (GRCm39) C392S probably damaging Het
Rabgap1l A G 1: 160,509,686 (GRCm39) S436P possibly damaging Het
Rfc2 A T 5: 134,624,135 (GRCm39) probably null Het
Rgs17 T A 10: 5,792,583 (GRCm39) R74S probably benign Het
Rnf139 C A 15: 58,771,264 (GRCm39) L430I probably damaging Het
Sgsm1 C A 5: 113,422,226 (GRCm39) probably benign Het
Skint6 T A 4: 112,668,698 (GRCm39) T1126S possibly damaging Het
Slc15a2 T C 16: 36,573,398 (GRCm39) E602G probably damaging Het
Stpg2 T C 3: 138,948,954 (GRCm39) probably benign Het
Sycp2l T C 13: 41,283,001 (GRCm39) probably benign Het
Tlr11 A T 14: 50,598,275 (GRCm39) N87I probably benign Het
Tril A G 6: 53,795,348 (GRCm39) F625L probably damaging Het
Ube3c T A 5: 29,812,062 (GRCm39) V434E probably damaging Het
Usp34 G A 11: 23,313,111 (GRCm39) G533R probably damaging Het
Utp25 A G 1: 192,810,778 (GRCm39) L75P probably damaging Het
Zfp93 G T 7: 23,974,900 (GRCm39) R295L 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
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
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'- AGCATAAAACAAGACAGTTCTATGAG -3'
Posted On 2013-05-09