Incidental Mutation 'R4618:Rfx4'
ID 345110
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 041884-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4618 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 84591926-84742402 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 84716760 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Serine at position 425 (A425S)
Ref Sequence ENSEMBL: ENSMUSP00000093035 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000060397] [ENSMUST00000095388] [ENSMUST00000166696]
AlphaFold Q7TNK1
Predicted Effect probably benign
Transcript: ENSMUST00000060397
AA Change: A519S

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: A519S

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: A425S

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: A425S

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: A376S

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
AA Change: A376S

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 0.0617 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.2%
Validation Efficiency 98% (89/91)
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: 77 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930432M17Rik A T 3: 121,473,095 (GRCm39) K83N unknown Het
Adamtsl3 T A 7: 82,255,728 (GRCm39) M1580K probably benign Het
Adprhl1 A G 8: 13,292,250 (GRCm39) probably null Het
Akap3 G T 6: 126,843,406 (GRCm39) C675F probably benign Het
Asap1 A T 15: 64,024,744 (GRCm39) H318Q probably damaging Het
Atf7ip G T 6: 136,542,104 (GRCm39) A18S probably damaging Het
Bcl2a1a A C 9: 88,839,357 (GRCm39) N85T probably damaging Het
Btnl6 G A 17: 34,733,120 (GRCm39) P248S probably damaging Het
C9 A G 15: 6,520,944 (GRCm39) D51G probably damaging Het
Ccdc14 T A 16: 34,526,865 (GRCm39) C257S probably benign Het
Cd5l A G 3: 87,275,926 (GRCm39) T299A probably benign Het
Cstdc3 T A 16: 36,132,952 (GRCm39) D76E possibly damaging Het
Endou C T 15: 97,611,763 (GRCm39) V292M possibly damaging Het
Fbxo36 T C 1: 84,877,749 (GRCm39) I137T probably damaging Het
Fcer1a T C 1: 173,050,208 (GRCm39) I161V possibly damaging Het
Fsip2 A G 2: 82,818,103 (GRCm39) Y4612C probably benign Het
Gcnt2 T A 13: 41,111,670 (GRCm39) L353* probably null Het
Ghrhr T C 6: 55,358,739 (GRCm39) F172S probably damaging Het
Gins1 T A 2: 150,759,781 (GRCm39) probably null Het
Gm16519 T G 17: 71,236,237 (GRCm39) L62R probably damaging Het
Gpr20 T C 15: 73,567,585 (GRCm39) N268S probably benign Het
Greb1l A G 18: 10,498,965 (GRCm39) T283A probably benign Het
Grin2c T A 11: 115,143,573 (GRCm39) D729V probably damaging Het
Heatr4 T G 12: 84,024,841 (GRCm39) T327P probably damaging Het
Hes2 A C 4: 152,244,845 (GRCm39) S105R probably benign Het
Hsph1 A G 5: 149,542,308 (GRCm39) V705A probably benign Het
Ighv1-82 T C 12: 115,916,280 (GRCm39) T77A probably benign Het
Itih1 A T 14: 30,651,788 (GRCm39) D851E probably benign Het
Klhdc7b A G 15: 89,271,472 (GRCm39) T785A probably benign Het
Lmbr1 G T 5: 29,551,863 (GRCm39) A74E probably damaging Het
Lonp1 A C 17: 56,929,511 (GRCm39) H175Q probably benign Het
Maml2 T C 9: 13,531,371 (GRCm39) F195S probably damaging Het
Man2b2 G T 5: 36,974,983 (GRCm39) T436K probably benign Het
Man2c1 T C 9: 57,049,439 (GRCm39) probably null Het
Mrps15 G A 4: 125,940,837 (GRCm39) probably benign Het
Mtrf1l C A 10: 5,767,586 (GRCm39) V177F probably benign Het
Naxd A T 8: 11,559,489 (GRCm39) I213F probably damaging Het
Nbeal1 T A 1: 60,267,890 (GRCm39) probably benign Het
Nfatc1 T C 18: 80,741,047 (GRCm39) I318V probably damaging Het
Nid2 T A 14: 19,858,078 (GRCm39) I1297N probably damaging Het
Nol10 T C 12: 17,398,562 (GRCm39) V3A probably damaging Het
Nop14 G T 5: 34,796,562 (GRCm39) P765Q probably damaging Het
Noxa1 C T 2: 24,981,761 (GRCm39) G114D probably damaging Het
Ntmt2 A T 1: 163,552,597 (GRCm39) F10I probably damaging Het
Opa1 T C 16: 29,405,857 (GRCm39) W141R probably damaging Het
Or10a2 G A 7: 106,673,761 (GRCm39) C242Y probably damaging Het
Or13p4 A T 4: 118,546,667 (GRCm39) probably benign Het
Or5d18 A G 2: 87,864,898 (GRCm39) V195A probably benign Het
Or8h10 A G 2: 86,808,618 (GRCm39) I174T possibly damaging Het
Pde4d A T 13: 110,070,411 (GRCm39) M7L probably benign Het
Phykpl G A 11: 51,483,056 (GRCm39) A188T probably damaging Het
Pkd2l1 C A 19: 44,142,573 (GRCm39) A490S probably damaging Het
Pkhd1l1 T A 15: 44,403,078 (GRCm39) V2260D probably damaging Het
Ptprt T C 2: 161,395,765 (GRCm39) E1136G probably damaging Het
Rad21 A T 15: 51,833,420 (GRCm39) L353Q probably damaging Het
Rnf38 A G 4: 44,142,450 (GRCm39) S169P probably damaging Het
Samd9l C A 6: 3,376,347 (GRCm39) V305F probably damaging Het
Serpini1 A G 3: 75,523,883 (GRCm39) K164E probably benign Het
Sirt6 A G 10: 81,462,408 (GRCm39) L37P probably damaging Het
Sorbs1 T C 19: 40,361,962 (GRCm39) T141A probably damaging Het
Tacc2 A T 7: 130,227,946 (GRCm39) T1563S probably benign Het
Tbc1d14 A C 5: 36,687,725 (GRCm39) probably benign Het
Tbrg4 G A 11: 6,570,185 (GRCm39) probably benign Het
Tox2 T C 2: 163,162,567 (GRCm39) L479P probably damaging Het
Tpp1 A T 7: 105,400,913 (GRCm39) L38Q probably benign Het
Trhr A G 15: 44,061,037 (GRCm39) N186D probably benign Het
Trmt1l C T 1: 151,329,799 (GRCm39) Q581* probably null Het
Tsen54 T A 11: 115,706,247 (GRCm39) probably benign Het
Tsg101 A G 7: 46,542,257 (GRCm39) I138T possibly damaging Het
Usp22 A G 11: 61,052,269 (GRCm39) S237P probably damaging Het
Vmn1r209 A G 13: 22,990,619 (GRCm39) S24P possibly damaging Het
Vmn2r18 A T 5: 151,508,424 (GRCm39) H233Q possibly damaging Het
Vmn2r45 A T 7: 8,486,436 (GRCm39) I284N probably benign Het
Vmn2r66 T C 7: 84,644,296 (GRCm39) I705V possibly damaging Het
Vsig1 G T X: 139,827,135 (GRCm39) A95S probably benign Het
Zdhhc11 T A 13: 74,127,349 (GRCm39) M242K probably benign Het
Zfp352 A G 4: 90,113,318 (GRCm39) K486R 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
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'- GCACTTGGGTGTATGGAAACC -3'
(R):5'- AGATTCCTGAGTTCTGGTATTCC -3'

Sequencing Primer
(F):5'- AGAAAGTGGGCTTCCTTTCC -3'
(R):5'- CCTTTTGTGTTTTGAGGAAGACCC -3'
Posted On 2015-09-25