Incidental Mutation 'R1738:Rfx4'
ID 199882
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 039770-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1738 (G1)
Quality Score 225
Status Not validated
Chromosome 10
Chromosomal Location 84591926-84742402 bp(+) (GRCm39)
Type of Mutation critical splice donor site (1 bp from exon)
DNA Base Change (assembly) G to A at 84716839 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000128690 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000060397] [ENSMUST00000095388] [ENSMUST00000166696]
AlphaFold Q7TNK1
Predicted Effect probably null
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
SMART Domains Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037

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 null
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
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 96.8%
  • 10x: 94.7%
  • 20x: 89.9%
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
4930562C15Rik A G 16: 4,682,475 (GRCm39) Y202C probably damaging Het
Adamts16 G A 13: 70,927,637 (GRCm39) probably benign Het
Adgrl3 T G 5: 81,535,826 (GRCm39) M155R probably damaging Het
Ak9 A T 10: 41,211,917 (GRCm39) Q218L possibly damaging Het
Akap13 G A 7: 75,326,942 (GRCm39) G647D probably damaging Het
Angptl3 A G 4: 98,921,499 (GRCm39) T206A probably benign Het
Arhgap19 A G 19: 41,772,820 (GRCm39) I291T probably benign Het
BC049715 C T 6: 136,817,306 (GRCm39) P182L probably damaging Het
Bsn T C 9: 107,984,133 (GRCm39) D3307G unknown Het
Cby2 C T 14: 75,830,497 (GRCm39) M1I probably null Het
Ces2h T A 8: 105,745,697 (GRCm39) probably null Het
Ces4a G A 8: 105,864,729 (GRCm39) G69S probably damaging Het
Col4a2 T A 8: 11,496,238 (GRCm39) F1620I probably damaging Het
Col6a3 T C 1: 90,744,083 (GRCm39) E88G probably damaging Het
Coro6 A G 11: 77,360,251 (GRCm39) D407G probably benign Het
Cpe A T 8: 65,064,475 (GRCm39) F241L probably damaging Het
Csde1 A G 3: 102,936,493 (GRCm39) probably benign Het
Cspg4b T G 13: 113,504,034 (GRCm39) L179R possibly damaging Het
Dgki A G 6: 37,034,367 (GRCm39) I361T possibly damaging Het
Dnah3 A G 7: 119,634,582 (GRCm39) V1298A probably damaging Het
Duox2 T A 2: 122,123,895 (GRCm39) I430F probably damaging Het
Gak T C 5: 108,764,842 (GRCm39) Y153C probably damaging Het
Gal3st2 T A 1: 93,802,318 (GRCm39) probably null Het
Gbp11 T C 5: 105,474,510 (GRCm39) N389D probably benign Het
Grm1 A G 10: 10,812,163 (GRCm39) V287A probably damaging Het
Hsp90ab1 T C 17: 45,882,732 (GRCm39) K36E probably damaging Het
Il24 T A 1: 130,815,099 (GRCm39) probably null Het
Ino80d T C 1: 63,132,624 (GRCm39) D13G probably damaging Het
Ipp G A 4: 116,387,618 (GRCm39) V399I probably benign Het
Kank3 A T 17: 34,036,168 (GRCm39) D12V probably damaging Het
Lcn12 A T 2: 25,383,263 (GRCm39) S74R probably damaging Het
Mast3 T C 8: 71,237,200 (GRCm39) T637A probably benign Het
Nes C A 3: 87,883,728 (GRCm39) Y662* probably null Het
Nudt13 A T 14: 20,359,762 (GRCm39) H163L probably damaging Het
Or1j17 T C 2: 36,578,797 (GRCm39) V261A probably benign Het
Or4a2 T C 2: 89,248,362 (GRCm39) T132A probably benign Het
Or4p7 G A 2: 88,221,671 (GRCm39) V27I probably benign Het
Or8k1 A T 2: 86,048,060 (GRCm39) probably null Het
Pde6b C T 5: 108,578,425 (GRCm39) R788* probably null Het
Pex13 A G 11: 23,599,458 (GRCm39) L351P probably benign Het
Phc1 A G 6: 122,295,525 (GRCm39) M942T probably damaging Het
Plch1 A T 3: 63,626,659 (GRCm39) D571E probably benign Het
Plec C T 15: 76,070,418 (GRCm39) V931M probably damaging Het
Plekhh2 A G 17: 84,874,125 (GRCm39) N470S possibly damaging Het
Primpol A G 8: 47,060,873 (GRCm39) S82P probably damaging Het
Prkg1 T C 19: 30,764,322 (GRCm39) D256G possibly damaging Het
Prune2 A G 19: 17,102,374 (GRCm39) E2511G probably benign Het
Rassf8 T C 6: 145,761,034 (GRCm39) I120T probably benign Het
Rtp2 A T 16: 23,746,423 (GRCm39) N69K probably benign Het
Sh3d19 A T 3: 86,027,913 (GRCm39) I597F probably damaging Het
Sorl1 T A 9: 42,001,261 (GRCm39) E246D probably benign Het
Tet2 T A 3: 133,187,148 (GRCm39) I1094L probably benign Het
Tlr4 A T 4: 66,759,313 (GRCm39) H702L probably benign Het
Tnfrsf14 T C 4: 155,009,788 (GRCm39) D47G probably damaging Het
Ttn T C 2: 76,777,157 (GRCm39) Y1415C probably damaging Het
Vmn2r17 T A 5: 109,576,377 (GRCm39) F416Y probably benign Het
Vmn2r54 A G 7: 12,369,815 (GRCm39) S83P probably benign Het
Vtn A G 11: 78,390,422 (GRCm39) D53G possibly damaging Het
Vwde A T 6: 13,190,723 (GRCm39) V456D probably damaging Het
Wdr91 G A 6: 34,861,243 (GRCm39) P653L probably damaging Het
Ythdf1 G A 2: 180,553,285 (GRCm39) A283V probably benign Het
Zfp975 C A 7: 42,312,373 (GRCm39) W80L 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
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'- TCTCTGTTTGCAGCAGAAGCCC -3'
(R):5'- TGTCTCTTGTTTCCAAGGATGCCTG -3'

Sequencing Primer
(F):5'- GCCCAGGAAGAGATTATCTTGAC -3'
(R):5'- GGATGCCTGTATACTAGCTTACACG -3'
Posted On 2014-05-23