Mutagenetix > Incidental Mutation

Incidental Mutation 'R5227:Rfx1'

402682

Institutional Source

Beutler Lab

Gene Symbol

Rfx1

Ensembl Gene

ENSMUSG00000031706

Gene Name

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

Synonyms

MMRRC Submission

042800-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5227 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

84793463-84823621 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 84800687 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 96 (V96A)

Ref Sequence

ENSEMBL: ENSMUSP00000005600 (fasta)

Gene Model

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

AlphaFold

P48377

Predicted Effect

probably damaging
Transcript: ENSMUST00000005600
AA Change: V96A

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000005600
Gene: ENSMUSG00000031706
AA Change: V96A

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 damaging
Transcript: ENSMUST00000211046
AA Change: V96A

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)

Coding Region Coverage

1x: 99.5%
3x: 99.0%
10x: 98.2%
20x: 97.2%

Validation Efficiency

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: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcg8	T	C	17: 84,999,249 (GRCm39)	L115P	probably damaging	Het
Adgrb3	A	C	1: 25,133,033 (GRCm39)	M481R	possibly damaging	Het
Adgrd1	C	A	5: 129,199,647 (GRCm39)	N161K	probably benign	Het
Alx4	T	A	2: 93,507,725 (GRCm39)	V340D	probably damaging	Het
Arid1a	A	G	4: 133,407,716 (GRCm39)	S2264P	unknown	Het
Azi2	A	T	9: 117,876,526 (GRCm39)	H14L	probably damaging	Het
Camsap2	A	G	1: 136,202,629 (GRCm39)		probably benign	Het
Ccpg1	T	A	9: 72,919,354 (GRCm39)	L323*	probably null	Het
Cpsf1	A	T	15: 76,483,148 (GRCm39)	I943N	probably damaging	Het
Crebrf	T	A	17: 26,978,739 (GRCm39)	Y476N	probably damaging	Het
Defb10	T	A	8: 22,351,894 (GRCm39)	Y46*	probably null	Het
Dock3	A	G	9: 106,863,269 (GRCm39)	L703P	probably damaging	Het
Ebf2	A	T	14: 67,484,518 (GRCm39)	I181F	probably damaging	Het
Eif3e	T	A	15: 43,114,917 (GRCm39)	M420L	probably benign	Het
Emilin3	T	A	2: 160,751,185 (GRCm39)	Q188L	probably damaging	Het
Fbxl4	C	T	4: 22,376,840 (GRCm39)	T92M	probably damaging	Het
Fer1l6	C	T	15: 58,453,752 (GRCm39)	Q687*	probably null	Het
Fkrp	T	C	7: 16,544,635 (GRCm39)	E409G	possibly damaging	Het
Fzd9	T	C	5: 135,278,460 (GRCm39)	D475G	probably benign	Het
Gabbr1	C	T	17: 37,380,958 (GRCm39)	T767I	possibly damaging	Het
Gdf2	G	A	14: 33,663,451 (GRCm39)		probably null	Het
Gpatch1	T	C	7: 35,008,776 (GRCm39)	N82D	probably benign	Het
Heg1	T	A	16: 33,583,961 (GRCm39)	L1256Q	probably damaging	Het
Ireb2	T	A	9: 54,803,885 (GRCm39)		probably null	Het
Kansl1	T	G	11: 104,247,640 (GRCm39)	H570P	probably benign	Het
Kcna10	T	G	3: 107,101,744 (GRCm39)	M125R	probably damaging	Het
Lrp1b	T	G	2: 40,741,805 (GRCm39)	I3041L	possibly damaging	Het
Mbtd1	T	C	11: 93,815,474 (GRCm39)	F354S	possibly damaging	Het
Mideas	A	T	12: 84,199,661 (GRCm39)	F1020I	probably benign	Het
Mov10	T	C	3: 104,709,894 (GRCm39)	T331A	probably benign	Het
Ms4a8a	A	T	19: 11,045,780 (GRCm39)	S243T	probably damaging	Het
Ndufa11	T	C	17: 57,024,867 (GRCm39)	S10P	probably benign	Het
Olfml3	A	G	3: 103,643,737 (GRCm39)	Y215H	possibly damaging	Het
Or2t45	T	A	11: 58,669,705 (GRCm39)	F251I	possibly damaging	Het
Or56b2j	A	G	7: 104,353,529 (GRCm39)	I252V	possibly damaging	Het
Pclo	T	C	5: 14,763,574 (GRCm39)	S4016P	probably benign	Het
Pcyox1	G	C	6: 86,368,726 (GRCm39)	A264G	probably damaging	Het
Pdzrn3	C	T	6: 101,130,272 (GRCm39)	D515N	probably damaging	Het
Pnisr	A	G	4: 21,874,587 (GRCm39)		probably benign	Het
Prc1	T	C	7: 79,962,927 (GRCm39)	S574P	probably damaging	Het
Ranbp3l	T	A	15: 9,037,186 (GRCm39)	V16D	probably damaging	Het
Rufy4	T	C	1: 74,186,822 (GRCm39)	C537R	probably damaging	Het
Sfmbt1	T	C	14: 30,537,211 (GRCm39)		probably null	Het
Siglecf	T	C	7: 43,001,364 (GRCm39)	Y111H	probably damaging	Het
Snx14	G	A	9: 88,280,347 (GRCm39)	T536I	possibly damaging	Het
Spindoc	A	G	19: 7,351,512 (GRCm39)	V204A	probably benign	Het
Sptbn5	A	G	2: 119,915,812 (GRCm39)		probably benign	Het
Swt1	G	A	1: 151,278,727 (GRCm39)	Q227*	probably null	Het
Tg	A	G	15: 66,631,416 (GRCm39)	I562V	possibly damaging	Het
Trip11	T	A	12: 101,851,179 (GRCm39)	I677F	probably damaging	Het
Vmn1r49	G	A	6: 90,049,753 (GRCm39)	T83I	probably benign	Het
Vmn1r90	T	C	7: 14,295,601 (GRCm39)	K166E	possibly damaging	Het
Vmn2r124	T	C	17: 18,269,819 (GRCm39)	I25T	possibly damaging	Het
Vps13d	A	T	4: 144,907,777 (GRCm39)		probably null	Het
Zfp106	T	C	2: 120,354,449 (GRCm39)	I170V	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
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'- ACAGTCCTATGTTACTGAGCTAC -3'
(R):5'- GTAGGATGAGAAGCTCCTCTGC -3'

Sequencing Primer
(F):5'- TGAGCTACAGGCAGCCC -3'
(R):5'- TCTGCTTGGCCCGAGTC -3'

Posted On

2016-07-22