Incidental Mutation 'R5157:Rfxap'
ID 396767
Institutional Source Beutler Lab
Gene Symbol Rfxap
Ensembl Gene ENSMUSG00000036615
Gene Name regulatory factor X-associated protein
Synonyms 5730495K23Rik
MMRRC Submission 042739-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.120) question?
Stock # R5157 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 54710536-54715212 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 54711938 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Isoleucine at position 215 (N215I)
Ref Sequence ENSEMBL: ENSMUSP00000040917 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029371] [ENSMUST00000044373] [ENSMUST00000217267]
AlphaFold Q8VCG9
Predicted Effect probably benign
Transcript: ENSMUST00000029371
SMART Domains Protein: ENSMUSP00000029371
Gene: ENSMUSG00000027796

DomainStartEndE-ValueType
DWA 29 138 3.47e-68 SMART
DWB 234 406 1.02e-106 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000044373
AA Change: N215I

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000040917
Gene: ENSMUSG00000036615
AA Change: N215I

DomainStartEndE-ValueType
low complexity region 42 65 N/A INTRINSIC
low complexity region 74 98 N/A INTRINSIC
Pfam:RFXA_RFXANK_bdg 100 226 6.5e-64 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000182084
Predicted Effect noncoding transcript
Transcript: ENSMUST00000182246
Predicted Effect probably damaging
Transcript: ENSMUST00000217267
AA Change: N215I

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
Meta Mutation Damage Score 0.0875 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.2%
Validation Efficiency 100% (57/57)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Major histocompatibility (MHC) class II molecules are transmembrane proteins that have a central role in development and control of the immune system. The protein encoded by this gene, along with regulatory factor X-associated ankyrin-containing protein and regulatory factor-5, forms a complex that binds to the X box motif of certain MHC class II gene promoters and activates their transcription. Once bound to the promoter, this complex associates with the non-DNA-binding factor MHC class II transactivator, which controls the cell type specificity and inducibility of MHC class II gene expression. Mutations in this gene have been linked to bare lymphocyte syndrome type II, complementation group D. Transcript variants utilizing different polyA signals have been found for this gene. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca3 C T 17: 24,627,096 (GRCm39) R1266C probably damaging Het
Adap2 T C 11: 80,047,772 (GRCm39) F76S probably damaging Het
Adgb T A 10: 10,274,710 (GRCm39) H747L probably damaging Het
Aox1 T A 1: 58,109,222 (GRCm39) V670D probably damaging Het
Ap4e1 A G 2: 126,903,615 (GRCm39) D839G probably benign Het
Arhgef11 T A 3: 87,635,817 (GRCm39) probably null Het
AY074887 T C 9: 54,858,102 (GRCm39) probably benign Het
Bicd1 C G 6: 149,421,912 (GRCm39) Q878E probably benign Het
Catspere1 A T 1: 177,707,348 (GRCm39) noncoding transcript Het
Cnmd T C 14: 79,894,126 (GRCm39) Q87R probably benign Het
Col24a1 G T 3: 145,051,712 (GRCm39) G661* probably null Het
Crtap G A 9: 114,213,860 (GRCm39) L232F probably damaging Het
Ctsq T C 13: 61,184,913 (GRCm39) T258A probably benign Het
Cyp2d26 T C 15: 82,675,190 (GRCm39) Q388R probably benign Het
Ddb1 A T 19: 10,599,728 (GRCm39) T646S probably benign Het
Dnah6 G T 6: 73,172,617 (GRCm39) S280R probably benign Het
Dzank1 T C 2: 144,325,332 (GRCm39) H545R probably damaging Het
Ehhadh T A 16: 21,585,261 (GRCm39) M207L probably benign Het
Elmo2 T A 2: 165,133,627 (GRCm39) probably benign Het
Golga3 G A 5: 110,350,537 (GRCm39) A731T probably benign Het
Igsf21 T C 4: 139,755,378 (GRCm39) T426A possibly damaging Het
Kcnf1 T C 12: 17,224,742 (GRCm39) E493G probably benign Het
Lmna A T 3: 88,391,414 (GRCm39) D364E probably damaging Het
Lsr T C 7: 30,665,465 (GRCm39) Y163C probably damaging Het
Map3k20 A T 2: 72,268,558 (GRCm39) T522S probably benign Het
Mroh9 C A 1: 162,871,690 (GRCm39) A598S probably damaging Het
Msln T C 17: 25,971,957 (GRCm39) M87V probably benign Het
Or14c39 A G 7: 86,344,440 (GRCm39) K259E probably benign Het
Or1e26 T C 11: 73,480,549 (GRCm39) N5S probably damaging Het
Or4a27 T A 2: 88,559,892 (GRCm39) Q17L probably benign Het
Or5d16 T A 2: 87,773,232 (GRCm39) M247L probably benign Het
Pals1 T A 12: 78,867,589 (GRCm39) M324K possibly damaging Het
Plekhg5 T A 4: 152,192,322 (GRCm39) probably benign Het
Pprc1 G T 19: 46,053,197 (GRCm39) probably benign Het
Ptprm T A 17: 67,264,092 (GRCm39) K385I probably benign Het
Slc16a7 A T 10: 125,069,333 (GRCm39) Y114* probably null Het
Smarcb1 G T 10: 75,747,628 (GRCm39) probably benign Het
Spef2 T A 15: 9,668,877 (GRCm39) R770* probably null Het
Stard9 A T 2: 120,528,342 (GRCm39) Y1533F probably benign Het
Tbcd A T 11: 121,500,853 (GRCm39) Y1142F probably benign Het
Trappc2b A T 11: 51,576,893 (GRCm39) S2T probably benign Het
Ttc23l G T 15: 10,551,636 (GRCm39) T30K possibly damaging Het
Uba7 G A 9: 107,857,246 (GRCm39) V703I probably benign Het
Upb1 T C 10: 75,248,638 (GRCm39) S53P possibly damaging Het
Zfp672 A G 11: 58,207,677 (GRCm39) S215P possibly damaging Het
Zfp978 T A 4: 147,475,437 (GRCm39) L328H probably damaging Het
Other mutations in Rfxap
AlleleSourceChrCoordTypePredicted EffectPPH Score
R1985:Rfxap UTSW 3 54,714,747 (GRCm39) missense probably damaging 1.00
R6073:Rfxap UTSW 3 54,714,708 (GRCm39) missense probably damaging 1.00
R8914:Rfxap UTSW 3 54,715,042 (GRCm39) missense probably benign
R9052:Rfxap UTSW 3 54,715,155 (GRCm39) unclassified probably benign
Predicted Primers PCR Primer
(F):5'- TCATTCGCTTCAGTAGGCATAAC -3'
(R):5'- GCATTGCTGTGAGCTCAAAG -3'

Sequencing Primer
(F):5'- GACAGGAACTTGCTATGTAGCCC -3'
(R):5'- AAAGCCTGCCTGTCTATGG -3'
Posted On 2016-06-21