Mutagenetix > Incidental Mutations

Incidental Mutation 'R4231:Rfx4'

320861

Institutional Source

Beutler Lab

Gene Symbol

Rfx4

Ensembl Gene

ENSMUSG00000020037

Gene Name

regulatory factor X, 4 (influences HLA class II expression)

Synonyms

4933412G19Rik

MMRRC Submission

041050-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R4231 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

84756062-84906538 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 84814694 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Leucine at position 84 (M84L)

Ref Sequence

ENSEMBL: ENSMUSP00000051107 (fasta)

Gene Model

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

AlphaFold

Q7TNK1

Predicted Effect

probably benign
Transcript: ENSMUST00000060397
AA Change: M84L

PolyPhen 2 Score 0.025 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: M84L

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

noncoding transcript
Transcript: ENSMUST00000158826

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000165868

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173479

Meta Mutation Damage Score

0.1419

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.2%

Validation Efficiency

99% (75/76)

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930567H17Rik	C	T	X: 70,394,529	A53T	probably benign	Het
4932438A13Rik	C	T	3: 36,920,236	T663I	probably benign	Het
Ajuba	T	C	14: 54,569,526	R490G	probably damaging	Het
Akap6	A	T	12: 53,141,038	D1745V	probably damaging	Het
Aldh5a1	C	T	13: 24,911,653	G494R	probably damaging	Het
Ankar	T	C	1: 72,658,542	D1034G	probably benign	Het
Aox3	T	A	1: 58,114,885	N23K	probably benign	Het
Arhgef18	T	C	8: 3,450,317	I541T	possibly damaging	Het
Atg14	T	C	14: 47,551,345	K184E	probably benign	Het
Cacnb2	A	G	2: 14,981,440	K343E	probably damaging	Het
Casp8	T	C	1: 58,844,770	V432A	probably damaging	Het
Cd93	A	T	2: 148,442,960	H155Q	probably benign	Het
Cox6b2	T	C	7: 4,752,835	M1V	probably null	Het
Crat	T	C	2: 30,413,011	E88G	possibly damaging	Het
Ddx1	C	T	12: 13,223,857	V590I	possibly damaging	Het
Dip2a	G	A	10: 76,319,470	P94S	probably damaging	Het
Dtx3	A	G	10: 127,193,189	I60T	possibly damaging	Het
Fam196b	A	T	11: 34,403,143	E395V	probably benign	Het
Filip1l	T	C	16: 57,506,768	S54P	probably benign	Het
Gm12887	A	T	4: 121,622,102	M1K	probably null	Het
Gm26678	T	C	3: 54,633,083		noncoding transcript	Het
Impg1	A	G	9: 80,345,329	L523P	probably damaging	Het
Ip6k2	G	A	9: 108,805,648	R319Q	probably benign	Het
Irak2	A	G	6: 113,690,856	E466G	probably damaging	Het
Irgm2	C	T	11: 58,219,478		probably benign	Het
Jak3	T	A	8: 71,685,545	V880D	probably damaging	Het
Jmy	G	T	13: 93,498,925	P128T	probably benign	Het
Kif20a	A	G	18: 34,632,038	N775S	probably benign	Het
Kremen1	G	A	11: 5,243,881	Q50*	probably null	Het
Lrrc71	A	G	3: 87,740,991	I438T	probably benign	Het
Map3k1	T	C	13: 111,768,494	T374A	probably benign	Het
Med12l	T	G	3: 59,257,223		probably null	Het
Mrps30	T	C	13: 118,386,840	D132G	probably damaging	Het
Mta1	T	C	12: 113,135,827	M603T	possibly damaging	Het
Myo5a	A	G	9: 75,189,997	N1319S	possibly damaging	Het
Nalcn	T	A	14: 123,599,913	Q13L	probably benign	Het
Nbas	A	G	12: 13,393,343	N1133S	probably damaging	Het
Nsun2	A	G	13: 69,619,541	N205D	probably damaging	Het
Nxpe4	A	T	9: 48,398,837	T467S	probably damaging	Het
Olfr1293-ps	C	T	2: 111,528,201	R314C	probably damaging	Het
Olfr53	T	C	7: 140,652,740	Y254H	probably damaging	Het
Olfr849	T	A	9: 19,441,590	L226I	probably damaging	Het
Pam	A	G	1: 97,884,124		probably null	Het
Pcdh7	G	A	5: 57,719,289	G62D	possibly damaging	Het
Plxna2	C	T	1: 194,644,454	T232I	probably damaging	Het
Prkar1b	A	G	5: 139,108,621	S71P	probably benign	Het
Ptprq	A	T	10: 107,686,283	Y602*	probably null	Het
Rfx7	A	T	9: 72,619,390	E1287D	possibly damaging	Het
Rin2	C	T	2: 145,860,446	T354I	probably benign	Het
Rnf216	A	T	5: 143,093,090	S35T	probably damaging	Het
Rps6kc1	A	G	1: 190,808,900	V402A	probably damaging	Het
Rufy4	T	C	1: 74,147,663	C537R	probably damaging	Het
Sart3	A	G	5: 113,771,418	M73T	probably benign	Het
Scn10a	G	T	9: 119,631,544	T1088K	probably damaging	Het
Senp2	T	C	16: 22,011,554		probably null	Het
Setd7	T	C	3: 51,542,730	N92D	probably benign	Het
Sipa1	A	T	19: 5,654,089	L735Q	probably damaging	Het
Skint11	C	A	4: 114,244,659	Q99K	probably benign	Het
Slitrk6	A	T	14: 110,751,388	S296T	probably benign	Het
Spc24	T	C	9: 21,756,202		probably null	Het
Tex15	T	C	8: 33,572,137	S806P	probably damaging	Het
Tgm3	A	T	2: 130,044,589	K577*	probably null	Het
Wscd2	A	G	5: 113,560,984	D200G	probably benign	Het
Xpo6	T	C	7: 126,174,182	T24A	possibly damaging	Het
Zfhx2	A	G	14: 55,073,534	C568R	possibly damaging	Het
Zfp599	T	A	9: 22,249,745	K375*	probably null	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
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
R8838:Rfx4	UTSW	10	84840894	missense	probably damaging	1.00
R8938:Rfx4	UTSW	10	84840072	missense	probably damaging	1.00
R9359:Rfx4	UTSW	10	84905057	missense	probably benign	0.00
RF010:Rfx4	UTSW	10	84858487	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'- ACTCTTTTGTATATGCCCAGCAG -3'
(R):5'- GTACCATGGAGTCCTTTTGCC -3'

Sequencing Primer
(F):5'- GCTCGGTCCACAGGTAATACTATG -3'
(R):5'- ACAAAGCCCTTGGTGACTG -3'

Posted On

2015-06-12