Incidental Mutation 'R4952:Rfx3'
ID 382113
Institutional Source Beutler Lab
Gene Symbol Rfx3
Ensembl Gene ENSMUSG00000040929
Gene Name regulatory factor X, 3 (influences HLA class II expression)
Synonyms MRFX3, C230093O12Rik
MMRRC Submission 042549-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4952 (G1)
Quality Score 225
Status Validated
Chromosome 19
Chromosomal Location 27739121-27988566 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 27808072 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 224 (S224P)
Ref Sequence ENSEMBL: ENSMUSP00000133367 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046898] [ENSMUST00000165566] [ENSMUST00000172907] [ENSMUST00000173863] [ENSMUST00000174850]
AlphaFold P48381
Predicted Effect probably damaging
Transcript: ENSMUST00000046898
AA Change: S199P

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: S199P

DomainStartEndE-ValueType
Pfam:RFX1_trans_act 1 140 6.3e-58 PFAM
Pfam:RFX_DNA_binding 150 235 6.9e-41 PFAM
low complexity region 274 283 N/A INTRINSIC
internal_repeat_1 326 414 1.39e-5 PROSPERO
internal_repeat_1 439 527 1.39e-5 PROSPERO
low complexity region 649 664 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000165566
AA Change: S224P

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: S224P

DomainStartEndE-ValueType
Pfam:RFX1_trans_act 4 138 9.7e-38 PFAM
Pfam:RFX_DNA_binding 181 258 6.2e-36 PFAM
low complexity region 299 308 N/A INTRINSIC
internal_repeat_1 351 439 1.82e-5 PROSPERO
internal_repeat_1 464 552 1.82e-5 PROSPERO
low complexity region 674 689 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000172498
Predicted Effect probably damaging
Transcript: ENSMUST00000172907
AA Change: S224P

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: S224P

DomainStartEndE-ValueType
Pfam:RFX1_trans_act 1 140 9.4e-58 PFAM
Pfam:RFX_DNA_binding 175 260 5.2e-41 PFAM
low complexity region 299 308 N/A INTRINSIC
internal_repeat_1 351 439 1.82e-5 PROSPERO
internal_repeat_1 464 552 1.82e-5 PROSPERO
low complexity region 674 689 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173161
Predicted Effect probably damaging
Transcript: ENSMUST00000173863
AA Change: S224P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000133367
Gene: ENSMUSG00000040929
AA Change: S224P

DomainStartEndE-ValueType
Pfam:RFX1_trans_act 1 140 3.3e-58 PFAM
Pfam:RFX_DNA_binding 175 246 3.7e-24 PFAM
low complexity region 285 294 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000174850
AA Change: S224P

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: S224P

DomainStartEndE-ValueType
Pfam:RFX1_trans_act 1 140 9.4e-58 PFAM
Pfam:RFX_DNA_binding 175 260 5.2e-41 PFAM
low complexity region 299 308 N/A INTRINSIC
internal_repeat_1 351 439 1.82e-5 PROSPERO
internal_repeat_1 464 552 1.82e-5 PROSPERO
low complexity region 674 689 N/A INTRINSIC
Meta Mutation Damage Score 0.9515 question?
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.3%
  • 10x: 96.5%
  • 20x: 93.0%
Validation Efficiency 99% (93/94)
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, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. Multiple transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2013]
PHENOTYPE: Homozygous null mice display embryonic and perinatal lethality, impaired development of cilia on the embryonic node, abnormal left-right patterning, meso- and dextrocardia, and situs inversus in surviving adults. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 84 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930522L14Rik A G 5: 109,887,063 (GRCm39) probably null Het
4933421I07Rik T C 7: 42,097,083 (GRCm39) Y76C possibly damaging Het
Adcy4 C T 14: 56,016,486 (GRCm39) D322N probably damaging Het
Ak9 A G 10: 41,296,585 (GRCm39) M1444V probably benign Het
Amfr A G 8: 94,699,787 (GRCm39) probably benign Het
Ankef1 A G 2: 136,392,449 (GRCm39) E546G probably damaging Het
Ankrd24 A G 10: 81,482,982 (GRCm39) M977V probably benign Het
Ap3m1 A T 14: 21,090,134 (GRCm39) S5T probably benign Het
Aqr C A 2: 113,940,418 (GRCm39) D1243Y probably damaging Het
Arhgef2 T C 3: 88,549,769 (GRCm39) L591P probably damaging Het
Arid4a C A 12: 71,070,299 (GRCm39) T70K possibly damaging Het
Asphd1 C T 7: 126,547,857 (GRCm39) A149T probably benign Het
Avpr1a T A 10: 122,285,659 (GRCm39) M317K probably damaging Het
Birc2 T C 9: 7,836,741 (GRCm39) I109V probably damaging Het
Catsperd A G 17: 56,939,303 (GRCm39) Y44C probably damaging Het
Crygb T G 1: 65,121,268 (GRCm39) S20R probably benign Het
Cyp3a25 T C 5: 145,928,334 (GRCm39) N237S probably benign Het
Dkk3 C T 7: 111,717,558 (GRCm39) A304T probably benign Het
Dst T C 1: 34,310,503 (GRCm39) L4101S probably damaging Het
Dysf A G 6: 84,126,968 (GRCm39) N1407S possibly damaging Het
Epb41 A G 4: 131,727,581 (GRCm39) V265A probably damaging Het
Faim2 C T 15: 99,419,109 (GRCm39) E75K possibly damaging Het
Fam237b T A 5: 5,625,387 (GRCm39) F28I probably benign Het
Fbn1 T A 2: 125,159,454 (GRCm39) D2208V probably damaging Het
Fbxo28 A G 1: 182,153,950 (GRCm39) S129P probably damaging Het
Fbxw14 T A 9: 109,105,269 (GRCm39) I299L probably benign Het
Fras1 C T 5: 96,795,357 (GRCm39) A1050V probably benign Het
Fyb1 C A 15: 6,668,292 (GRCm39) T495K probably damaging Het
Ghdc A T 11: 100,659,977 (GRCm39) W257R probably damaging Het
Gm10719 T C 9: 3,018,962 (GRCm39) L69S probably benign Het
Gm12250 G T 11: 58,079,210 (GRCm39) noncoding transcript Het
Gm4846 A T 1: 166,311,503 (GRCm39) F452Y probably damaging Het
Gpbp1 T C 13: 111,577,284 (GRCm39) D202G probably damaging Het
Gpd2 C A 2: 57,197,025 (GRCm39) Y193* probably null Het
Grhl2 G T 15: 37,287,493 (GRCm39) R229L probably benign Het
Gtf2a1 A G 12: 91,542,523 (GRCm39) F59L possibly damaging Het
Heatr1 G T 13: 12,425,480 (GRCm39) W640L probably benign Het
Kalrn A T 16: 34,177,785 (GRCm39) probably null Het
Keap1 T C 9: 21,148,582 (GRCm39) T142A probably damaging Het
Kpna2 G A 11: 106,882,061 (GRCm39) T255M probably damaging Het
Kpna3 A G 14: 61,607,838 (GRCm39) C456R probably damaging Het
Lama1 G A 17: 68,074,561 (GRCm39) probably null Het
Lrrc37 T C 11: 103,505,033 (GRCm39) T2312A possibly damaging Het
Mag C A 7: 30,608,581 (GRCm39) E178* probably null Het
Map3k13 A G 16: 21,729,769 (GRCm39) I467V probably benign Het
Mga A G 2: 119,733,782 (GRCm39) E210G probably damaging Het
Msi2 C T 11: 88,257,610 (GRCm39) probably null Het
Naa16 A T 14: 79,582,525 (GRCm39) D521E probably damaging Het
Nav2 C T 7: 48,954,288 (GRCm39) probably benign Het
Nek10 T A 14: 14,860,986 (GRCm38) L513M possibly damaging Het
Nek5 T C 8: 22,586,815 (GRCm39) K332R probably benign Het
Nek5 T A 8: 22,569,104 (GRCm39) I573L probably benign Het
Ntn1 CCTTCTTCT CCTTCT 11: 68,103,852 (GRCm39) probably benign Het
Odad1 A C 7: 45,591,615 (GRCm39) E293A probably damaging Het
Or2w1 G A 13: 21,317,514 (GRCm39) V190I probably benign Het
Or5v1b A T 17: 37,841,641 (GRCm39) T258S possibly damaging Het
Or6c204 T A 10: 129,022,466 (GRCm39) T275S probably benign Het
Or8b12b T A 9: 37,684,360 (GRCm39) M135K probably damaging Het
Orai1 T G 5: 123,167,313 (GRCm39) V162G probably damaging Het
P2rx6 T C 16: 17,385,308 (GRCm39) S134P probably damaging Het
Pappa2 G A 1: 158,684,706 (GRCm39) T811I probably null Het
Pcdhga10 T C 18: 37,880,213 (GRCm39) probably benign Het
Pex16 C T 2: 92,209,405 (GRCm39) R241* probably null Het
Plxnb1 T C 9: 108,943,904 (GRCm39) F1969L probably damaging Het
Postn A G 3: 54,297,736 (GRCm39) probably benign Het
Prdm15 A T 16: 97,607,277 (GRCm39) I752N probably damaging Het
Rasgef1c A T 11: 49,870,339 (GRCm39) K468M probably damaging Het
Rbfox1 A G 16: 7,094,952 (GRCm39) S111G probably benign Het
Rbm28 T C 6: 29,138,597 (GRCm39) D405G probably damaging Het
Rell1 A G 5: 64,097,010 (GRCm39) probably benign Het
Scarb2 A T 5: 92,602,636 (GRCm39) I260K probably damaging Het
Septin4 A G 11: 87,458,598 (GRCm39) N324S probably benign Het
Slc15a4 A G 5: 127,680,901 (GRCm39) F72L probably damaging Het
Spg7 C A 8: 123,816,910 (GRCm39) R534S probably damaging Het
Stoml2 T C 4: 43,029,589 (GRCm39) T164A probably benign Het
Syt11 C T 3: 88,669,590 (GRCm39) G101S possibly damaging Het
Traj12 A G 14: 54,444,013 (GRCm39) probably benign Het
Traj7 A T 14: 54,448,981 (GRCm39) probably benign Het
Tysnd1 C T 10: 61,537,855 (GRCm39) T175I possibly damaging Het
Usp48 T G 4: 137,334,004 (GRCm39) Y139* probably null Het
Vmn2r72 A G 7: 85,400,317 (GRCm39) L244P probably benign Het
Wasf1 C A 10: 40,812,186 (GRCm39) P325Q unknown Het
Zc3h18 T A 8: 123,137,639 (GRCm39) probably benign Het
Zfp712 A G 13: 67,188,905 (GRCm39) S541P possibly damaging Het
Other mutations in Rfx3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00548:Rfx3 APN 19 27,783,586 (GRCm39) critical splice donor site probably null
IGL00588:Rfx3 APN 19 27,803,476 (GRCm39) nonsense probably null
IGL01408:Rfx3 APN 19 27,746,050 (GRCm39) missense probably benign 0.04
IGL01937:Rfx3 APN 19 27,808,129 (GRCm39) missense probably damaging 1.00
IGL02668:Rfx3 APN 19 27,793,014 (GRCm39) splice site probably benign
IGL02679:Rfx3 APN 19 27,827,137 (GRCm39) missense possibly damaging 0.95
R0267:Rfx3 UTSW 19 27,771,188 (GRCm39) missense probably benign 0.00
R0336:Rfx3 UTSW 19 27,783,662 (GRCm39) missense probably benign 0.00
R0838:Rfx3 UTSW 19 27,827,367 (GRCm39) missense possibly damaging 0.92
R0967:Rfx3 UTSW 19 27,783,751 (GRCm39) splice site probably benign
R1102:Rfx3 UTSW 19 27,845,000 (GRCm39) missense possibly damaging 0.51
R1507:Rfx3 UTSW 19 27,745,913 (GRCm39) missense probably benign 0.00
R2172:Rfx3 UTSW 19 27,792,894 (GRCm39) nonsense probably null
R2844:Rfx3 UTSW 19 27,784,186 (GRCm39) splice site probably benign
R2960:Rfx3 UTSW 19 27,878,211 (GRCm39) nonsense probably null
R4291:Rfx3 UTSW 19 27,777,632 (GRCm39) missense probably damaging 1.00
R5198:Rfx3 UTSW 19 27,808,176 (GRCm39) missense probably damaging 1.00
R5451:Rfx3 UTSW 19 27,827,359 (GRCm39) missense probably damaging 1.00
R5590:Rfx3 UTSW 19 27,779,780 (GRCm39) critical splice donor site probably null
R5641:Rfx3 UTSW 19 27,771,008 (GRCm39) splice site probably null
R5663:Rfx3 UTSW 19 27,771,017 (GRCm39) missense probably damaging 1.00
R5899:Rfx3 UTSW 19 27,808,165 (GRCm39) missense probably damaging 1.00
R6049:Rfx3 UTSW 19 27,779,795 (GRCm39) missense probably damaging 0.99
R6368:Rfx3 UTSW 19 27,746,009 (GRCm39) missense possibly damaging 0.92
R7131:Rfx3 UTSW 19 27,746,028 (GRCm39) nonsense probably null
R7273:Rfx3 UTSW 19 27,779,858 (GRCm39) missense probably damaging 1.00
R7593:Rfx3 UTSW 19 27,827,139 (GRCm39) missense probably benign 0.00
R7814:Rfx3 UTSW 19 27,803,470 (GRCm39) missense probably benign 0.01
R7815:Rfx3 UTSW 19 27,803,448 (GRCm39) missense probably benign 0.00
R8458:Rfx3 UTSW 19 27,771,072 (GRCm39) missense possibly damaging 0.71
R8995:Rfx3 UTSW 19 27,783,725 (GRCm39) missense probably benign 0.14
R9147:Rfx3 UTSW 19 27,878,207 (GRCm39) missense possibly damaging 0.84
R9148:Rfx3 UTSW 19 27,878,207 (GRCm39) missense possibly damaging 0.84
R9310:Rfx3 UTSW 19 27,827,329 (GRCm39) missense probably benign 0.00
Z1088:Rfx3 UTSW 19 27,814,850 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGGAGGTCCATTCTATAGTTTTCTCC -3'
(R):5'- GAAGAGATTCCAAGTAGCTGTGC -3'

Sequencing Primer
(F):5'- GCTCACTTTCCAACACTG -3'
(R):5'- CCAAGTAGCTGTGCATATATTGTACC -3'
Posted On 2016-04-27