Mutagenetix > Incidental Mutation

Incidental Mutation 'R4995:Rfx1'

385180

Institutional Source

Beutler Lab

Gene Symbol

Rfx1

Ensembl Gene

ENSMUSG00000031706

Gene Name

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

Synonyms

MMRRC Submission

042589-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4995 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

84793463-84823621 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

T to A at 84806743 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000147677 (fasta)

Gene Model

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

AlphaFold

P48377

Predicted Effect

probably null
Transcript: ENSMUST00000005600

SMART Domains

Protein: ENSMUSP00000005600
Gene: ENSMUSG00000031706

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 null
Transcript: ENSMUST00000005600

SMART Domains

Protein: ENSMUSP00000005600
Gene: ENSMUSG00000031706

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 null
Transcript: ENSMUST00000005600

SMART Domains

Protein: ENSMUSP00000005600
Gene: ENSMUSG00000031706

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 null
Transcript: ENSMUST00000005600

SMART Domains

Protein: ENSMUSP00000005600
Gene: ENSMUSG00000031706

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

noncoding transcript
Transcript: ENSMUST00000209362

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000210660

Predicted Effect

probably null
Transcript: ENSMUST00000211046

Predicted Effect

probably null
Transcript: ENSMUST00000211046

Predicted Effect

probably null
Transcript: ENSMUST00000211046

Predicted Effect

probably null
Transcript: ENSMUST00000211046

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.6%

Validation Efficiency

99% (86/87)

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921504E06Rik	G	A	2: 19,498,995 (GRCm39)	Q333*	probably null	Het
4930505A04Rik	C	T	11: 30,376,349 (GRCm39)	V173M	probably damaging	Het
Acvrl1	G	A	15: 101,033,741 (GRCm39)	R141H	probably benign	Het
Adprm	A	G	11: 66,932,436 (GRCm39)	F158L	possibly damaging	Het
Aldoart2	C	T	12: 55,613,038 (GRCm39)	T321M	probably benign	Het
Ap3m2	A	G	8: 23,293,792 (GRCm39)	V86A	probably benign	Het
Arhgef19	T	A	4: 140,974,826 (GRCm39)		probably null	Het
Bcl2l12	T	G	7: 44,643,615 (GRCm39)		probably null	Het
Bptf	T	C	11: 106,945,391 (GRCm39)	Q2501R	probably damaging	Het
C230029F24Rik	A	T	1: 49,377,295 (GRCm39)		noncoding transcript	Het
C7	C	T	15: 5,079,074 (GRCm39)	G78D	probably damaging	Het
Caly	T	C	7: 139,650,538 (GRCm39)	T135A	probably benign	Het
Cbl	A	G	9: 44,065,108 (GRCm39)	M740T	possibly damaging	Het
Cbx4	A	G	11: 118,972,037 (GRCm39)	V446A	probably benign	Het
Celsr1	C	A	15: 85,822,112 (GRCm39)	R1735L	probably damaging	Het
Cep250	A	G	2: 155,830,236 (GRCm39)	D135G	probably damaging	Het
Cgn	T	C	3: 94,687,246 (GRCm39)	T19A	probably damaging	Het
Chic2	A	T	5: 75,204,865 (GRCm39)	V32D	probably damaging	Het
Cntln	A	G	4: 84,968,120 (GRCm39)	K780E	probably benign	Het
Col8a2	A	T	4: 126,204,581 (GRCm39)	D197V	probably damaging	Het
Crot	A	T	5: 9,024,000 (GRCm39)	V372E	probably damaging	Het
Cyb561d2	C	T	9: 107,418,747 (GRCm39)	V26M	probably damaging	Het
Ddx5	G	A	11: 106,676,062 (GRCm39)	T237I	probably damaging	Het
Dmxl2	G	T	9: 54,408,725 (GRCm39)		probably benign	Het
Dock8	T	A	19: 25,135,747 (GRCm39)	S1188R	probably benign	Het
Ehbp1	T	A	11: 22,051,073 (GRCm39)	H493L	probably damaging	Het
Eif5b	T	A	1: 38,090,792 (GRCm39)	*1217K	probably null	Het
Eprs1	A	G	1: 185,142,336 (GRCm39)		probably benign	Het
Etfdh	T	C	3: 79,513,095 (GRCm39)	D376G	probably benign	Het
Fam186a	T	C	15: 99,842,980 (GRCm39)	Q1088R	probably benign	Het
Fbxw16	G	T	9: 109,270,318 (GRCm39)	T141N	probably damaging	Het
Fgf11	G	A	11: 69,689,585 (GRCm39)	H138Y	probably damaging	Het
Htra3	T	C	5: 35,828,418 (GRCm39)	E154G	probably damaging	Het
Hydin	T	A	8: 111,296,274 (GRCm39)	V3601D	probably damaging	Het
Jup	G	T	11: 100,270,367 (GRCm39)	S380*	probably null	Het
Klrg1	T	A	6: 122,255,234 (GRCm39)	D66V	probably benign	Het
Llgl1	C	T	11: 60,600,550 (GRCm39)	A633V	probably benign	Het
Lmln	T	A	16: 32,894,467 (GRCm39)	Y203*	probably null	Het
Lrrc58	T	G	16: 37,697,418 (GRCm39)	C165G	probably benign	Het
Lss	T	C	10: 76,383,371 (GRCm39)	V557A	probably benign	Het
Mast4	T	C	13: 103,042,262 (GRCm39)		probably benign	Het
Med13l	C	A	5: 118,869,014 (GRCm39)	P754Q	possibly damaging	Het
Mga	C	T	2: 119,763,063 (GRCm39)	R1240*	probably null	Het
Mgat5b	T	A	11: 116,865,025 (GRCm39)		probably null	Het
Mtor	A	G	4: 148,610,209 (GRCm39)	D1572G	probably damaging	Het
Muc4	T	A	16: 32,754,214 (GRCm38)	S1363T	probably benign	Het
Muc4	T	A	16: 32,575,332 (GRCm39)	S1306T	probably benign	Het
Myo18b	A	G	5: 112,908,258 (GRCm39)	V2005A	probably damaging	Het
Myo1e	G	A	9: 70,260,554 (GRCm39)	D571N	probably benign	Het
Mypn	T	C	10: 62,955,747 (GRCm39)		probably null	Het
Ndufb10	T	C	17: 24,941,731 (GRCm39)		probably null	Het
Nelfb	G	T	2: 25,096,208 (GRCm39)	D300E	probably benign	Het
Nicol1	G	A	5: 34,142,270 (GRCm39)	R79H	probably damaging	Het
Odad2	G	A	18: 7,223,663 (GRCm39)	T460M	probably damaging	Het
Or2y1d	T	A	11: 49,321,482 (GRCm39)	Y60N	probably damaging	Het
Or4e5	A	T	14: 52,727,988 (GRCm39)	C61*	probably null	Het
Or52n2c	T	A	7: 104,574,942 (GRCm39)	T10S	probably benign	Het
Or52z15	T	A	7: 103,332,574 (GRCm39)	D206E	probably damaging	Het
Pcdha11	C	T	18: 37,144,080 (GRCm39)	T57M	probably benign	Het
Pkp1	A	T	1: 135,808,593 (GRCm39)	I458N	possibly damaging	Het
Prr12	T	A	7: 44,700,653 (GRCm39)		probably benign	Het
Prrc2c	A	T	1: 162,532,879 (GRCm39)		probably benign	Het
Psd4	T	C	2: 24,287,259 (GRCm39)	F397S	probably benign	Het
Pygm	T	C	19: 6,448,169 (GRCm39)	I737T	probably damaging	Het
Rsl1	A	G	13: 67,330,313 (GRCm39)	T254A	possibly damaging	Het
Sh3rf3	A	G	10: 58,922,646 (GRCm39)	Q574R	probably benign	Het
Spire1	T	C	18: 67,685,849 (GRCm39)		probably null	Het
St6galnac4	G	A	2: 32,484,075 (GRCm39)	G91D	probably damaging	Het
Sytl2	T	C	7: 90,031,465 (GRCm39)		probably benign	Het
Tbpl2	T	A	2: 23,983,872 (GRCm39)	K188N	possibly damaging	Het
Tenm3	A	T	8: 48,682,172 (GRCm39)	M2486K	possibly damaging	Het
Tgoln1	A	C	6: 72,593,123 (GRCm39)	V119G	possibly damaging	Het
Tpgs1	A	T	10: 79,505,325 (GRCm39)	N28Y	probably benign	Het
U2surp	A	C	9: 95,344,847 (GRCm39)		probably benign	Het
Vmn2r103	A	G	17: 19,993,773 (GRCm39)	H50R	probably benign	Het
Vmn2r19	A	G	6: 123,306,869 (GRCm39)	N459S	probably benign	Het
Vmn2r72	T	C	7: 85,387,693 (GRCm39)	S624G	probably damaging	Het
Vps13c	A	G	9: 67,826,603 (GRCm39)	T1415A	probably benign	Het
Vwa5b1	G	A	4: 138,336,154 (GRCm39)	P147S	probably damaging	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
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
R6920:Rfx1	UTSW	8	84,822,117 (GRCm39)	missense	probably damaging	1.00
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'- AGACTGTGTCAGAAGCCAGC -3'
(R):5'- GGACTCTGGCAAGAACAGAC -3'

Sequencing Primer
(F):5'- AGTTCCACGGCAAGCCAG -3'
(R):5'- TCTGGCAAGAACAGACACAAG -3'

Posted On

2016-05-10