Incidental Mutation 'R5996:Rfx4'
ID 481137
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 044175-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5996 (G1)
Quality Score 225.009
Status Validated
Chromosome 10
Chromosomal Location 84591926-84742402 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) G to A at 84675881 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tryptophan to Stop codon at position 32 (W32*)
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 silent
Transcript: ENSMUST00000060397
SMART Domains Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037

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 null
Transcript: ENSMUST00000095388
AA Change: W32*
SMART Domains Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: W32*

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
SMART Domains Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037

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 0.9714 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.6%
  • 20x: 92.4%
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
1700093K21Rik A G 11: 23,468,928 (GRCm39) M1T probably null Het
A2m T A 6: 121,636,353 (GRCm39) W741R probably damaging Het
Abcb8 C T 5: 24,605,137 (GRCm39) R108C possibly damaging Het
Acan A G 7: 78,761,068 (GRCm39) T1927A probably damaging Het
Agbl4 A G 4: 110,812,869 (GRCm39) probably null Het
Bltp1 T C 3: 36,985,265 (GRCm39) F865S probably benign Het
Ccr8 T A 9: 119,923,529 (GRCm39) C215S probably damaging Het
Cd209b T C 8: 3,968,688 (GRCm39) T314A probably benign Het
Cd244a T G 1: 171,409,208 (GRCm39) probably null Het
Cdh23 T C 10: 60,249,356 (GRCm39) E849G possibly damaging Het
Cep57 A G 9: 13,721,175 (GRCm39) V268A probably damaging Het
Clip4 T C 17: 72,163,305 (GRCm39) S626P probably damaging Het
Col19a1 C T 1: 24,367,152 (GRCm39) G477R probably damaging Het
Col4a4 T C 1: 82,433,449 (GRCm39) D1498G unknown Het
Coro6 T C 11: 77,357,322 (GRCm39) V177A probably benign Het
Crip3 T C 17: 46,742,210 (GRCm39) S202P possibly damaging Het
Cxcr2 T C 1: 74,197,619 (GRCm39) C38R probably damaging Het
Cyp4f13 C T 17: 33,148,447 (GRCm39) G327R possibly damaging Het
Dab2 C T 15: 6,464,792 (GRCm39) Q415* probably null Het
Dennd5b A G 6: 148,969,593 (GRCm39) F287L probably benign Het
Dlg4 G A 11: 69,908,057 (GRCm39) R6K probably benign Het
Edc4 A G 8: 106,614,033 (GRCm39) K429E probably damaging Het
Fam107b T A 2: 3,780,667 (GRCm39) probably null Het
Flt4 A T 11: 49,541,897 (GRCm39) D1360V probably damaging Het
Gm1043 A T 5: 37,317,168 (GRCm39) probably benign Het
Gm4894 A T 9: 49,189,970 (GRCm39) I82L unknown Het
Gm7247 C T 14: 51,601,805 (GRCm39) S26F probably benign Het
Gpr176 A C 2: 118,114,385 (GRCm39) probably null Het
Gtse1 T C 15: 85,748,381 (GRCm39) L262P probably benign Het
Il4ra T C 7: 125,166,393 (GRCm39) W46R probably damaging Het
Itga11 A G 9: 62,662,955 (GRCm39) Y557C probably benign Het
Kcnab2 A C 4: 152,519,287 (GRCm39) probably null Het
Kcnh7 G A 2: 63,014,441 (GRCm39) probably benign Het
Ly9 T A 1: 171,429,396 (GRCm39) Q230L probably damaging Het
Map2 C A 1: 66,454,043 (GRCm39) H978N possibly damaging Het
Map2k6 A G 11: 110,388,732 (GRCm39) I225V possibly damaging Het
Map3k13 A G 16: 21,723,995 (GRCm39) N326D possibly damaging Het
Mdga2 A G 12: 66,844,537 (GRCm39) F85L probably benign Het
Mmp13 C T 9: 7,274,269 (GRCm39) P192L probably damaging Het
Mrpl37 T C 4: 106,923,704 (GRCm39) T97A probably benign Het
Mycbpap C T 11: 94,404,420 (GRCm39) G121D probably benign Het
Nabp1 A G 1: 51,510,544 (GRCm39) S153P probably benign Het
Nsun3 A T 16: 62,590,049 (GRCm39) F222I probably benign Het
Or4q3 A G 14: 50,582,969 (GRCm39) V310A possibly damaging Het
Pcdhga4 A T 18: 37,818,991 (GRCm39) D180V probably benign Het
Pex6 C A 17: 47,025,384 (GRCm39) probably null Het
Phrf1 C A 7: 140,839,015 (GRCm39) probably benign Het
Ppp1r36 A G 12: 76,485,936 (GRCm39) T365A possibly damaging Het
Ranbp10 A G 8: 106,499,672 (GRCm39) M519T probably benign Het
Ryr1 T C 7: 28,723,666 (GRCm39) N4131S probably benign Het
Slc27a6 A G 18: 58,745,306 (GRCm39) E580G possibly damaging Het
Slc7a14 T C 3: 31,263,385 (GRCm39) D719G probably benign Het
Slfn9 A G 11: 82,878,310 (GRCm39) I273T possibly damaging Het
Spice1 A G 16: 44,205,037 (GRCm39) E781G probably benign Het
Sspo C T 6: 48,471,110 (GRCm39) P4686S possibly damaging Het
Stab1 G T 14: 30,861,508 (GRCm39) R2500S probably benign Het
Stox2 A T 8: 47,656,182 (GRCm39) M98K possibly damaging Het
Tacc2 T C 7: 130,225,213 (GRCm39) S633P probably damaging Het
Tex51 G T 18: 32,595,545 (GRCm39) probably benign Het
Tm9sf4 T C 2: 153,037,491 (GRCm39) probably null Het
Togaram2 T A 17: 72,011,778 (GRCm39) F486I probably damaging Het
Trappc12 A G 12: 28,797,113 (GRCm39) S140P possibly damaging Het
Ttc29 A T 8: 79,003,525 (GRCm39) N247I probably damaging Het
Uso1 A T 5: 92,340,589 (GRCm39) E668D probably benign Het
Vmn2r69 A T 7: 85,061,117 (GRCm39) probably null Het
Xirp2 T A 2: 67,341,994 (GRCm39) L1412I possibly damaging Het
Xrcc5 T A 1: 72,349,617 (GRCm39) D15E probably damaging Het
Zfp661 T C 2: 127,418,968 (GRCm39) K391E probably damaging Het
Zfp729b A G 13: 67,741,977 (GRCm39) I106T probably benign Het
Zfyve9 A C 4: 108,576,557 (GRCm39) S175A 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
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
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'- TCTGATTGATGGCTGGCAAC -3'
(R):5'- ACTGGCTGGCAGATTTAGGTC -3'

Sequencing Primer
(F):5'- TGGCAACATGGAACTTTGGC -3'
(R):5'- CTGGCAGATTTAGGTCTTTGAC -3'
Posted On 2017-06-26