Mutagenetix > Incidental Mutation

Incidental Mutation 'R4690:Rfx1'

354849

Institutional Source

Beutler Lab

Gene Symbol

Rfx1

Ensembl Gene

ENSMUSG00000031706

Gene Name

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

Synonyms

MMRRC Submission

041941-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4690 (G1)

Quality Score

142

Status

Validated

Chromosome

Chromosomal Location

84793463-84823621 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 84809374 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 233 (V233A)

Ref Sequence

ENSEMBL: ENSMUSP00000005600 (fasta)

Gene Model

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

AlphaFold

P48377

Predicted Effect

possibly damaging
Transcript: ENSMUST00000005600
AA Change: V233A

PolyPhen 2 Score 0.496 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000005600
Gene: ENSMUSG00000031706
AA Change: V233A

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: ENSMUST00000102190

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000209362

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000210660

Predicted Effect

probably benign
Transcript: ENSMUST00000211046
AA Change: V233A

PolyPhen 2 Score 0.316 (Sensitivity: 0.90; Specificity: 0.89)

Meta Mutation Damage Score

0.0632

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.9%
20x: 94.5%

Validation Efficiency

98% (89/91)

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca9	A	G	11: 110,039,706 (GRCm39)	F436L	probably damaging	Het
Adam28	G	T	14: 68,879,497 (GRCm39)	Q184K	probably benign	Het
Adh6a	A	G	3: 138,031,932 (GRCm39)	T275A	possibly damaging	Het
Agap2	A	G	10: 126,927,244 (GRCm39)	D1082G	possibly damaging	Het
Alox5	A	T	6: 116,400,150 (GRCm39)	V263E	probably damaging	Het
Arhgef16	C	T	4: 154,372,420 (GRCm39)		probably null	Het
Bspry	G	A	4: 62,404,762 (GRCm39)	R186Q	probably damaging	Het
Ccdc188	T	A	16: 18,036,159 (GRCm39)	H111Q	probably damaging	Het
Cd40	T	C	2: 164,911,615 (GRCm39)	F209S	possibly damaging	Het
Cfap43	C	A	19: 47,736,298 (GRCm39)	V1398L	probably benign	Het
Cln3	A	T	7: 126,174,565 (GRCm39)	I286N	possibly damaging	Het
Col9a1	T	C	1: 24,263,787 (GRCm39)		probably null	Het
Cpne9	A	G	6: 113,279,016 (GRCm39)	E470G	probably damaging	Het
Cul5	A	T	9: 53,534,171 (GRCm39)	W654R	probably damaging	Het
Cyp2a22	T	A	7: 26,638,634 (GRCm39)	K51*	probably null	Het
Dcaf10	G	A	4: 45,372,769 (GRCm39)	R394Q	possibly damaging	Het
Dot1l	C	A	10: 80,622,016 (GRCm39)	S556*	probably null	Het
Eif3d	A	T	15: 77,851,516 (GRCm39)	M98K	probably benign	Het
Fiz1	A	G	7: 5,012,167 (GRCm39)	V117A	probably benign	Het
Fryl	A	G	5: 73,257,636 (GRCm39)	V722A	probably benign	Het
Ftdc1	G	A	16: 58,434,333 (GRCm39)	T128I	probably benign	Het
Gm3095	G	T	14: 3,964,471 (GRCm38)	R63I	probably benign	Het
Gm7133	A	T	1: 97,197,224 (GRCm39)		noncoding transcript	Het
Hoxb8	A	T	11: 96,175,286 (GRCm39)	D241V	probably benign	Het
Hrnr	A	G	3: 93,230,959 (GRCm39)	Q399R	unknown	Het
Itpk1	A	T	12: 102,572,434 (GRCm39)	V93D	probably damaging	Het
Kars1	C	T	8: 112,729,216 (GRCm39)	A164T	probably benign	Het
Kcnq4	A	T	4: 120,574,208 (GRCm39)	I150N	probably damaging	Het
Kcnrg	A	T	14: 61,849,176 (GRCm39)	L212F	probably damaging	Het
Kif5b	A	T	18: 6,216,759 (GRCm39)	D521E	probably benign	Het
Klf11	C	T	12: 24,705,071 (GRCm39)	T158M	probably damaging	Het
Klhl6	T	C	16: 19,776,034 (GRCm39)	I175V	probably benign	Het
Lsm1	A	G	8: 26,283,708 (GRCm39)	N40S	probably damaging	Het
Map1b	T	C	13: 99,567,576 (GRCm39)	E1715G	unknown	Het
Mecom	C	A	3: 30,292,459 (GRCm39)	A4S	probably benign	Het
Muc5b	G	A	7: 141,396,031 (GRCm39)	V96M	unknown	Het
Mug2	A	T	6: 122,013,255 (GRCm39)	I341L	probably benign	Het
Mxra7	A	T	11: 116,707,078 (GRCm39)		probably null	Het
Myo5a	T	C	9: 75,061,105 (GRCm39)	L537P	probably damaging	Het
Myo5b	A	T	18: 74,855,533 (GRCm39)	N1241Y	probably damaging	Het
Naa16	T	C	14: 79,582,497 (GRCm39)	R531G	probably damaging	Het
Neb	T	A	2: 52,134,087 (GRCm39)	M3299L	probably benign	Het
Nlrp4b	T	A	7: 10,453,130 (GRCm39)	Y76N	probably benign	Het
Nmral1	T	C	16: 4,534,205 (GRCm39)	T79A	probably damaging	Het
Noct	C	T	3: 51,155,300 (GRCm39)	Q23*	probably null	Het
Nrxn1	A	T	17: 90,344,509 (GRCm39)	V438D	probably damaging	Het
Or5b109	A	C	19: 13,212,132 (GRCm39)	N173H	possibly damaging	Het
Or5m9	T	A	2: 85,877,242 (GRCm39)	C139S	probably damaging	Het
Oxct2a	T	C	4: 123,216,836 (GRCm39)	T182A	probably benign	Het
Pank2	T	C	2: 131,115,945 (GRCm39)	I121T	probably damaging	Het
Pcdh1	T	A	18: 38,336,528 (GRCm39)	T36S	probably benign	Het
Pfdn1	A	T	18: 36,584,133 (GRCm39)	M67K	possibly damaging	Het
Plec	T	C	15: 76,058,456 (GRCm39)	E3849G	probably damaging	Het
Polr3a	A	T	14: 24,514,349 (GRCm39)	S817T	possibly damaging	Het
Pomgnt1	T	A	4: 116,012,707 (GRCm39)	D401E	probably damaging	Het
Ppp1r13b	T	A	12: 111,798,992 (GRCm39)	D891V	probably damaging	Het
Prr14l	A	G	5: 33,001,500 (GRCm39)		probably benign	Het
Ptk2b	A	G	14: 66,410,749 (GRCm39)		probably null	Het
Rab13	G	C	3: 90,128,330 (GRCm39)		probably null	Het
Rexo1	C	T	10: 80,382,255 (GRCm39)	A751T	probably benign	Het
Rnf149	C	T	1: 39,616,295 (GRCm39)		probably benign	Het
Rrm1	A	G	7: 102,097,086 (GRCm39)	D122G	probably benign	Het
Serpina1b	A	G	12: 103,698,639 (GRCm39)	F70S	probably damaging	Het
Serpinb13	C	T	1: 106,910,574 (GRCm39)	S66L	probably damaging	Het
Sh3rf3	T	C	10: 58,649,526 (GRCm39)	S44P	possibly damaging	Het
Shroom1	A	G	11: 53,356,549 (GRCm39)	T471A	possibly damaging	Het
Slc6a1	A	G	6: 114,279,792 (GRCm39)	Y152C	probably damaging	Het
Spata31f3	T	A	4: 42,873,032 (GRCm39)		probably null	Het
Spata6	A	T	4: 111,632,023 (GRCm39)	T145S	probably damaging	Het
Srcap	G	A	7: 127,137,186 (GRCm39)	G956D	probably damaging	Het
Ssh2	A	T	11: 77,346,031 (GRCm39)	I1339F	possibly damaging	Het
Tardbp	A	T	4: 148,697,078 (GRCm39)	*99K	probably null	Het
Tbc1d22a	A	G	15: 86,196,037 (GRCm39)	Y336C	probably damaging	Het
Tmcc3	G	A	10: 94,381,419 (GRCm39)		probably benign	Het
Tmem178b	T	G	6: 40,222,547 (GRCm39)	D87E	probably benign	Het
Tmem184a	A	C	5: 139,791,377 (GRCm39)	S380A	probably benign	Het
Tnfaip2	A	G	12: 111,411,682 (GRCm39)	K84R	possibly damaging	Het
Tpgs1	A	G	10: 79,511,235 (GRCm39)	T126A	probably benign	Het
Traf3ip1	A	G	1: 91,447,834 (GRCm39)	E437G	possibly damaging	Het
Trpc4ap	C	T	2: 155,477,053 (GRCm39)	C755Y	probably damaging	Het
Tsfm	A	G	10: 126,866,547 (GRCm39)		probably benign	Het
Tulp1	A	C	17: 28,570,811 (GRCm39)		probably benign	Het
Vmn1r23	A	T	6: 57,903,010 (GRCm39)	M256K	probably benign	Het
Zdhhc8	T	C	16: 18,044,605 (GRCm39)	D305G	probably damaging	Het
Zfp326	G	A	5: 106,054,942 (GRCm39)	R282H	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
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
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'- TGAGGCAGGTTGTTAGAGCC -3'
(R):5'- TAATGTGCCCTGTGAGGCAC -3'

Sequencing Primer
(F):5'- TGTTAGAGCCTGGGTGCCC -3'
(R):5'- TGTGAGGCACCTCTACAACTG -3'

Posted On

2015-10-21