Mutagenetix > Incidental Mutation

Incidental Mutation 'R6920:Rfx1'

539583

Institutional Source

Beutler Lab

Gene Symbol

Rfx1

Ensembl Gene

ENSMUSG00000031706

Gene Name

regulatory factor X, 1 (influences HLA class II expression)

Synonyms

MMRRC Submission

045040-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6920 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

84793463-84823621 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 84822117 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 872 (Y872C)

Ref Sequence

ENSEMBL: ENSMUSP00000147677 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000005600] [ENSMUST00000041367] [ENSMUST00000210279] [ENSMUST00000211046]

AlphaFold

P48377

Predicted Effect

probably damaging
Transcript: ENSMUST00000005600
AA Change: Y872C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000005600
Gene: ENSMUSG00000031706
AA Change: Y872C

Domain	Start	End	E-Value	Type
low complexity region	11	47	N/A	INTRINSIC
low complexity region	53	67	N/A	INTRINSIC
low complexity region	73	92	N/A	INTRINSIC
Pfam:RFX1_trans_act	106	176	9.6e-9	PFAM
Pfam:RFX1_trans_act	211	366	1.8e-59	PFAM
Pfam:RFX_DNA_binding	420	498	2.5e-35	PFAM
Blast:HisKA	705	768	3e-28	BLAST
low complexity region	908	920	N/A	INTRINSIC
low complexity region	932	948	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000041367

SMART Domains

Protein: ENSMUSP00000038568
Gene: ENSMUSG00000037103

Domain	Start	End	E-Value	Type
low complexity region	12	33	N/A	INTRINSIC
Pfam:DCAF15_WD40	48	259	1.1e-84	PFAM
low complexity region	275	294	N/A	INTRINSIC
low complexity region	343	359	N/A	INTRINSIC
low complexity region	374	384	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000210279

Predicted Effect

probably damaging
Transcript: ENSMUST00000211046
AA Change: Y872C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.1%
20x: 97.2%

Validation Efficiency

100% (65/65)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the regulatory factor X (RFX) family of transcription factors, which are characterized by a winged-helix DNA-binding domain. The encoded transcription factor contains an N-terminal activation domain and a C-terminal repression domain, and may activate or repress target gene expression depending on cellular context. This transcription factor has been shown to regulate a wide variety of genes involved in immunity and cancer, including the MHC class II genes and genes that may be involved in cancer progression. This gene exhibits altered expression in glioblastoma and the autoimmune disease systemic lupus erythematosis (SLE). [provided by RefSeq, Jul 2016]
PHENOTYPE: Mice homozygous for a gene trap allele die prior to implantation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	A	T	3: 137,773,811 (GRCm39)	Y1000F	probably damaging	Het
1700018B08Rik	A	G	8: 122,262,160 (GRCm39)		probably null	Het
Aadat	T	C	8: 60,982,467 (GRCm39)	F245L	probably damaging	Het
Adcy10	T	G	1: 165,403,227 (GRCm39)	L1575W	probably damaging	Het
Anks4b	A	T	7: 119,782,231 (GRCm39)	T421S	probably damaging	Het
Anpep	A	T	7: 79,475,097 (GRCm39)	I155N	probably damaging	Het
Arnt	T	C	3: 95,397,932 (GRCm39)	F572L	probably damaging	Het
Brip1	G	A	11: 86,039,362 (GRCm39)	Q391*	probably null	Het
Brpf3	C	A	17: 29,042,970 (GRCm39)	H1004N	probably benign	Het
Cand2	T	A	6: 115,768,250 (GRCm39)	V465D	possibly damaging	Het
Card10	G	T	15: 78,686,609 (GRCm39)	Y69*	probably null	Het
Catsperd	A	T	17: 56,962,175 (GRCm39)	K450*	probably null	Het
Ccdc137	T	C	11: 120,351,009 (GRCm39)	L137P	probably damaging	Het
Cic	T	C	7: 24,990,107 (GRCm39)	S1905P	probably damaging	Het
Csmd3	C	T	15: 47,507,601 (GRCm39)	G2971S	probably damaging	Het
Dmxl2	A	G	9: 54,379,496 (GRCm39)	Y183H	probably damaging	Het
Drosha	T	C	15: 12,834,396 (GRCm39)	Y167H	unknown	Het
E330034G19Rik	A	G	14: 24,358,310 (GRCm39)	K214R	unknown	Het
Fam180a	T	G	6: 35,290,765 (GRCm39)	I73L	possibly damaging	Het
Fbxo28	G	T	1: 182,168,986 (GRCm39)	H51N	probably benign	Het
Gm12728	T	G	4: 105,647,533 (GRCm39)		probably null	Het
Gm973	T	C	1: 59,591,620 (GRCm39)	C335R	possibly damaging	Het
Gpx8	A	G	13: 113,179,770 (GRCm39)	V177A	probably damaging	Het
Hdlbp	A	G	1: 93,340,083 (GRCm39)		probably null	Het
Htt	T	G	5: 35,034,444 (GRCm39)	Y1972D	probably null	Het
Igkv6-14	T	C	6: 70,412,116 (GRCm39)	Y56C	possibly damaging	Het
Kcnma1	A	G	14: 23,576,602 (GRCm39)		probably null	Het
Klc1	T	C	12: 111,754,019 (GRCm39)	S105P	probably damaging	Het
Klhl20	T	C	1: 160,921,266 (GRCm39)	D63G	possibly damaging	Het
Lamc3	A	G	2: 31,798,701 (GRCm39)	D469G	probably damaging	Het
Lrit1	G	C	14: 36,782,052 (GRCm39)	V242L	probably damaging	Het
Mboat4	G	A	8: 34,591,865 (GRCm39)	R434H	probably benign	Het
Mttp	T	C	3: 137,821,043 (GRCm39)	K270E	possibly damaging	Het
Muc5ac	G	A	7: 141,347,035 (GRCm39)	C337Y	possibly damaging	Het
Nars1	A	G	18: 64,634,471 (GRCm39)	V484A	probably damaging	Het
Noxa1	G	T	2: 24,981,844 (GRCm39)		probably null	Het
Or14c45	A	G	7: 86,176,522 (GRCm39)	T186A	probably benign	Het
Or7g18	T	A	9: 18,786,821 (GRCm39)	L63H	probably damaging	Het
Osbpl7	G	A	11: 96,941,584 (GRCm39)	G36S	probably damaging	Het
P4htm	C	T	9: 108,460,812 (GRCm39)	G220D	probably benign	Het
Pcdhga7	A	G	18: 37,848,199 (GRCm39)	I69V	probably benign	Het
Pla2g4e	C	T	2: 120,015,795 (GRCm39)	E250K	possibly damaging	Het
Plcd4	A	G	1: 74,604,994 (GRCm39)		probably benign	Het
Ppfia3	C	A	7: 45,008,231 (GRCm39)	G213V	possibly damaging	Het
Ppp1r1a	A	G	15: 103,441,513 (GRCm39)	S67P	probably damaging	Het
Prss43	T	C	9: 110,657,680 (GRCm39)	F193S	probably benign	Het
Rhot1	T	A	11: 80,132,921 (GRCm39)	N218K	probably benign	Het
Sall1	A	G	8: 89,757,021 (GRCm39)	F1028L	probably damaging	Het
Siglec1	G	A	2: 130,919,997 (GRCm39)	Q845*	probably null	Het
Slc38a9	C	T	13: 112,838,060 (GRCm39)	T275I	possibly damaging	Het
Slc39a4	A	T	15: 76,497,470 (GRCm39)	S481T	probably damaging	Het
Ssr1	A	T	13: 38,169,998 (GRCm39)	N191K	probably damaging	Het
Tenm4	A	T	7: 96,544,757 (GRCm39)	S2258C	probably damaging	Het
Tm7sf3	T	G	6: 146,507,645 (GRCm39)	R472S	possibly damaging	Het
Tmprss11a	G	A	5: 86,576,494 (GRCm39)	T119M	probably benign	Het
Traip	C	T	9: 107,838,240 (GRCm39)	R142*	probably null	Het
Utrn	T	C	10: 12,626,214 (GRCm39)	N100D	probably damaging	Het
Vmn1r74	T	C	7: 11,581,575 (GRCm39)	S292P	probably benign	Het
Vmn2r71	A	T	7: 85,273,108 (GRCm39)	I641F	probably damaging	Het
Vmn2r9	T	A	5: 108,996,912 (GRCm39)	Y119F	possibly damaging	Het
Vmn2r98	A	G	17: 19,285,510 (GRCm39)	N110S	probably damaging	Het
Vwce	A	G	19: 10,642,057 (GRCm39)	T928A	probably benign	Het
Zfp608	T	A	18: 55,121,337 (GRCm39)	K83N	probably damaging	Het
Zfp808	A	G	13: 62,320,982 (GRCm39)	H737R	probably benign	Het
Zswim4	T	C	8: 84,940,714 (GRCm39)	N795S	probably benign	Het

Other mutations in Rfx1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01612:Rfx1	APN	8	84,819,601 (GRCm39)	critical splice acceptor site	probably null
IGL01779:Rfx1	APN	8	84,819,291 (GRCm39)	splice site	probably benign
IGL02505:Rfx1	APN	8	84,822,438 (GRCm39)	missense	possibly damaging	0.79
IGL02741:Rfx1	APN	8	84,822,471 (GRCm39)	missense	possibly damaging	0.94
R1565:Rfx1	UTSW	8	84,800,575 (GRCm39)	missense	probably benign
R1793:Rfx1	UTSW	8	84,793,050 (GRCm39)	unclassified	probably benign
R1808:Rfx1	UTSW	8	84,821,677 (GRCm39)	missense	probably damaging	1.00
R1971:Rfx1	UTSW	8	84,822,126 (GRCm39)	missense	probably damaging	1.00
R4542:Rfx1	UTSW	8	84,816,866 (GRCm39)	missense	probably damaging	1.00
R4690:Rfx1	UTSW	8	84,809,374 (GRCm39)	missense	possibly damaging	0.50
R4995:Rfx1	UTSW	8	84,806,743 (GRCm39)	splice site	probably null
R5163:Rfx1	UTSW	8	84,819,840 (GRCm39)	missense	probably damaging	0.98
R5212:Rfx1	UTSW	8	84,793,221 (GRCm39)	unclassified	probably benign
R5227:Rfx1	UTSW	8	84,800,687 (GRCm39)	missense	probably damaging	0.99
R5401:Rfx1	UTSW	8	84,793,005 (GRCm39)	splice site	probably null
R5431:Rfx1	UTSW	8	84,809,349 (GRCm39)	nonsense	probably null
R5584:Rfx1	UTSW	8	84,814,706 (GRCm39)	splice site	probably null
R5693:Rfx1	UTSW	8	84,800,533 (GRCm39)	missense	unknown
R6210:Rfx1	UTSW	8	84,819,647 (GRCm39)	missense	probably damaging	1.00
R6715:Rfx1	UTSW	8	84,822,444 (GRCm39)	missense	possibly damaging	0.49
R7131:Rfx1	UTSW	8	84,821,708 (GRCm39)	missense	probably damaging	0.96
R7155:Rfx1	UTSW	8	84,821,455 (GRCm39)	missense	probably damaging	0.99
R7336:Rfx1	UTSW	8	84,800,385 (GRCm39)	start gained	probably benign
R7467:Rfx1	UTSW	8	84,800,542 (GRCm39)	missense	possibly damaging	0.86
R8105:Rfx1	UTSW	8	84,814,505 (GRCm39)	missense	possibly damaging	0.92
R8145:Rfx1	UTSW	8	84,800,657 (GRCm39)	missense	probably benign	0.06
R8261:Rfx1	UTSW	8	84,819,479 (GRCm39)	missense	probably benign	0.00
R8263:Rfx1	UTSW	8	84,821,483 (GRCm39)	missense	probably damaging	1.00
R8443:Rfx1	UTSW	8	84,806,515 (GRCm39)	missense	probably benign	0.00
R8680:Rfx1	UTSW	8	84,818,084 (GRCm39)	missense	possibly damaging	0.82
R9302:Rfx1	UTSW	8	84,817,662 (GRCm39)	missense	possibly damaging	0.50
R9473:Rfx1	UTSW	8	84,819,903 (GRCm39)	missense	probably damaging	0.96
R9766:Rfx1	UTSW	8	84,814,376 (GRCm39)	missense	probably damaging	1.00
Z1177:Rfx1	UTSW	8	84,816,906 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGCTTGCAAGAGACACTGGG -3'
(R):5'- CATGCATGGCTACCTTTGTC -3'

Sequencing Primer
(F):5'- CTTGCAAGAGACACTGGGGAAAAC -3'
(R):5'- CCTTTGTCAGGGTCCAAGG -3'

Posted On

2018-11-06