Mutagenetix > Incidental Mutation

Incidental Mutation 'R5590:Rfx3'

437498

Institutional Source

Beutler Lab

Gene Symbol

Rfx3

Ensembl Gene

ENSMUSG00000040929

Gene Name

regulatory factor X, 3 (influences HLA class II expression)

Synonyms

MRFX3, C230093O12Rik

MMRRC Submission

043143-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5590 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

27739121-27988566 bp(-) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

A to T at 27779780 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000133461 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000046898] [ENSMUST00000165566] [ENSMUST00000165566] [ENSMUST00000172907] [ENSMUST00000173863] [ENSMUST00000174850]

AlphaFold

P48381

Predicted Effect

probably null
Transcript: ENSMUST00000046898

SMART Domains

Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929

Domain	Start	End	E-Value	Type
Pfam:RFX1_trans_act	1	140	6.3e-58	PFAM
Pfam:RFX_DNA_binding	150	235	6.9e-41	PFAM
low complexity region	274	283	N/A	INTRINSIC
internal_repeat_1	326	414	1.39e-5	PROSPERO
internal_repeat_1	439	527	1.39e-5	PROSPERO
low complexity region	649	664	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000165566

SMART Domains

Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929

Domain	Start	End	E-Value	Type
Pfam:RFX1_trans_act	4	138	9.7e-38	PFAM
Pfam:RFX_DNA_binding	181	258	6.2e-36	PFAM
low complexity region	299	308	N/A	INTRINSIC
internal_repeat_1	351	439	1.82e-5	PROSPERO
internal_repeat_1	464	552	1.82e-5	PROSPERO
low complexity region	674	689	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000165566

SMART Domains

Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929

Domain	Start	End	E-Value	Type
Pfam:RFX1_trans_act	4	138	9.7e-38	PFAM
Pfam:RFX_DNA_binding	181	258	6.2e-36	PFAM
low complexity region	299	308	N/A	INTRINSIC
internal_repeat_1	351	439	1.82e-5	PROSPERO
internal_repeat_1	464	552	1.82e-5	PROSPERO
low complexity region	674	689	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000172498

Predicted Effect

probably null
Transcript: ENSMUST00000172907

SMART Domains

Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929

Domain	Start	End	E-Value	Type
Pfam:RFX1_trans_act	1	140	9.4e-58	PFAM
Pfam:RFX_DNA_binding	175	260	5.2e-41	PFAM
low complexity region	299	308	N/A	INTRINSIC
internal_repeat_1	351	439	1.82e-5	PROSPERO
internal_repeat_1	464	552	1.82e-5	PROSPERO
low complexity region	674	689	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173161

Predicted Effect

probably benign
Transcript: ENSMUST00000173863

SMART Domains

Protein: ENSMUSP00000133367
Gene: ENSMUSG00000040929

Domain	Start	End	E-Value	Type
Pfam:RFX1_trans_act	1	140	3.3e-58	PFAM
Pfam:RFX_DNA_binding	175	246	3.7e-24	PFAM
low complexity region	285	294	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000174850

SMART Domains

Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929

Domain	Start	End	E-Value	Type
Pfam:RFX1_trans_act	1	140	9.4e-58	PFAM
Pfam:RFX_DNA_binding	175	260	5.2e-41	PFAM
low complexity region	299	308	N/A	INTRINSIC
internal_repeat_1	351	439	1.82e-5	PROSPERO
internal_repeat_1	464	552	1.82e-5	PROSPERO
low complexity region	674	689	N/A	INTRINSIC

Meta Mutation Damage Score

0.9500

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.6%
20x: 96.2%

Validation Efficiency

100% (108/108)

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, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. Multiple transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2013]
PHENOTYPE: Homozygous null mice display embryonic and perinatal lethality, impaired development of cilia on the embryonic node, abnormal left-right patterning, meso- and dextrocardia, and situs inversus in surviving adults. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3100002H09Rik	T	G	4: 124,504,280 (GRCm39)	M91L	unknown	Het
A2m	C	T	6: 121,653,891 (GRCm39)	T1408M	probably damaging	Het
Abca16	C	T	7: 120,143,995 (GRCm39)	T1671M	probably damaging	Het
Adamts8	A	T	9: 30,862,632 (GRCm39)	N279I	probably damaging	Het
Adgre1	T	A	17: 57,752,034 (GRCm39)	I594N	probably damaging	Het
Aldh4a1	T	A	4: 139,369,415 (GRCm39)	V322E	probably damaging	Het
Atp12a	A	T	14: 56,610,837 (GRCm39)	Y327F	probably benign	Het
C4b	T	C	17: 34,959,309 (GRCm39)	T422A	probably damaging	Het
Cacna1c	A	T	6: 118,664,143 (GRCm39)	S668T	probably damaging	Het
Cchcr1	A	T	17: 35,837,577 (GRCm39)	E426D	probably damaging	Het
Ccr3	G	A	9: 123,828,830 (GRCm39)	G55D	probably damaging	Het
Cdipt	T	A	7: 126,578,704 (GRCm39)		probably null	Het
Cep19	A	G	16: 31,922,716 (GRCm39)		probably benign	Het
Cts6	T	A	13: 61,349,626 (GRCm39)	M56L	probably benign	Het
Cyp3a11	C	A	5: 145,802,787 (GRCm39)	M235I	probably benign	Het
Dnajc21	A	T	15: 10,462,363 (GRCm39)	D87E	possibly damaging	Het
Ell	A	C	8: 70,992,357 (GRCm39)	M1L	possibly damaging	Het
Esyt3	T	C	9: 99,240,466 (GRCm39)		probably benign	Het
Ets1	T	C	9: 32,640,094 (GRCm39)		probably benign	Het
Fam222b	T	A	11: 78,045,858 (GRCm39)	M473K	probably benign	Het
Fanca	T	C	8: 124,030,702 (GRCm39)		probably benign	Het
Fbrsl1	G	T	5: 110,529,484 (GRCm39)	A67D	probably damaging	Het
Fchsd1	G	A	18: 38,094,380 (GRCm39)	P622L	probably damaging	Het
Gal3st2c	T	G	1: 93,936,023 (GRCm39)		probably null	Het
Gins2	T	G	8: 121,308,486 (GRCm39)	H166P	possibly damaging	Het
Gm10118	A	T	10: 63,762,845 (GRCm39)		probably benign	Het
Gm9979	A	T	13: 40,859,289 (GRCm39)		noncoding transcript	Het
Hspbap1	A	G	16: 35,622,033 (GRCm39)	Y126C	probably damaging	Het
Hspd1	A	T	1: 55,123,928 (GRCm39)	I64N	probably damaging	Het
Igkv3-4	A	T	6: 70,649,267 (GRCm39)	S89C	probably damaging	Het
Il10ra	T	A	9: 45,176,924 (GRCm39)	K134*	probably null	Het
Il12rb1	G	A	8: 71,266,411 (GRCm39)	C252Y	possibly damaging	Het
Il24	A	T	1: 130,810,253 (GRCm39)	V201E	possibly damaging	Het
Inpp1	A	G	1: 52,833,820 (GRCm39)	I92T	probably damaging	Het
Kcnh5	T	C	12: 75,023,463 (GRCm39)	D535G	probably benign	Het
Kcnq4	T	A	4: 120,573,082 (GRCm39)	I240F	probably damaging	Het
Kctd17	G	A	15: 78,321,502 (GRCm39)		probably benign	Het
Leo1	T	A	9: 75,364,423 (GRCm39)	I521N	possibly damaging	Het
Mdga1	A	G	17: 30,058,841 (GRCm39)	L722P	probably damaging	Het
Met	G	T	6: 17,548,781 (GRCm39)	V942L	probably benign	Het
Mfn1	A	T	3: 32,617,996 (GRCm39)	T110S	probably benign	Het
Mrps15	T	C	4: 125,942,488 (GRCm39)	I79T	probably benign	Het
Mycbp2	A	C	14: 103,360,791 (GRCm39)	M4497R	probably damaging	Het
Mylk	T	A	16: 34,699,722 (GRCm39)	S362T	probably benign	Het
Mypn	A	G	10: 62,955,827 (GRCm39)	F1209L	probably benign	Het
Nab2	T	C	10: 127,500,526 (GRCm39)	S189G	probably damaging	Het
Naxe	A	C	3: 87,963,840 (GRCm39)		probably null	Het
Ncf1	A	G	5: 134,252,355 (GRCm39)	V232A	probably damaging	Het
Nell1	A	G	7: 49,929,359 (GRCm39)	Y422C	probably damaging	Het
Nmnat2	G	T	1: 152,969,807 (GRCm39)	G176V	probably damaging	Het
Npr1	A	G	3: 90,362,149 (GRCm39)	S999P	probably damaging	Het
Nuak1	T	C	10: 84,211,119 (GRCm39)	D323G	probably benign	Het
Or4d10b	A	G	19: 12,036,642 (GRCm39)	V158A	probably benign	Het
Or5h23	A	G	16: 58,906,360 (GRCm39)	F162S	probably benign	Het
Or8b3b	T	A	9: 38,584,261 (GRCm39)	T160S	probably damaging	Het
Osbpl8	T	C	10: 111,108,029 (GRCm39)	S342P	probably damaging	Het
Pag1	A	T	3: 9,764,482 (GRCm39)	Y224N	probably damaging	Het
Pald1	T	A	10: 61,179,489 (GRCm39)	H460L	probably damaging	Het
Per2	G	A	1: 91,355,578 (GRCm39)	Q727*	probably null	Het
Pex19	T	C	1: 171,960,779 (GRCm39)	V134A	probably benign	Het
Phlpp1	A	T	1: 106,320,657 (GRCm39)	I1551F	possibly damaging	Het
Ppef2	A	T	5: 92,386,998 (GRCm39)	V313D	probably damaging	Het
Prorp	T	C	12: 55,351,257 (GRCm39)	S189P	possibly damaging	Het
Pzp	A	C	6: 128,500,759 (GRCm39)	F153C	probably damaging	Het
Rasl11a	A	G	5: 146,782,052 (GRCm39)	H9R	probably benign	Het
Rmnd5b	A	T	11: 51,518,789 (GRCm39)	I68N	probably damaging	Het
Senp5	T	A	16: 31,808,331 (GRCm39)	S281C	probably damaging	Het
Sh3rf1	G	A	8: 61,814,766 (GRCm39)	E442K	probably benign	Het
Slc12a3	G	A	8: 95,072,416 (GRCm39)	V645M	probably damaging	Het
Slc22a16	T	C	10: 40,457,337 (GRCm39)	F193L	possibly damaging	Het
Slc35f1	A	T	10: 52,984,274 (GRCm39)	T345S	possibly damaging	Het
Slc9a1	G	A	4: 133,148,874 (GRCm39)	R704H	probably damaging	Het
Spta1	A	T	1: 174,003,336 (GRCm39)	Y89F	possibly damaging	Het
Sspo	A	G	6: 48,451,425 (GRCm39)	E2741G	probably damaging	Het
Strn4	G	A	7: 16,567,799 (GRCm39)		probably null	Het
Tanc2	A	G	11: 105,814,132 (GRCm39)	T1859A	probably damaging	Het
Tbc1d14	A	T	5: 36,682,389 (GRCm39)	Y3N	probably damaging	Het
Tdrd9	C	A	12: 112,018,414 (GRCm39)	R1278S	probably benign	Het
Tenm4	C	A	7: 96,446,608 (GRCm39)	A826E	possibly damaging	Het
Tenm4	G	T	7: 96,446,607 (GRCm39)	A826S	possibly damaging	Het
Tet2	C	T	3: 133,182,241 (GRCm39)		probably null	Het
Tfec	A	G	6: 16,834,199 (GRCm39)	L236P	probably benign	Het
Tjap1	A	G	17: 46,569,797 (GRCm39)	S388P	probably damaging	Het
Tle1	T	C	4: 72,043,208 (GRCm39)	T554A	possibly damaging	Het
Tmem17	G	A	11: 22,467,450 (GRCm39)	V83I	probably benign	Het
Tnrc6b	C	T	15: 80,760,703 (GRCm39)	H137Y	probably damaging	Het
Tomm5	T	C	4: 45,106,679 (GRCm39)		probably benign	Het
Top3b	T	A	16: 16,709,441 (GRCm39)		probably benign	Het
Tph1	T	C	7: 46,303,216 (GRCm39)	H254R	probably damaging	Het
Tpte	T	C	8: 22,841,468 (GRCm39)	Y487H	probably damaging	Het
Trappc13	T	A	13: 104,284,749 (GRCm39)	D241V	probably damaging	Het
Trrap	A	G	5: 144,719,075 (GRCm39)	I193V	probably benign	Het
Tspear	A	T	10: 77,706,199 (GRCm39)	H323L	probably benign	Het
Ttc39a	A	T	4: 109,290,184 (GRCm39)		probably null	Het
Ttn	A	T	2: 76,641,587 (GRCm39)	L5176Q	possibly damaging	Het
Tubg1	A	G	11: 101,014,858 (GRCm39)	D200G	probably damaging	Het
Ugdh	C	A	5: 65,580,217 (GRCm39)		probably benign	Het
Uso1	A	G	5: 92,328,467 (GRCm39)	N355D	probably benign	Het
Vamp4	T	C	1: 162,420,248 (GRCm39)		probably null	Het
Vmn2r5	T	C	3: 64,411,497 (GRCm39)	D357G	probably damaging	Het
Vps52	A	G	17: 34,180,195 (GRCm39)	T300A	probably benign	Het
Wt1	A	T	2: 104,957,629 (GRCm39)	H163L	probably damaging	Het
Xirp2	T	C	2: 67,344,379 (GRCm39)	S2207P	probably benign	Het
Xpo6	A	T	7: 125,706,250 (GRCm39)	I30N	probably damaging	Het
Zfp386	T	A	12: 116,023,347 (GRCm39)	I320K	probably benign	Het

Other mutations in Rfx3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00548:Rfx3	APN	19	27,783,586 (GRCm39)	critical splice donor site	probably null
IGL00588:Rfx3	APN	19	27,803,476 (GRCm39)	nonsense	probably null
IGL01408:Rfx3	APN	19	27,746,050 (GRCm39)	missense	probably benign	0.04
IGL01937:Rfx3	APN	19	27,808,129 (GRCm39)	missense	probably damaging	1.00
IGL02668:Rfx3	APN	19	27,793,014 (GRCm39)	splice site	probably benign
IGL02679:Rfx3	APN	19	27,827,137 (GRCm39)	missense	possibly damaging	0.95
R0267:Rfx3	UTSW	19	27,771,188 (GRCm39)	missense	probably benign	0.00
R0336:Rfx3	UTSW	19	27,783,662 (GRCm39)	missense	probably benign	0.00
R0838:Rfx3	UTSW	19	27,827,367 (GRCm39)	missense	possibly damaging	0.92
R0967:Rfx3	UTSW	19	27,783,751 (GRCm39)	splice site	probably benign
R1102:Rfx3	UTSW	19	27,845,000 (GRCm39)	missense	possibly damaging	0.51
R1507:Rfx3	UTSW	19	27,745,913 (GRCm39)	missense	probably benign	0.00
R2172:Rfx3	UTSW	19	27,792,894 (GRCm39)	nonsense	probably null
R2844:Rfx3	UTSW	19	27,784,186 (GRCm39)	splice site	probably benign
R2960:Rfx3	UTSW	19	27,878,211 (GRCm39)	nonsense	probably null
R4291:Rfx3	UTSW	19	27,777,632 (GRCm39)	missense	probably damaging	1.00
R4952:Rfx3	UTSW	19	27,808,072 (GRCm39)	missense	probably damaging	1.00
R5198:Rfx3	UTSW	19	27,808,176 (GRCm39)	missense	probably damaging	1.00
R5451:Rfx3	UTSW	19	27,827,359 (GRCm39)	missense	probably damaging	1.00
R5641:Rfx3	UTSW	19	27,771,008 (GRCm39)	splice site	probably null
R5663:Rfx3	UTSW	19	27,771,017 (GRCm39)	missense	probably damaging	1.00
R5899:Rfx3	UTSW	19	27,808,165 (GRCm39)	missense	probably damaging	1.00
R6049:Rfx3	UTSW	19	27,779,795 (GRCm39)	missense	probably damaging	0.99
R6368:Rfx3	UTSW	19	27,746,009 (GRCm39)	missense	possibly damaging	0.92
R7131:Rfx3	UTSW	19	27,746,028 (GRCm39)	nonsense	probably null
R7273:Rfx3	UTSW	19	27,779,858 (GRCm39)	missense	probably damaging	1.00
R7593:Rfx3	UTSW	19	27,827,139 (GRCm39)	missense	probably benign	0.00
R7814:Rfx3	UTSW	19	27,803,470 (GRCm39)	missense	probably benign	0.01
R7815:Rfx3	UTSW	19	27,803,448 (GRCm39)	missense	probably benign	0.00
R8458:Rfx3	UTSW	19	27,771,072 (GRCm39)	missense	possibly damaging	0.71
R8995:Rfx3	UTSW	19	27,783,725 (GRCm39)	missense	probably benign	0.14
R9147:Rfx3	UTSW	19	27,878,207 (GRCm39)	missense	possibly damaging	0.84
R9148:Rfx3	UTSW	19	27,878,207 (GRCm39)	missense	possibly damaging	0.84
R9310:Rfx3	UTSW	19	27,827,329 (GRCm39)	missense	probably benign	0.00
Z1088:Rfx3	UTSW	19	27,814,850 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATCTGGAATCCTCAAGGCATG -3'
(R):5'- GCCGAGTCTAGTATTTTGAGACG -3'

Sequencing Primer
(F):5'- TCAAGGCATGAGTAACAGCTCTG -3'
(R):5'- GTCTAGTATTTTGAGACGCACTAAG -3'

Posted On

2016-10-26