Mutagenetix > Incidental Mutation

Incidental Mutation 'R7248:Rfx4'

563694

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

045311-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7248 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

84591926-84742402 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 84740919 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Leucine at position 679 (P679L)

Ref Sequence

ENSEMBL: ENSMUSP00000051107 (fasta)

Gene Model

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

AlphaFold

Q7TNK1

Predicted Effect

probably benign
Transcript: ENSMUST00000060397
AA Change: P679L

PolyPhen 2 Score 0.054 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: P679L

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
AA Change: P585L

PolyPhen 2 Score 0.392 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: P585L

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
AA Change: P536L

PolyPhen 2 Score 0.054 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
AA Change: P536L

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: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.4%

Validation Efficiency

97% (75/77)

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006A11Rik	A	G	3: 124,207,959 (GRCm39)		probably null	Het
Aldh16a1	A	G	7: 44,795,018 (GRCm39)	Y484H	probably damaging	Het
Arhgap26	T	C	18: 39,439,907 (GRCm39)		probably null	Het
Atxn7l1	A	G	12: 33,417,194 (GRCm39)	T452A	probably benign	Het
Baz1a	C	T	12: 54,947,293 (GRCm39)	E1119K	probably damaging	Het
Btaf1	A	T	19: 36,922,714 (GRCm39)	E39D	possibly damaging	Het
Bud13	G	T	9: 46,194,413 (GRCm39)	E29*	probably null	Het
Ccdc150	C	T	1: 54,344,057 (GRCm39)	T530I	probably benign	Het
Chd6	G	A	2: 160,803,199 (GRCm39)	Q2160*	probably null	Het
Cluap1	T	A	16: 3,737,364 (GRCm39)	I172N	possibly damaging	Het
Cnot2	T	C	10: 116,334,278 (GRCm39)	N329S	probably benign	Het
Cog4	A	T	8: 111,608,834 (GRCm39)	T175S	unknown	Het
Coq7	C	A	7: 118,128,897 (GRCm39)	R46L	probably benign	Het
D630045J12Rik	A	T	6: 38,145,198 (GRCm39)	V1276E	probably damaging	Het
Dcaf15	A	G	8: 84,829,394 (GRCm39)	V116A	possibly damaging	Het
Ddr2	C	T	1: 169,822,198 (GRCm39)	V417I	probably benign	Het
Defa25	G	A	8: 21,575,216 (GRCm39)	C65Y	probably damaging	Het
Dhx38	T	C	8: 110,285,559 (GRCm39)	T425A	probably benign	Het
Diaph1	T	C	18: 38,022,829 (GRCm39)	T782A	probably benign	Het
Dnah7b	T	A	1: 46,181,245 (GRCm39)	M1044K	possibly damaging	Het
Dusp16	G	A	6: 134,695,940 (GRCm39)	T297M	probably benign	Het
Esyt2	A	G	12: 116,305,858 (GRCm39)	N363D	probably damaging	Het
Fasl	C	T	1: 161,615,760 (GRCm39)	C32Y	possibly damaging	Het
Flg	T	C	3: 93,189,041 (GRCm39)	V137A	probably benign	Het
Gm57858	T	A	3: 36,080,086 (GRCm39)	T224S	probably benign	Het
Gpr150	G	A	13: 76,204,126 (GRCm39)	A273V	probably benign	Het
Grk5	A	G	19: 60,879,045 (GRCm39)	T10A	probably benign	Het
Hivep2	A	G	10: 14,006,909 (GRCm39)	K1169R	possibly damaging	Het
Ido2	A	C	8: 25,030,657 (GRCm39)	Y224*	probably null	Het
Ido2	A	G	8: 25,038,839 (GRCm39)	I149T	probably damaging	Het
Iqca1l	C	T	5: 24,749,269 (GRCm39)	S743N	probably benign	Het
Kctd2	A	G	11: 115,312,845 (GRCm39)	T126A	possibly damaging	Het
Khdc4	T	C	3: 88,600,886 (GRCm39)	S228P	probably damaging	Het
Kif1a	T	C	1: 92,969,305 (GRCm39)	D1090G	probably benign	Het
Klrb1a	A	T	6: 128,586,697 (GRCm39)	H222Q	possibly damaging	Het
Kndc1	A	C	7: 139,500,699 (GRCm39)	H688P	probably damaging	Het
Lrriq1	C	A	10: 103,059,611 (GRCm39)	V141F	possibly damaging	Het
Malrd1	A	G	2: 16,106,722 (GRCm39)	I1845V	unknown	Het
Mob3c	G	A	4: 115,688,881 (GRCm39)	R138H	probably benign	Het
Mre11a	T	A	9: 14,723,209 (GRCm39)	D394E	possibly damaging	Het
Myh7b	A	T	2: 155,464,106 (GRCm39)	I536F	probably damaging	Het
Nacad	T	A	11: 6,548,589 (GRCm39)	K1382*	probably null	Het
Ncor1	T	C	11: 62,275,598 (GRCm39)	K128R	possibly damaging	Het
Or10am5	T	C	7: 6,517,520 (GRCm39)	N303D	probably damaging	Het
Ostn	T	A	16: 27,165,719 (GRCm39)		probably null	Het
Pacs1	G	A	19: 5,189,003 (GRCm39)	T793I	probably damaging	Het
Pcdhb2	T	C	18: 37,429,547 (GRCm39)	S507P	probably damaging	Het
Pde2a	A	G	7: 101,152,597 (GRCm39)	K393E	possibly damaging	Het
Pfkl	T	A	10: 77,825,423 (GRCm39)	N656Y	probably damaging	Het
Phf20	T	A	2: 156,135,331 (GRCm39)		probably null	Het
Plekha6	G	T	1: 133,203,586 (GRCm39)	E550*	probably null	Het
Plxna4	A	T	6: 32,139,095 (GRCm39)	V1691E	probably damaging	Het
Rag1	A	T	2: 101,472,123 (GRCm39)	H1006Q	probably damaging	Het
Ripor2	A	G	13: 24,878,128 (GRCm39)	H301R	probably damaging	Het
Rrp12	A	T	19: 41,871,877 (GRCm39)	I469N	possibly damaging	Het
Serpinb6b	A	G	13: 33,161,559 (GRCm39)	T211A	probably benign	Het
Sf1	A	T	19: 6,426,383 (GRCm39)	H547L	unknown	Het
Slc29a1	T	C	17: 45,903,108 (GRCm39)	D9G	probably damaging	Het
Sptan1	T	A	2: 29,892,311 (GRCm39)	M1075K	probably benign	Het
Syngap1	A	G	17: 27,176,741 (GRCm39)	D474G	probably damaging	Het
Syt16	C	T	12: 74,313,483 (GRCm39)	R470C	probably damaging	Het
Timeless	A	G	10: 128,087,870 (GRCm39)	T1148A	probably benign	Het
Tmem116	A	T	5: 121,601,899 (GRCm39)		probably null	Het
Tmem158	A	T	9: 123,089,390 (GRCm39)	I74N	probably damaging	Het
Traf5	T	A	1: 191,743,432 (GRCm39)	D174V	probably benign	Het
Trim65	A	T	11: 116,018,534 (GRCm39)	I247N	probably benign	Het
Tsfm	A	T	10: 126,847,500 (GRCm39)	V197E	probably benign	Het
Utrn	A	G	10: 12,604,562 (GRCm39)	C539R	possibly damaging	Het
Vps13a	A	T	19: 16,655,406 (GRCm39)	F1874Y	probably benign	Het
Wdr6	A	G	9: 108,453,238 (GRCm39)	M215T	possibly damaging	Het
Wdr75	T	A	1: 45,856,560 (GRCm39)	W528R	probably damaging	Het
Zc3h7b	A	G	15: 81,655,988 (GRCm39)	D112G	possibly damaging	Het
Zc3hav1	C	T	6: 38,330,911 (GRCm39)	D83N	probably benign	Het
Zfp369	T	A	13: 65,443,931 (GRCm39)	V358E	probably damaging	Het
Zfp946	T	A	17: 22,672,489 (GRCm39)	C29*	probably null	Het
Zng1	A	G	19: 24,898,505 (GRCm39)	S318P	probably damaging	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
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
RF062:Rfx4	UTSW	10	84,694,345 (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'- CTGTTCCATCAACTCCCGAG -3'
(R):5'- TGAAAGCAGTCACTTAGCCC -3'

Sequencing Primer
(F):5'- CTCCCGAGAATAGCGTCTTGAAATG -3'
(R):5'- AGTCACTTAGCCCATCCAGTG -3'

Posted On

2019-06-26