Mutagenetix > Incidental Mutation

Incidental Mutation 'RF062:Rfx4'

605441

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

Essential gene?

Essential (E-score: 1.000) question?

Stock #

RF062 (G1)

Quality Score

135.467

Status

Not validated

Chromosome

Chromosomal Location

84591926-84742402 bp(+) (GRCm39)

Type of Mutation

critical splice acceptor site

DNA Base Change (assembly)

CTCTCTCTCTCTCT to CTCTCTCTCTCTCTCTATCTCTCTCTCTCT at 84694345 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000051107 (fasta)

Gene Model

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

AlphaFold

Q7TNK1

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: 99.6%
10x: 99.3%
20x: 98.6%

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: 19 list
Gene	Ref	Var	Chr/Loc	Predicted Effect	Zygosity
Anapc2	GTGGCGGCGGCGGC	G	2: 25,162,549 (GRCm39)	probably null	Het
Ankhd1	GGCGGC	GGCGGCAGCGGC	18: 36,693,971 (GRCm39)	probably benign	Het
Cckbr	CAG	C	7: 105,083,894 (GRCm39)	probably null	Het
Defb22	TGGCCT	TGGCCTCTGCGGCAGAGCCGGCCT	2: 152,327,745 (GRCm39)	probably benign	Het
Dennd2b	GGGCAGCCCTCACTGA	G	7: 109,156,153 (GRCm39)	probably benign	Het
Dmkn	GGTGGAAGTGGTGGAAGTGGTGGAAGT	GGTGGAAGTGGTGGAAGTGGTGGAAGTCGTGGAAGTGGTGGAAGTGGTGGAAGT	7: 30,466,600 (GRCm39)	probably benign	Het
Efhd2	GCCGCC	GCCGCCTCCGCC	4: 141,602,066 (GRCm39)	probably benign	Het
Efhd2	CC	CCGCCGAC	4: 141,602,085 (GRCm39)	probably benign	Het
Fsip2	TTTT	TTTTGTTT	2: 82,814,707 (GRCm39)	probably benign	Het
Gm11060	CTGTGTG	CTG	2: 104,922,385 (GRCm39)	probably null	Het
Gm5591	GC	G	7: 38,221,759 (GRCm39)	probably null	Het
Krt10	CGCC	CGCCGCC	11: 99,277,025 (GRCm39)	probably benign	Het
Krt10	ACCACCGCC	ACCACCGCCACCGCC	11: 99,280,090 (GRCm39)	probably benign	Het
Nefh	TGGGGACTTGGCCTCACCTGGGGACTTGGCCTC	TGGGGACTTGGCCTCACCGGGGGACTTGGCCTCACCTGGGGACTTGGCCTC	11: 4,891,028 (GRCm39)	probably benign	Het
Nusap1	CAAGCTGAGA	CAAGCTGAGATACACGTTAGCAGTGAGGAGGAAGCTGAGA	2: 119,458,082 (GRCm39)	probably benign	Het
Nusap1	A	ATACACGTTAGCAGTGAGGAGCAAGCTGAGG	2: 119,458,091 (GRCm39)	probably benign	Het
Tfeb	GCA	GCATCA	17: 48,097,025 (GRCm39)	probably benign	Het
Tnfaip8	ACACACACACACACACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC	AC	18: 50,179,898 (GRCm39)	probably benign	Het
Zfp384	CCCAGGCCCAGGCCCAGGCCCAGG	CCCAGGCCCAGGACCAGGCCCAGGCCCAGGCCCAGG	6: 125,013,429 (GRCm39)	probably benign	Het

Other mutations in Rfx4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00094:Rfx4	APN	10	84,676,063 (GRCm39)	missense	probably damaging	1.00
IGL00334:Rfx4	APN	10	84,615,917 (GRCm39)	missense	possibly damaging	0.91
IGL00928:Rfx4	APN	10	84,675,978 (GRCm39)	missense	probably benign	0.04
IGL01063:Rfx4	APN	10	84,704,246 (GRCm39)	missense	possibly damaging	0.90
IGL01490:Rfx4	APN	10	84,676,715 (GRCm39)	missense	possibly damaging	0.85
IGL02390:Rfx4	APN	10	84,676,014 (GRCm39)	missense	probably damaging	1.00
IGL02454:Rfx4	APN	10	84,675,970 (GRCm39)	missense	possibly damaging	0.83
R0099:Rfx4	UTSW	10	84,730,168 (GRCm39)	missense	probably benign
R0503:Rfx4	UTSW	10	84,730,196 (GRCm39)	missense	possibly damaging	0.56
R0924:Rfx4	UTSW	10	84,704,291 (GRCm39)	missense	probably damaging	1.00
R0930:Rfx4	UTSW	10	84,704,291 (GRCm39)	missense	probably damaging	1.00
R1386:Rfx4	UTSW	10	84,699,149 (GRCm39)	missense	probably damaging	1.00
R1715:Rfx4	UTSW	10	84,680,144 (GRCm39)	missense	probably damaging	1.00
R1738:Rfx4	UTSW	10	84,716,839 (GRCm39)	critical splice donor site	probably null
R1987:Rfx4	UTSW	10	84,731,952 (GRCm39)	missense	possibly damaging	0.87
R3717:Rfx4	UTSW	10	84,716,088 (GRCm39)	missense	probably damaging	1.00
R4231:Rfx4	UTSW	10	84,650,558 (GRCm39)	missense	probably benign	0.03
R4300:Rfx4	UTSW	10	84,740,966 (GRCm39)	missense	probably damaging	0.98
R4581:Rfx4	UTSW	10	84,680,164 (GRCm39)	missense	possibly damaging	0.93
R4582:Rfx4	UTSW	10	84,680,164 (GRCm39)	missense	possibly damaging	0.93
R4618:Rfx4	UTSW	10	84,716,760 (GRCm39)	missense	probably benign	0.01
R5156:Rfx4	UTSW	10	84,704,218 (GRCm39)	missense	probably damaging	1.00
R5185:Rfx4	UTSW	10	84,699,114 (GRCm39)	missense	probably damaging	1.00
R5377:Rfx4	UTSW	10	84,696,406 (GRCm39)	missense	possibly damaging	0.81
R5601:Rfx4	UTSW	10	84,634,442 (GRCm39)	missense	probably damaging	1.00
R5879:Rfx4	UTSW	10	84,650,625 (GRCm39)	critical splice donor site	probably null
R5996:Rfx4	UTSW	10	84,675,881 (GRCm39)	nonsense	probably null
R6358:Rfx4	UTSW	10	84,680,099 (GRCm39)	missense	probably damaging	1.00
R6805:Rfx4	UTSW	10	84,676,092 (GRCm39)	missense	possibly damaging	0.86
R7248:Rfx4	UTSW	10	84,740,919 (GRCm39)	missense	probably benign	0.05
R7427:Rfx4	UTSW	10	84,731,876 (GRCm39)	missense	probably benign	0.28
R7428:Rfx4	UTSW	10	84,731,876 (GRCm39)	missense	probably benign	0.28
R7514:Rfx4	UTSW	10	84,716,090 (GRCm39)	missense	probably damaging	1.00
R7576:Rfx4	UTSW	10	84,699,213 (GRCm39)	missense	probably damaging	0.98
R8002:Rfx4	UTSW	10	84,676,721 (GRCm39)	missense	probably damaging	0.97
R8838:Rfx4	UTSW	10	84,676,758 (GRCm39)	missense	probably damaging	1.00
R8938:Rfx4	UTSW	10	84,675,936 (GRCm39)	missense	probably damaging	1.00
R9359:Rfx4	UTSW	10	84,740,921 (GRCm39)	missense	probably benign	0.00
R9513:Rfx4	UTSW	10	84,674,050 (GRCm39)	start codon destroyed	probably null	0.01
RF010:Rfx4	UTSW	10	84,694,351 (GRCm39)	critical splice acceptor site	probably benign
RF014:Rfx4	UTSW	10	84,694,353 (GRCm39)	critical splice acceptor site	probably benign
RF015:Rfx4	UTSW	10	84,694,353 (GRCm39)	critical splice acceptor site	probably benign
RF023:Rfx4	UTSW	10	84,694,349 (GRCm39)	critical splice acceptor site	probably benign
RF030:Rfx4	UTSW	10	84,694,344 (GRCm39)	critical splice acceptor site	probably benign
RF035:Rfx4	UTSW	10	84,694,344 (GRCm39)	critical splice acceptor site	probably benign
RF046:Rfx4	UTSW	10	84,694,345 (GRCm39)	critical splice acceptor site	probably benign
RF060:Rfx4	UTSW	10	84,694,358 (GRCm39)	critical splice acceptor site	probably benign
X0024:Rfx4	UTSW	10	84,615,938 (GRCm39)	missense	possibly damaging	0.82
Z1177:Rfx4	UTSW	10	84,731,955 (GRCm39)	missense	probably benign	0.30
Z1177:Rfx4	UTSW	10	84,650,548 (GRCm39)	missense	possibly damaging	0.85

Predicted Primers

PCR Primer
(F):5'- TTGGATTCTGGATGCCACCG -3'
(R):5'- AGCTTTGAACTGTTGCCCTC -3'

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

Posted On

2019-12-04