Mutagenetix > Incidental Mutations

Incidental Mutation 'RF010:Rfx4'

603140

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

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

RF010 (G1)

Quality Score

217.468

Status

Not validated

Chromosome

Chromosomal Location

84756062-84906538 bp(+) (GRCm38)

Type of Mutation

critical splice acceptor site

DNA Base Change (assembly)

CTCTCTCT to CTCTCTCTCTCTCTCTATCTCTCT at 84858487 bp

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000051107 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000060397] [ENSMUST00000095388] [ENSMUST00000166696]

Predicted Effect

probably benign
Transcript: ENSMUST00000060397

SMART Domains

Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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: 98.8%

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2300002M23Rik	GGGTTATGGTCAGTACCCCCCAGTAGGGACCTGGGGCGGTTATGGTCAGTACCCCCCAGTAGGGCCCTGGGGCGGTTATGGTCAGTACCCCCCAGTAGGGACCTGGGG	GGGTTATGGTCAGTACCCCCCAGTAGGGCCCTGGGGCGGTTATGGTCAGTACCCCCCAGTAGGGACCTGGGG	17: 35,568,576		probably benign	Het
Acap3	CCTGGGCTGCTG	CCTGGGCTGCTGCATACTGGGCTGCTG	4: 155,905,096		probably benign	Het
Ankrd28	A	G	14: 31,778,986	I16T	probably damaging	Het
AY761185	GCACTGTGGGC	G	8: 20,943,911		probably null	Het
B020031M17Rik	A	T	13: 119,950,046	V8E	probably benign	Het
Bend3	T	A	10: 43,510,184	F191Y	possibly damaging	Het
Calhm1	GTGGC	GTGGCTGTGGCTATGGC	19: 47,141,273		probably benign	Het
Camkv	CGCTGCTGC	CGC	9: 107,947,860		probably benign	Het
Chga	GCA	GCATCA	12: 102,561,403		probably benign	Het
Cngb1	CTCTGGCTCTGGCTCTGGCTCTG	C	8: 95,303,650		probably null	Het
Cnot3	T	C	7: 3,656,069	V438A	probably benign	Het
Cntnap5c	T	A	17: 58,286,795	W710R	probably damaging	Het
Dyrk1a	A	G	16: 94,677,563	S404G	probably benign	Het
Efhd2	GCCGCC	GCCGCCTCCGCC	4: 141,874,764		probably benign	Het
Flywch1	GTGT	GTGTGGGGAGGCTACGTACTCACCCACACCTGTTGT	17: 23,762,175		probably null	Het
Fmn2	T	A	1: 174,582,015	S605T	unknown	Het
Gab3	TCT	TCTGCT	X: 75,000,011		probably benign	Het
Gabre	GCTC	GCTCCGTCTC	X: 72,270,060		probably benign	Het
Gli3	A	G	13: 15,726,369	Y1447C	probably damaging	Het
Hibch	T	C	1: 52,913,732	V297A	probably benign	Het
Ifi213	C	G	1: 173,582,153	D462H	probably damaging	Het
Kcnh8	G	A	17: 52,978,239	R1079H	probably benign	Het
Lce1m	GCTGCTGCC	GCTGCTGCCCCCACTGCTGCC	3: 93,018,290		probably benign	Het
Lpo	A	G	11: 87,821,102	V43A	probably benign	Het
Map1a	A	AGCTCCAGCTCCAGCCCCACCTCCAGCTCCC	2: 121,306,318		probably benign	Het
Mapk9	A	G	11: 49,854,256		probably benign	Het
Mep1a	G	A	17: 43,486,235	H314Y	probably damaging	Het
Myh3	ATTAC	ATTACTTAC	11: 67,086,356		probably null	Het
Myh3	AC	ACTTCC	11: 67,086,359		probably null	Het
Nusap1	ACGTTAGCAGTGAGGAGCAA	ACGTTAGCAGTGAGGAGCAAACTGAGATACTCGTTAGCAGTGAGGAGCAA	2: 119,627,584		probably benign	Het
Olfr1118	T	A	2: 87,308,840	V37E	possibly damaging	Het
Olfr305	T	C	7: 86,363,386	Q317R	probably benign	Het
Pdcd11	AGGAGG	A	19: 47,113,451		probably null	Het
Pfkm	T	A	15: 98,129,793	I651N	possibly damaging	Het
Phldb3	CCCCCGCCCC	CCCCC	7: 24,626,495		probably null	Het
Prkce	T	C	17: 86,488,199	V288A	probably damaging	Het
Pxmp4	A	G	2: 154,592,263	S93P	probably damaging	Het
Rfc4	T	C	16: 23,127,482	T17A	probably benign	Het
Ryr3	G	T	2: 112,775,670	A2415E	probably damaging	Het
Sbp	ACAAAGATGCTGACAACAAAGATGCTGACA	ACAAAGATGCTGACACCAAAGATGCTGACAACAAAGATGCTGACA	17: 23,945,351		probably benign	Het
Sec24c	T	A	14: 20,688,715		probably null	Het
Sec63	C	A	10: 42,806,624	A437E	probably benign	Het
Six3	GCG	GCGTCG	17: 85,621,355		probably benign	Het
Slco5a1	G	A	1: 12,871,947	T825I	probably damaging	Het
Stard8	GGA	GGAAGA	X: 99,066,517		probably benign	Het
Stxbp1	A	G	2: 32,821,915	V30A	probably benign	Het
Supt20	AGCAGC	AGCAGCGGCAGC	3: 54,727,662		probably benign	Het
Syne1	T	A	10: 5,246,386	D3882V	possibly damaging	Het
T	A	G	17: 8,441,708	T384A	probably benign	Het
Tbc1d12	CGGGGCGG	CG	19: 38,836,940		probably benign	Het
Tcof1	CAG	CAGAAG	18: 60,835,744		probably benign	Het
Tfeb	GCA	GCAACA	17: 47,786,094		probably benign	Het
Tfeb	CAG	CAGAAG	17: 47,786,107		probably benign	Het
Thegl	CAG	CAGCGATCCTCCCCAGTCCCGCAAGGCGAG	5: 77,016,427		probably benign	Het
Thumpd3	C	T	6: 113,056,045	A248V	probably damaging	Het
Tmem181a	T	C	17: 6,280,703		probably null	Het
Tmem56	T	A	3: 121,228,884	I103L	probably benign	Het
Trim41	A	T	11: 48,807,338	H600Q	probably damaging	Het
Ttbk2	A	T	2: 120,790,339	C147*	probably null	Het
Ttll2	C	T	17: 7,351,338	A397T	probably benign	Het
Unc79	T	A	12: 103,112,787	L1737Q	probably benign	Het
Usp47	T	A	7: 112,092,938	V869E	probably damaging	Het
Vmn1r231	T	A	17: 20,889,993	Q220L	probably damaging	Het
Vmn2r26	C	T	6: 124,039,489	T304I	possibly damaging	Het
Wdr66	TCTCA	T	5: 123,274,161		probably benign	Het
Wrn	T	C	8: 33,288,765	N839S	probably benign	Het
Zfp384	GCCCAGGCCCAGGCCCAGGCCCAG	GCCCAGGCCCAGTCCCAGGCCCAGGCCCAGGCCCAG	6: 125,036,471		probably benign	Het
Zfp384	GGCCCAGG	GGCCCAGGAGCACGCCCAGG	6: 125,036,488		probably benign	Het
Zfyve26	C	T	12: 79,255,338	C1828Y	probably damaging	Het
Znrd1as	CACCACCAC	CACCACCACCACCACCACCACTACCACCAC	17: 36,965,063		probably benign	Het

Other mutations in Rfx4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00094:Rfx4	APN	10	84840199	missense	probably damaging	1.00
IGL00334:Rfx4	APN	10	84780053	missense	possibly damaging	0.91
IGL00928:Rfx4	APN	10	84840114	missense	probably benign	0.04
IGL01063:Rfx4	APN	10	84868382	missense	possibly damaging	0.90
IGL01490:Rfx4	APN	10	84840851	missense	possibly damaging	0.85
IGL02390:Rfx4	APN	10	84840150	missense	probably damaging	1.00
IGL02454:Rfx4	APN	10	84840106	missense	possibly damaging	0.83
R0099:Rfx4	UTSW	10	84894304	missense	probably benign
R0503:Rfx4	UTSW	10	84894332	missense	possibly damaging	0.56
R0924:Rfx4	UTSW	10	84868427	missense	probably damaging	1.00
R0930:Rfx4	UTSW	10	84868427	missense	probably damaging	1.00
R1386:Rfx4	UTSW	10	84863285	missense	probably damaging	1.00
R1715:Rfx4	UTSW	10	84844280	missense	probably damaging	1.00
R1738:Rfx4	UTSW	10	84880975	critical splice donor site	probably null
R1987:Rfx4	UTSW	10	84896088	missense	possibly damaging	0.87
R3717:Rfx4	UTSW	10	84880224	missense	probably damaging	1.00
R4231:Rfx4	UTSW	10	84814694	missense	probably benign	0.03
R4300:Rfx4	UTSW	10	84905102	missense	probably damaging	0.98
R4581:Rfx4	UTSW	10	84844300	missense	possibly damaging	0.93
R4582:Rfx4	UTSW	10	84844300	missense	possibly damaging	0.93
R4618:Rfx4	UTSW	10	84880896	missense	probably benign	0.01
R5156:Rfx4	UTSW	10	84868354	missense	probably damaging	1.00
R5185:Rfx4	UTSW	10	84863250	missense	probably damaging	1.00
R5377:Rfx4	UTSW	10	84860542	missense	possibly damaging	0.81
R5601:Rfx4	UTSW	10	84798578	missense	probably damaging	1.00
R5879:Rfx4	UTSW	10	84814761	critical splice donor site	probably null
R5996:Rfx4	UTSW	10	84840017	nonsense	probably null
R6358:Rfx4	UTSW	10	84844235	missense	probably damaging	1.00
R6805:Rfx4	UTSW	10	84840228	missense	possibly damaging	0.86
R7248:Rfx4	UTSW	10	84905055	missense	probably benign	0.05
R7427:Rfx4	UTSW	10	84896012	missense	probably benign	0.28
R7428:Rfx4	UTSW	10	84896012	missense	probably benign	0.28
R7514:Rfx4	UTSW	10	84880226	missense	probably damaging	1.00
R7576:Rfx4	UTSW	10	84863349	missense	probably damaging	0.98
R8002:Rfx4	UTSW	10	84840857	missense	probably damaging	0.97
RF005:Rfx4	UTSW	10	84858494	critical splice acceptor site	probably benign
RF014:Rfx4	UTSW	10	84858489	critical splice acceptor site	probably benign
RF015:Rfx4	UTSW	10	84858489	critical splice acceptor site	probably benign
RF023:Rfx4	UTSW	10	84858485	critical splice acceptor site	probably benign
RF030:Rfx4	UTSW	10	84858480	critical splice acceptor site	probably benign
RF035:Rfx4	UTSW	10	84858480	critical splice acceptor site	probably benign
RF046:Rfx4	UTSW	10	84858481	critical splice acceptor site	probably benign
RF060:Rfx4	UTSW	10	84858494	critical splice acceptor site	probably benign
RF062:Rfx4	UTSW	10	84858481	critical splice acceptor site	probably benign
X0024:Rfx4	UTSW	10	84780074	missense	possibly damaging	0.82
Z1177:Rfx4	UTSW	10	84814684	missense	possibly damaging	0.85
Z1177:Rfx4	UTSW	10	84896091	missense	probably benign	0.30

Predicted Primers

PCR Primer
(F):5'- TCTCCCGAAGTGACCAGATC -3'
(R):5'- CGCACATGGGAAACACTTAGC -3'

Sequencing Primer
(F):5'- AGTGACCAGATCTTCAAAGGC -3'
(R):5'- TGGGAAACACTTAGCCTAATTCTGGG -3'

Posted On

2019-12-04