Mutagenetix > Incidental Mutations

Incidental Mutation 'RF014:Rfx4'

603420

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 #

RF014 (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)

CTCTCT to CTCTCTCTCTCTCTCTTTCTCT at 84858489 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: 98.6%

Validation Efficiency

98% (49/50)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5430401F13Rik	AGAAAGGAAAAGGTGGCCAGCAAAAACAGAAAGGAAAAGGTGGCCAG	AGAAAGGAAAAGGTGGCCAGCAAAAACAGAAAGGAAAAGGTGGCCAGCAAAAACAGAAAGGAAAAGGTGGCCAG	6: 131,552,857		probably benign	Het
9530003J23Rik	A	G	10: 117,234,417	*152Q	probably null	Het
A2ml1	T	C	6: 128,570,068	N366S	probably damaging	Het
Abca5	T	C	11: 110,279,754		probably null	Het
Acaca	T	C	11: 84,231,724	V323A	probably benign	Het
Agbl3	T	A	6: 34,799,358	D266E	possibly damaging	Het
Aggf1	A	T	13: 95,370,768	S170T	possibly damaging	Het
Amhr2	A	T	15: 102,453,154	S467C	probably benign	Het
Begain	GCCGCC	GCCGCCACCGCC	12: 109,033,422		probably benign	Het
Best3	A	T	10: 117,004,505	Q280L	probably damaging	Het
Calhm1	CTGTGGCTGTGG	CTGTGGCTGTGGGTGTGGCTGTGG	19: 47,141,265		probably benign	Het
Ccdc186	A	G	19: 56,813,472	L71S	probably benign	Het
Ces1d	C	A	8: 93,176,165		probably null	Het
Chga	AGC	AGCGGC	12: 102,561,393		probably benign	Het
Chga	AGC	AGCTGC	12: 102,561,405		probably benign	Het
Clstn3	T	A	6: 124,459,266	K212*	probably null	Het
Col16a1	TTTTT	TTTTTCTTTT	4: 130,093,067		probably benign	Het
Cpxm2	G	T	7: 132,070,863	T319K	possibly damaging	Het
Cyb5r4	TGCCCAGGGATGTGACAGACACAC	TGCCCAGGGATGTGACAGACACACCGCCCAGGGATGTGACAGACACAC	9: 87,040,415		probably benign	Het
Dst	T	C	1: 34,247,679	S3364P	probably benign	Het
Edc4	C	T	8: 105,884,600	T61M	probably benign	Het
Fndc5	A	G	4: 129,142,167	H199R	probably benign	Het
Gm43302	T	A	5: 105,274,757	I470F	possibly damaging	Het
Gne	G	T	4: 44,060,045	A147D	probably damaging	Het
Igkv12-89	G	GCAACGCCAC	6: 68,835,286		probably benign	Het
Irf9	C	T	14: 55,605,877	R179*	probably null	Het
Jakmip1	A	T	5: 37,174,526	K850M	possibly damaging	Het
Kalrn	G	A	16: 34,039,933	T1884I	probably benign	Het
Krtap28-10	CCACCACAGCCACAGCCACCACAGCCACAG	CCACCACAGCCACAGACACCACAGCCACAGCCACCACAGCCACAG	1: 83,042,251		probably benign	Het
Las1l	CTCCTCCTTCTCCTCTTCCTC	CTCCTC	X: 95,940,657		probably benign	Het
Lctl	A	G	9: 64,118,930	Y89C	probably damaging	Het
Lpgat1	GCC	GCCTCC	1: 191,718,553		probably benign	Het
Luzp2	A	T	7: 55,172,205	I157F	probably damaging	Het
Mamld1	GCA	GCACCA	X: 71,118,845		probably benign	Het
Map1a	GCTCCAGCTCCAGCTCCAGCTCCA	GCTCCAGCTCCAGCTCCAGCTCCAGCTCCACCTCCAGCTCCAGCTCCAGCTCCA	2: 121,306,295		probably benign	Het
Mbd3l1	A	T	9: 18,485,000	E140D	possibly damaging	Het
Mlh3	T	A	12: 85,268,029	Q461L	probably benign	Het
Mto1	G	T	9: 78,448,316	R7L	probably benign	Het
Muc4	A	T	16: 32,751,858	S579C	probably damaging	Het
Ngfr	T	C	11: 95,578,201	Y117C	probably damaging	Het
Olfr432	A	T	1: 174,050,987	I205F	possibly damaging	Het
Olfr537-ps1	A	T	7: 140,538,777	M87L	probably benign	Het
Olfr926	C	A	9: 38,877,900	H241Q	probably benign	Het
Plch2	A	G	4: 155,007,120	S179P	probably damaging	Het
Pogz	T	G	3: 94,878,247	S838A	possibly damaging	Het
Pot1b	T	A	17: 55,674,106	T303S	probably benign	Het
Pou2f2	T	A	7: 25,115,737	I72L	unknown	Het
Ppil2	C	T	16: 17,097,418	V109M	probably damaging	Het
Ptpn4	A	G	1: 119,684,465		probably null	Het
Ptprs	A	T	17: 56,416,935	I1686N	probably damaging	Het
Rnf14	T	A	18: 38,309,570	V308E	probably damaging	Het
Setd1a	TGGTGGTGG	TGGTGGTGGGGGTGGTGG	7: 127,785,346		probably benign	Het
Sgo2b	T	C	8: 63,931,405	T186A	possibly damaging	Het
Six3	CGG	CGGTGG	17: 85,621,356		probably benign	Het
Six4	TG	T	12: 73,103,582		probably null	Het
Stox1	T	A	10: 62,664,246	H845L	probably benign	Het
Supt20	AGCAGC	AGCAGCGGCAGC	3: 54,727,665		probably benign	Het
Thegl	CAGCGATCCTCCCCAGTCCCGCA	CAGCGATCCTCCCCAGTCCCGCAGGGCGAGCGATCCTCCCCAGTCCCGCA	5: 77,016,400		probably benign	Het
Trappc9	A	AGCTGCTGCTGCTGCT	15: 72,801,283		probably benign	Het
Trim33	T	C	3: 103,329,092	V506A	possibly damaging	Het
Uckl1	T	C	2: 181,570,194	D373G	probably benign	Het
Vmn2r94	G	T	17: 18,253,287	C492*	probably null	Het
Wdr33	A	G	18: 31,881,273	D396G	probably damaging	Het
Zbtb11	A	T	16: 55,980,597	I105L	probably damaging	Het
Zbtb40	A	T	4: 137,017,306	C268S	probably benign	Het
Zfp36l1	T	A	12: 80,109,744	M288L	probably benign	Het
Zfp384	CC	CCAAGGCCCAGGAC	6: 125,036,466		probably benign	Het
Zfp72	A	G	13: 74,375,054	F15S	probably benign	Het
Znrd1as	CACCACCACCAC	CACCACCACCACCACCACCACGACCACCACCAC	17: 36,965,060		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
RF010:Rfx4	UTSW	10	84858487	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'- GCCACCGTGTTGGCTTTTAC -3'
(R):5'- GACTTACGAGAATGGAGTAGCTTTG -3'

Sequencing Primer
(F):5'- ACCACTGTGCATCATGGACTG -3'
(R):5'- AGTAGCTTTGAACTGTTGCCC -3'

Posted On

2019-12-04