Incidental Mutation 'RF035:Rfx4'
ID 604534
Institutional Source Beutler Lab
Gene Symbol Rfx4
Ensembl Gene ENSMUSG00000020037
Gene Name regulatory factor X, 4 (influences HLA class II expression)
Synonyms 4933412G19Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # RF035 (G1)
Quality Score 217.468
Status Not validated
Chromosome 10
Chromosomal Location 84591926-84742402 bp(+) (GRCm39)
Type of Mutation critical splice acceptor site
DNA Base Change (assembly) TCTCTCTCTCTCTCT to TCTCTCTCTCTCTCTCGCTCTCTCTCTCTCT at 84694344 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000051107 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000060397] [ENSMUST00000095388] [ENSMUST00000166696]
AlphaFold Q7TNK1
Predicted Effect probably benign
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 benign
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 benign
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: 99.8%
  • 3x: 99.7%
  • 10x: 99.4%
  • 20x: 98.7%
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: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A030005L19Rik T TTTGGCTGCC 1: 82,891,310 (GRCm39) probably benign Het
Acap3 TGCATCCTGGGCTGC TGCATCCTGGGCTGCCGCATCCTGGGCTGC 4: 155,989,548 (GRCm39) probably benign Het
AI837181 G GGCT 19: 5,475,266 (GRCm39) probably benign Het
Amfr GCC GCCGGCGCGAGCTCC 8: 94,738,920 (GRCm39) probably benign Het
Amot GGAGCAGCAA G X: 144,233,984 (GRCm39) probably benign Het
Bltp1 TAT TATTATTATTATTATGAT 3: 37,104,907 (GRCm39) probably benign Het
Cacna1f GAG GAGTAG X: 7,486,293 (GRCm39) probably null Het
Calhm1 CTGTGGCTGTGGCTGTGGCTGTGG CTGTGGCTGTGGTTGTGGCTGTGGCTGTGGCTGTGG 19: 47,129,692 (GRCm39) probably benign Het
Chga G GCAT 12: 102,527,686 (GRCm39) probably benign Het
E4f1 CGC CGCTGC 17: 24,674,164 (GRCm39) probably benign Het
E4f1 CCG CCGGCG 17: 24,674,169 (GRCm39) probably benign Het
Eps8 C CTCAG 6: 137,494,068 (GRCm39) probably null Het
Exd2 GCAGCCACAGCAGCCGCAGCAGCCGCAGCCACAGCCACAGCCACAGCCACAGCCACAGC GCAGCCACAGC 12: 80,522,674 (GRCm39) probably benign Het
Exd2 CAGCCAGAGC CAGC 12: 80,522,729 (GRCm39) probably benign Het
Gm10447 AAAAAAAAAGAAAAA AAAAAA 11: 53,347,165 (GRCm39) probably benign Het
Gm10521 CTCTCTCTCT CTCTCTCTCTCTCT 1: 171,723,860 (GRCm39) probably null Het
Gm8369 TGTG TGTGCGAGTG 19: 11,489,137 (GRCm39) probably benign Het
Gucy1b2 CACACACACACACACACTTAC CAC 14: 62,646,090 (GRCm39) probably benign Het
Ier5l TTGCTGCTGCTGCTGCTG TTGCTGCTGCTGCTG 2: 30,363,832 (GRCm39) probably benign Het
Kmt2b TTCTCCT TTCTCCTTCTCCT 7: 30,285,782 (GRCm39) probably benign Het
Krtap28-10 CAG CAGCCAAAG 1: 83,019,867 (GRCm39) probably benign Het
Krtap28-10 CCACCACAGC CCACCACAGCCACAGTCACCACAGC 1: 83,020,002 (GRCm39) probably benign Het
Lmx1b TCCATCTTGATGCCGTCCAACATCTTGATGCCGTCCA TACATCTTGATGCCGTCCA 2: 33,530,501 (GRCm39) probably null Het
Mamld1 GCAACA GCAACAACA X: 70,162,418 (GRCm39) probably benign Het
Mamld1 AGC AGCGGC X: 70,162,456 (GRCm39) probably benign Het
Mamld1 AGC AGCCGC X: 70,162,444 (GRCm39) probably benign Het
Manbal CGATAGAAT C 2: 157,237,932 (GRCm39) probably null Het
Map1a GCTCCAGCTCCAGCTCCA GCTCCAGCTCCAGCTCCAGCTCCAGCTCCATCTCCAGCTCCAGCTCCA 2: 121,136,782 (GRCm39) probably benign Het
Mcph1 CTCT CTCTTCT 8: 18,702,541 (GRCm39) probably benign Het
Nefh CCTCACCTGGGGACTTGG CCTCACCTGGGGACTTGGGCTCACCTGGGGACTTGG 11: 4,891,039 (GRCm39) probably benign Het
Nusap1 GATACACGTTAGCAGTGAGGAGCAAGCTGA GATACACGTTAGCAGTGAGGAGCAAGCTGATATACACGTTAGCAGTGAGGAGCAAGCTGA 2: 119,458,060 (GRCm39) probably benign Het
Or2t49 TGGAGGTGGATTGG TG 11: 58,393,208 (GRCm39) probably benign Het
P4ha2 CCAGGTG C 11: 54,001,061 (GRCm39) probably benign Het
Pdik1l CCACCA CCACCAACACCA 4: 134,006,821 (GRCm39) probably benign Het
Polr1has CACCAC CACCACCCCCACCACCACCACAACCAC 17: 37,275,958 (GRCm39) probably benign Het
Rassf6 GCCTCACTCATGGTCCTGTAGAGCAATGGGGATTC GCCTCACTCATGGTCCTGTAGAGCAATGGGGATTCTTCCTCACTCATGGTCCTGTAGAGCAATGGGGATTC 5: 90,756,767 (GRCm39) probably benign Het
Rgs22 GCTAAAAAAAAAAAAAAAAA G 15: 36,010,981 (GRCm39) probably benign Het
Rpgrip1 AGG AGGGGG 14: 52,386,850 (GRCm39) probably benign Het
Slc39a4 TGTGGTC TGTGGTCATCATGATCACCATGGTCACCATGAGCACGGTGGTC 15: 76,499,066 (GRCm39) probably benign Het
Srpk2 ATCCT AT 5: 23,730,573 (GRCm39) probably benign Het
Strn AGTC AGTCCGTGCTCCCTTACCCCAGTCCGTGCTCCCTTACCCCTGTC 17: 78,984,714 (GRCm39) probably null Het
Tcof1 AAGAT AAGATTGGCCCTTTCCCAGAGATGCCCTTGGCTGCTGAGAT 18: 60,966,625 (GRCm39) probably benign Het
Tfeb AGC AGCCGC 17: 48,097,036 (GRCm39) probably benign Het
Tmem59 T TGTTTGTTG 4: 107,047,729 (GRCm39) probably benign Het
Trav6d-5 ATTTTT ATTTTTTTTTT 14: 53,032,791 (GRCm39) probably benign Het
Triobp CAGGACTCCCTGTGCCCAACGG CAGGACTCCCTGTGCCCAACGGAACAACCCAAGGACTCCCTGTGCCCAACGG 15: 78,851,239 (GRCm39) probably benign Het
Tsen2 GGA GGATGA 6: 115,537,028 (GRCm39) probably benign Het
Ttf2 TTCT TTCTTCT 3: 100,870,473 (GRCm39) probably benign Het
Vat1l C T 8: 115,016,069 (GRCm39) L320F probably damaging Het
Xirp2 TT TTTAT 2: 67,355,888 (GRCm39) probably benign Het
Yipf3 AGAGGA AGA 17: 46,559,898 (GRCm39) probably benign Het
Zfp933 TT TTTGCGT 4: 147,910,188 (GRCm39) probably null 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
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
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'- ATTGGATTCTGGATGCCACCG -3'
(R):5'- AGTAGCTTTGAACTGTTGCCC -3'

Sequencing Primer
(F):5'- ACCACTGTGCATCATGGACTG -3'
(R):5'- GAACTGTTGCCCTCACTTTCAG -3'
Posted On 2019-12-04