Mutagenetix > Incidental Mutation

Incidental Mutation 'R7427:Rfx4'

576192

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

045505-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7427 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

84591926-84742402 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 84731876 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Lysine at position 618 (Q618K)

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: Q618K

PolyPhen 2 Score 0.285 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: Q618K

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

possibly damaging
Transcript: ENSMUST00000095388
AA Change: Q524K

PolyPhen 2 Score 0.487 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: Q524K

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: Q475K

PolyPhen 2 Score 0.285 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
AA Change: Q475K

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: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

100% (78/78)

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adck5	T	A	15: 76,478,585 (GRCm39)	C318S	possibly damaging	Het
Aspm	T	A	1: 139,385,354 (GRCm39)	C333S	probably benign	Het
B3gnt4	A	G	5: 123,648,794 (GRCm39)	N53S	probably damaging	Het
Bpifb5	G	A	2: 154,067,042 (GRCm39)	M98I	probably benign	Het
Cacna2d3	A	G	14: 28,786,232 (GRCm39)	M585T	probably damaging	Het
Cbarp	T	C	10: 79,967,138 (GRCm39)	D701G	probably damaging	Het
Ccn2	T	G	10: 24,473,397 (GRCm39)	M312R	probably damaging	Het
Cntrl	T	A	2: 35,060,546 (GRCm39)	W1913R	probably benign	Het
Cry2	T	C	2: 92,243,392 (GRCm39)	D483G	possibly damaging	Het
Csmd1	A	G	8: 16,073,864 (GRCm39)	F2044L	possibly damaging	Het
Cxcl16	A	G	11: 70,349,630 (GRCm39)	V78A	possibly damaging	Het
Cxcr6	A	T	9: 123,639,305 (GRCm39)	Y109F	probably benign	Het
Cyb5b	A	G	8: 107,897,048 (GRCm39)	D106G	probably benign	Het
D630036H23Rik	T	C	12: 36,431,537 (GRCm39)	R154G	unknown	Het
Dnah9	T	C	11: 65,846,045 (GRCm39)	T2998A	probably benign	Het
Focad	T	C	4: 88,286,988 (GRCm39)	S1254P	unknown	Het
Gm21886	A	T	18: 80,132,867 (GRCm39)	L97Q	probably damaging	Het
Gpr158	A	C	2: 21,832,129 (GRCm39)	L1076F	probably benign	Het
Hivep2	T	C	10: 14,009,485 (GRCm39)	M1714T	possibly damaging	Het
Hlcs	A	G	16: 94,068,758 (GRCm39)	V154A	probably benign	Het
Hpdl	A	T	4: 116,678,062 (GRCm39)	L133Q	probably damaging	Het
Il1rn	C	A	2: 24,239,554 (GRCm39)	T150K	probably benign	Het
Il6st	A	G	13: 112,625,094 (GRCm39)	I237V	probably benign	Het
Inpp5f	A	G	7: 128,281,529 (GRCm39)	D510G	probably damaging	Het
Ism2	G	T	12: 87,333,769 (GRCm39)	T92K	possibly damaging	Het
Kif13b	T	C	14: 65,025,909 (GRCm39)	I1422T	probably benign	Het
Kit	G	A	5: 75,806,507 (GRCm39)	V671I	possibly damaging	Het
Klhdc8a	A	T	1: 132,230,705 (GRCm39)	N190I	probably damaging	Het
Lad1	C	T	1: 135,753,576 (GRCm39)	T41I	probably damaging	Het
Lrrc7	G	T	3: 157,903,778 (GRCm39)	T294K	probably benign	Het
Megf8	C	T	7: 25,037,796 (GRCm39)	R771C	probably benign	Het
Micu3	A	C	8: 40,831,955 (GRCm39)	N440T	possibly damaging	Het
Mnx1	T	C	5: 29,679,211 (GRCm39)	N291D	unknown	Het
Mthfr	A	G	4: 148,136,060 (GRCm39)	M378V	probably benign	Het
Mup2	A	T	4: 60,138,454 (GRCm39)	D79E	probably benign	Het
Myzap	T	C	9: 71,412,465 (GRCm39)	T451A	probably benign	Het
Nlrp9c	T	C	7: 26,070,860 (GRCm39)	D907G	probably benign	Het
Nr1h4	T	C	10: 89,334,267 (GRCm39)	E41G	probably benign	Het
Nup98	A	T	7: 101,784,208 (GRCm39)		probably null	Het
Nxpe5	A	C	5: 138,238,022 (GRCm39)	Y194S	probably damaging	Het
Omd	A	T	13: 49,745,745 (GRCm39)	E385V	possibly damaging	Het
Or12d15	T	C	17: 37,694,190 (GRCm39)	V244A	probably damaging	Het
Or12e9	G	T	2: 87,202,034 (GRCm39)	V53L	probably benign	Het
Or2av9	A	G	11: 58,380,606 (GRCm39)	I325T	probably benign	Het
Or52m1	A	G	7: 102,289,533 (GRCm39)	I27V	probably benign	Het
Or5m12	T	A	2: 85,734,475 (GRCm39)	R308*	probably null	Het
Or5m3	A	T	2: 85,838,563 (GRCm39)	I148L	probably benign	Het
Or9s18	A	G	13: 65,300,866 (GRCm39)	Y276C	probably damaging	Het
Pcdh9	G	T	14: 94,124,547 (GRCm39)	T541K	probably damaging	Het
Pdia6	T	C	12: 17,328,546 (GRCm39)	V167A	probably damaging	Het
Phf7	C	T	14: 30,962,370 (GRCm39)	R145Q	possibly damaging	Het
Pitx3	T	C	19: 46,125,863 (GRCm39)	D20G	possibly damaging	Het
Plxnb1	T	C	9: 108,937,236 (GRCm39)	V1139A	probably benign	Het
Pon2	A	T	6: 5,268,995 (GRCm39)	N226K	probably damaging	Het
Potegl	C	T	2: 23,147,006 (GRCm39)	R337C	probably benign	Het
Ppp1r10	T	A	17: 36,241,025 (GRCm39)	H642Q	possibly damaging	Het
Prom2	A	G	2: 127,381,731 (GRCm39)	L195P	probably damaging	Het
Psg23	C	T	7: 18,345,908 (GRCm39)		probably null	Het
Rhobtb1	T	A	10: 69,084,654 (GRCm39)	I15N	probably damaging	Het
Rhot2	A	T	17: 26,060,583 (GRCm39)	V233E	probably damaging	Het
Ripply2	T	C	9: 86,901,809 (GRCm39)	S112P	possibly damaging	Het
Slc12a1	C	A	2: 125,056,052 (GRCm39)	T861N	probably benign	Het
Slc35f1	T	A	10: 52,965,510 (GRCm39)	S308R	probably damaging	Het
Slc35f4	T	A	14: 49,536,355 (GRCm39)	I427F	probably damaging	Het
Slco1a8	T	G	6: 141,949,234 (GRCm39)		probably null	Het
Sned1	G	A	1: 93,217,080 (GRCm39)	V1322I	probably benign	Het
Sprr2f	G	A	3: 92,273,251 (GRCm39)	V17M	unknown	Het
Srd5a3	A	G	5: 76,302,490 (GRCm39)	H285R	probably benign	Het
Stab1	T	C	14: 30,881,216 (GRCm39)	T605A	probably benign	Het
Syne1	T	C	10: 5,223,718 (GRCm39)	Q3054R	probably damaging	Het
Tas1r1	T	C	4: 152,122,765 (GRCm39)	T27A	probably benign	Het
Tmem150b	A	T	7: 4,719,209 (GRCm39)	V237E	probably benign	Het
Trpv6	C	T	6: 41,602,087 (GRCm39)	M407I	probably benign	Het
Ttn	T	G	2: 76,550,698 (GRCm39)	D31528A	probably damaging	Het
Uroc1	A	T	6: 90,323,344 (GRCm39)	D354V	possibly damaging	Het
Vmn2r69	T	C	7: 85,060,467 (GRCm39)	I372M	probably benign	Het
Vmn2r93	A	T	17: 18,546,672 (GRCm39)	H848L	probably benign	Het
Zfp971	T	A	2: 177,674,967 (GRCm39)	C189S	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
R7248:Rfx4	UTSW	10	84,740,919 (GRCm39)	missense	probably benign	0.05
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'- TTTAAAGCTCACCACAGCAAGG -3'
(R):5'- CACAGCGGACTTATTAACTGTGG -3'

Sequencing Primer
(F):5'- CACAGCAAGGCCAGCAGG -3'
(R):5'- ACTTATTAACTGTGGGTAGTTGGC -3'

Posted On

2019-10-07