Incidental Mutation 'IGL01408:Rfx3'
ID 79862
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Rfx3
Ensembl Gene ENSMUSG00000040929
Gene Name regulatory factor X, 3 (influences HLA class II expression)
Synonyms MRFX3, C230093O12Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # IGL01408
Quality Score
Status
Chromosome 19
Chromosomal Location 27739121-27988566 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 27746050 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 685 (D685E)
Ref Sequence ENSEMBL: ENSMUSP00000133461 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046898] [ENSMUST00000165566] [ENSMUST00000172907] [ENSMUST00000173863] [ENSMUST00000174850]
AlphaFold P48381
Predicted Effect probably benign
Transcript: ENSMUST00000046898
AA Change: D660E

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: D660E

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 benign
Transcript: ENSMUST00000165566
AA Change: D685E

PolyPhen 2 Score 0.044 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: D685E

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 benign
Transcript: ENSMUST00000172907
AA Change: D685E

PolyPhen 2 Score 0.044 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: D685E

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 probably benign
Transcript: ENSMUST00000173863
SMART Domains Protein: ENSMUSP00000133367
Gene: ENSMUSG00000040929

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 benign
Transcript: ENSMUST00000174850
AA Change: D685E

PolyPhen 2 Score 0.044 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: D685E

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
Coding Region Coverage
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, 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: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9530068E07Rik A G 11: 52,294,193 (GRCm39) R145G probably damaging Het
Akr1c21 T A 13: 4,627,431 (GRCm39) M175K probably benign Het
Apol7a C T 15: 77,273,530 (GRCm39) A311T probably damaging Het
Atxn10 G T 15: 85,260,896 (GRCm39) E214* probably null Het
Bmp2k C T 5: 97,234,823 (GRCm39) Q749* probably null Het
Ccdc141 G A 2: 76,876,023 (GRCm39) A669V probably benign Het
Cndp2 A C 18: 84,689,036 (GRCm39) C249G probably benign Het
Cnr1 A G 4: 33,944,802 (GRCm39) I397V possibly damaging Het
Col19a1 T C 1: 24,345,331 (GRCm39) probably benign Het
Dbn1 T C 13: 55,630,117 (GRCm39) probably benign Het
Dmgdh C T 13: 93,845,803 (GRCm39) P486S probably damaging Het
Dpys A G 15: 39,656,702 (GRCm39) V455A possibly damaging Het
Farp2 A G 1: 93,546,702 (GRCm39) N907S probably benign Het
Fndc3c1 C T X: 105,476,378 (GRCm39) E894K probably benign Het
Gm6685 A T 11: 28,289,473 (GRCm39) N114K probably damaging Het
Golga3 A T 5: 110,365,675 (GRCm39) probably null Het
Grin2c A G 11: 115,151,708 (GRCm39) L84P probably damaging Het
Gucy2c A G 6: 136,675,009 (GRCm39) F1001L probably benign Het
Hcn4 A G 9: 58,767,169 (GRCm39) H910R unknown Het
Kdm4b T C 17: 56,660,518 (GRCm39) probably benign Het
Lrrfip2 A G 9: 111,043,284 (GRCm39) T497A probably benign Het
Man2c1 A G 9: 57,048,884 (GRCm39) Y924C probably damaging Het
Nkain2 T A 10: 32,278,237 (GRCm39) T63S probably damaging Het
Nlrp1a T A 11: 71,013,742 (GRCm39) T503S probably benign Het
Or52n3 T C 7: 104,530,037 (GRCm39) V41A probably benign Het
Or52n4 T A 7: 104,294,136 (GRCm39) I146F possibly damaging Het
Pitrm1 T A 13: 6,623,078 (GRCm39) C780S probably damaging Het
Plekha5 C T 6: 140,516,042 (GRCm39) probably benign Het
Rapgef4 C T 2: 72,005,185 (GRCm39) R193* probably null Het
Rbm20 A G 19: 53,840,044 (GRCm39) E1011G possibly damaging Het
Ror1 T C 4: 100,190,984 (GRCm39) S114P probably damaging Het
Slc17a6 A G 7: 51,318,863 (GRCm39) K502E probably benign Het
Spink2 A T 5: 77,359,174 (GRCm39) probably benign Het
Sptb A T 12: 76,659,921 (GRCm39) I993N possibly damaging Het
Stxbp4 A G 11: 90,512,475 (GRCm39) probably benign Het
Tes A T 6: 17,099,878 (GRCm39) Y291F probably damaging Het
Tmtc4 G T 14: 123,163,366 (GRCm39) probably benign Het
Trpa1 T C 1: 14,959,637 (GRCm39) E683G probably benign Het
Vmn2r73 T C 7: 85,521,455 (GRCm39) D171G probably benign Het
Wbp11 A G 6: 136,791,612 (GRCm39) probably benign Het
Wfdc12 A G 2: 164,031,581 (GRCm39) *86R probably null Het
Zfp281 T C 1: 136,553,853 (GRCm39) V277A probably 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
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
R4952:Rfx3 UTSW 19 27,808,072 (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
Posted On 2013-11-05