Incidental Mutation 'R8002:Rfx4'
ID 616415
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 046042-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8002 (G1)
Quality Score 225.009
Status Not validated
Chromosome 10
Chromosomal Location 84591926-84742402 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 84676721 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Leucine at position 204 (M204L)
Ref Sequence ENSEMBL: ENSMUSP00000051107 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000060397] [ENSMUST00000095388] [ENSMUST00000166696]
AlphaFold Q7TNK1
Predicted Effect probably damaging
Transcript: ENSMUST00000060397
AA Change: M204L

PolyPhen 2 Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: M204L

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: M110L

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: M110L

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 damaging
Transcript: ENSMUST00000166696
AA Change: M61L

PolyPhen 2 Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
AA Change: M61L

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: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
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: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acsm2 C T 7: 119,172,480 (GRCm39) R133C possibly damaging Het
Adgrf4 T C 17: 42,978,683 (GRCm39) E220G probably benign Het
Alx3 T A 3: 107,508,055 (GRCm39) L188* probably null Het
Arhgef2 A T 3: 88,554,117 (GRCm39) I969F probably damaging Het
Atf6 A G 1: 170,646,823 (GRCm39) V350A probably benign Het
Atp1a3 C A 7: 24,700,096 (GRCm39) G88V probably damaging Het
Brd8 T C 18: 34,741,609 (GRCm39) T360A probably benign Het
Casp1 C A 9: 5,303,164 (GRCm39) T206K possibly damaging Het
Ccdc150 A G 1: 54,311,656 (GRCm39) E214G probably damaging Het
Ccdc81 T C 7: 89,525,343 (GRCm39) E477G probably benign Het
Celsr2 G T 3: 108,311,285 (GRCm39) R1409S probably damaging Het
Chd6 T C 2: 160,832,241 (GRCm39) D977G probably damaging Het
Cpne3 A T 4: 19,528,232 (GRCm39) F342I probably damaging Het
Crot A C 5: 9,043,599 (GRCm39) S8A probably benign Het
Cyp11b2 T C 15: 74,727,881 (GRCm39) H67R probably damaging Het
Dnah1 A T 14: 31,020,679 (GRCm39) L1230H probably damaging Het
Dqx1 G A 6: 83,035,558 (GRCm39) D24N probably damaging Het
Gabrg3 T C 7: 56,384,716 (GRCm39) T282A possibly damaging Het
Gm13199 A G 2: 5,867,458 (GRCm39) S13P unknown Het
Gnptab A T 10: 88,276,130 (GRCm39) D1139V probably benign Het
Hdac1-ps T C 17: 78,799,716 (GRCm39) S236P probably damaging Het
Jtb T C 3: 90,141,251 (GRCm39) S76P probably benign Het
Klk1b27 T A 7: 43,705,445 (GRCm39) D172E probably benign Het
Lpcat4 G A 2: 112,074,699 (GRCm39) V307I probably benign Het
Ltn1 A C 16: 87,212,835 (GRCm39) S575R probably benign Het
Map3k13 A G 16: 21,723,878 (GRCm39) T287A probably benign Het
Marco T G 1: 120,422,509 (GRCm39) I58L probably benign Het
Nadk G T 4: 155,661,655 (GRCm39) probably null Het
Or11h7 A T 14: 50,891,314 (GRCm39) I207F probably damaging Het
Otof G A 5: 30,537,954 (GRCm39) T1215I probably benign Het
Pigw A T 11: 84,769,249 (GRCm39) C27S probably benign Het
Pla2g10 A T 16: 13,542,912 (GRCm39) M125K unknown Het
Septin1 T C 7: 126,815,074 (GRCm39) D209G probably damaging Het
Slc1a7 G A 4: 107,869,473 (GRCm39) V513M probably benign Het
Slc26a4 T C 12: 31,597,969 (GRCm39) D159G probably benign Het
Sptbn4 C A 7: 27,117,417 (GRCm39) S444I possibly damaging Het
Srebf2 C T 15: 82,062,966 (GRCm39) R468C probably damaging Het
Stard6 T A 18: 70,633,597 (GRCm39) D201E possibly damaging Het
Tas2r114 T C 6: 131,666,102 (GRCm39) T309A probably damaging Het
Tdrd6 C A 17: 43,940,710 (GRCm39) A113S probably damaging Het
Tigd2 T G 6: 59,187,494 (GRCm39) N120K probably damaging Het
Tomm70a A G 16: 56,957,097 (GRCm39) N224S probably damaging Het
Tspo T C 15: 83,455,640 (GRCm39) V9A probably benign Het
Vmn1r21 T A 6: 57,821,199 (GRCm39) I82L probably benign Het
Vmn2r103 T A 17: 20,019,511 (GRCm39) C532S probably damaging Het
Vmn2r76 T C 7: 85,879,271 (GRCm39) N343S probably benign Het
Wdr62 T C 7: 29,951,785 (GRCm39) K665E probably damaging Het
Xpc T A 6: 91,469,287 (GRCm39) N820I probably damaging Het
Zfp418 A G 7: 7,184,873 (GRCm39) T279A 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
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
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'- GGGCTACAATTCCCCTTCAG -3'
(R):5'- TGGCCTTCCCAGTATGTGTC -3'

Sequencing Primer
(F):5'- CAGGTCTTTCCGGATGCATAG -3'
(R):5'- CTGCCTTGAAGCATCACTGTGAAG -3'
Posted On 2020-01-23