Mutagenetix > Incidental Mutation

Incidental Mutation 'R7131:Rfx3'

552715

Institutional Source

Beutler Lab

Gene Symbol

Rfx3

Ensembl Gene

ENSMUSG00000040929

Gene Name

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

Synonyms

C230093O12Rik, MRFX3

MMRRC Submission

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R7131 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

27761721-28011166 bp(-) (GRCm38)

Type of Mutation

nonsense

DNA Base Change (assembly)

T to A at 27768628 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Stop codon at position 668 (K668*)

Ref Sequence

ENSEMBL: ENSMUSP00000038760 (fasta)

Gene Model

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

AlphaFold

P48381

Predicted Effect

probably null
Transcript: ENSMUST00000046898
AA Change: K668*

SMART Domains

Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: K668*

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
AA Change: K693*

SMART Domains

Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: K693*

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: ENSMUST00000172907
AA Change: K693*

SMART Domains

Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: K693*

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

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
AA Change: K693*

SMART Domains

Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: K693*

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

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, 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: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931409K22Rik	A	G	5: 24,548,956	V435A	possibly damaging	Het
Abca13	A	G	11: 9,291,893	N1252S	probably benign	Het
Abcc3	A	T	11: 94,365,031	F543I	probably damaging	Het
Adam15	T	A	3: 89,346,980	Q170L	possibly damaging	Het
AF366264	A	T	8: 13,836,982	W370R	probably damaging	Het
Aldoc	A	G	11: 78,324,456	I19V	possibly damaging	Het
Atrip	T	C	9: 109,060,420	I711M	probably benign	Het
Brwd1	A	C	16: 96,066,498	L149R	probably damaging	Het
Capn9	A	T	8: 124,576,278	D45V	probably damaging	Het
Card9	G	A	2: 26,358,835	R101C	probably damaging	Het
Casc1	A	T	6: 145,177,406	L578Q	probably null	Het
Ccdc36	A	T	9: 108,417,420	D98E	probably benign	Het
Ccdc87	A	G	19: 4,841,757	E759G	probably damaging	Het
Cep250	T	C	2: 155,965,077	M193T	probably damaging	Het
Cfap54	T	C	10: 92,821,104	K3029E	probably benign	Het
Chrna9	G	A	5: 65,977,141	G445D	possibly damaging	Het
Cluap1	C	T	16: 3,940,775	S367L	probably benign	Het
Col5a1	A	G	2: 27,929,486	D200G	unknown	Het
Crhr2	T	C	6: 55,092,127	N388D		Het
Cyp2b23	A	G	7: 26,681,413	L129P	probably benign	Het
Cyr61	T	C	3: 145,648,781	D125G	probably damaging	Het
Dctd	A	G	8: 48,112,040	S67G	probably benign	Het
Dhtkd1	C	G	2: 5,904,070	V738L	probably benign	Het
Dnah17	C	T	11: 118,079,658	D2173N	probably benign	Het
Dnah7c	G	T	1: 46,681,772	A2819S	probably benign	Het
Dot1l	A	G	10: 80,792,341	H1071R	unknown	Het
Doxl2	T	A	6: 48,976,372	Y410*	probably null	Het
Dync2h1	T	A	9: 7,075,786	D3027V	probably damaging	Het
Efl1	A	G	7: 82,658,064	Y56C	probably damaging	Het
Eif4e1b	A	T	13: 54,784,100	R29W	probably null	Het
Evc2	A	G	5: 37,410,258	R860G	probably damaging	Het
Fbxl12	G	A	9: 20,644,383		probably benign	Het
Fibp	T	A	19: 5,461,491	I129N	probably damaging	Het
Folh1	G	T	7: 86,726,112	H555Q	probably damaging	Het
Gcnt4	A	T	13: 96,946,519	T108S	probably damaging	Het
Gm436	A	G	4: 144,670,067	V365A	probably damaging	Het
H1fnt	T	A	15: 98,256,369	K300*	probably null	Het
Hecw2	A	T	1: 53,865,121	V1156E	probably damaging	Het
Herc3	C	G	6: 58,887,424	A681G	probably damaging	Het
Igkv13-84	T	A	6: 68,939,780	C20*	probably null	Het
Ivd	C	A	2: 118,869,774	T94K	probably damaging	Het
Kank2	C	T	9: 21,794,679	A348T	probably benign	Het
Kcnma1	T	C	14: 23,367,494	Y889C	probably damaging	Het
Kif13b	T	C	14: 64,773,068	V1272A	probably damaging	Het
Kmt2d	GCTGCTGCT	GCTGCTGCTCCTGCTGCT	15: 98,849,616		probably benign	Het
Kmt5b	T	A	19: 3,815,412	D825E	probably benign	Het
Krt39	C	T	11: 99,520,871	A130T	probably benign	Het
Krtap4-9	C	T	11: 99,785,457	T68I	unknown	Het
Lmbr1l	A	T	15: 98,906,323	V365E	probably benign	Het
Lonp1	C	T	17: 56,617,814	R531Q	probably damaging	Het
Mecom	T	A	3: 29,980,945	H194L	probably damaging	Het
Mlx	C	T	11: 101,089,242	H188Y	probably damaging	Het
Mrps10	T	C	17: 47,375,015	S77P	probably damaging	Het
Mst1	A	G	9: 108,084,931	E716G	probably null	Het
Mttp	C	T	3: 138,116,132	V210I	probably benign	Het
Mug2	T	C	6: 122,075,247	V988A	probably damaging	Het
Ndufb6	A	G	4: 40,279,336	M1T	probably null	Het
Neurog1	A	T	13: 56,251,750	N61K	probably benign	Het
Nlrp14	A	G	7: 107,184,814	D581G	possibly damaging	Het
Nlrp4a	C	A	7: 26,449,833	N288K	probably benign	Het
Notch3	T	A	17: 32,144,217	H1264L	probably benign	Het
Olfr384	A	T	11: 73,602,736	D52V	possibly damaging	Het
Olfr394	A	T	11: 73,887,954	C139*	probably null	Het
Olfr402	A	G	11: 74,155,780	M209V	probably benign	Het
Patl2	A	T	2: 122,121,782		probably null	Het
Pfkfb4	A	G	9: 109,007,302	T133A	probably benign	Het
Pla2g4f	T	C	2: 120,304,554	E471G	probably null	Het
Postn	T	C	3: 54,362,635	V45A	probably damaging	Het
Ppan	T	A	9: 20,891,154	V257E	possibly damaging	Het
Ptcra	C	G	17: 46,763,596	A7P	probably damaging	Het
Ptprd	C	T	4: 76,066,340	R523H	probably damaging	Het
Pycrl	A	T	15: 75,918,695	I105N	possibly damaging	Het
Rfx1	C	A	8: 84,095,079	Q815K	probably damaging	Het
Ryr2	A	T	13: 11,640,327	D3661E	possibly damaging	Het
Ryr2	A	G	13: 11,668,811		probably null	Het
Sec23ip	T	A	7: 128,779,640	S974T	probably damaging	Het
Setbp1	A	G	18: 79,086,960	F19S	probably benign	Het
Setd1a	AAGCAGCAGCAGCAGCAGCAG	AAGCAGCAGCAGCAGCAG	7: 127,796,418		probably benign	Het
Sh3pxd2b	A	G	11: 32,422,072	K413R	probably damaging	Het
Slc39a12	T	C	2: 14,449,803	V544A	probably damaging	Het
Slc6a7	T	C	18: 61,002,202	Y418C	probably damaging	Het
Snx19	T	G	9: 30,427,893	I109S	probably damaging	Het
Spg20	T	C	3: 55,121,799		probably null	Het
Sptbn2	A	T	19: 4,749,460	Q2097L	probably null	Het
Syne1	T	C	10: 5,228,221	K4751R	probably damaging	Het
Tigit	C	A	16: 43,662,252	G40C	probably damaging	Het
Tmem181a	T	A	17: 6,297,972	I264K	probably damaging	Het
Tom1	T	A	8: 75,057,249	I287N	possibly damaging	Het
Top2a	G	A	11: 99,004,182	P864L	possibly damaging	Het
Trmt44	A	T	5: 35,571,066	V290E	probably damaging	Het
Try4	T	C	6: 41,304,403	I93T	probably benign	Het
Usp24	T	A	4: 106,382,303	H1147Q	possibly damaging	Het
Uspl1	A	T	5: 149,193,935	R109S	probably benign	Het
Vav3	T	A	3: 109,664,346	F755I	probably damaging	Het
Vezt	A	T	10: 93,970,547	Y667*	probably null	Het
Vmn1r231	T	A	17: 20,889,878	L258F	possibly damaging	Het
Zfp207	T	C	11: 80,395,528	M489T	unknown	Het
Zfp462	A	G	4: 55,009,380	T449A	probably benign	Het
Zfp956	C	A	6: 47,955,847	Q19K	probably benign	Het
Zkscan8	A	T	13: 21,525,273	W152R	probably damaging	Het

Other mutations in Rfx3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00548:Rfx3	APN	19	27806186	critical splice donor site	probably null
IGL00588:Rfx3	APN	19	27826076	nonsense	probably null
IGL01408:Rfx3	APN	19	27768650	missense	probably benign	0.04
IGL01937:Rfx3	APN	19	27830729	missense	probably damaging	1.00
IGL02668:Rfx3	APN	19	27815614	splice site	probably benign
IGL02679:Rfx3	APN	19	27849737	missense	possibly damaging	0.95
R0267:Rfx3	UTSW	19	27793788	missense	probably benign	0.00
R0336:Rfx3	UTSW	19	27806262	missense	probably benign	0.00
R0838:Rfx3	UTSW	19	27849967	missense	possibly damaging	0.92
R0967:Rfx3	UTSW	19	27806351	splice site	probably benign
R1102:Rfx3	UTSW	19	27867600	missense	possibly damaging	0.51
R1507:Rfx3	UTSW	19	27768513	missense	probably benign	0.00
R2172:Rfx3	UTSW	19	27815494	nonsense	probably null
R2844:Rfx3	UTSW	19	27806786	splice site	probably benign
R2960:Rfx3	UTSW	19	27900811	nonsense	probably null
R4291:Rfx3	UTSW	19	27800232	missense	probably damaging	1.00
R4952:Rfx3	UTSW	19	27830672	missense	probably damaging	1.00
R5198:Rfx3	UTSW	19	27830776	missense	probably damaging	1.00
R5451:Rfx3	UTSW	19	27849959	missense	probably damaging	1.00
R5590:Rfx3	UTSW	19	27802380	critical splice donor site	probably null
R5641:Rfx3	UTSW	19	27793608	splice site	probably null
R5663:Rfx3	UTSW	19	27793617	missense	probably damaging	1.00
R5899:Rfx3	UTSW	19	27830765	missense	probably damaging	1.00
R6049:Rfx3	UTSW	19	27802395	missense	probably damaging	0.99
R6368:Rfx3	UTSW	19	27768609	missense	possibly damaging	0.92
R7273:Rfx3	UTSW	19	27802458	missense	probably damaging	1.00
R7593:Rfx3	UTSW	19	27849739	missense	probably benign	0.00
R7814:Rfx3	UTSW	19	27826070	missense	probably benign	0.01
R7815:Rfx3	UTSW	19	27826048	missense	probably benign	0.00
R8458:Rfx3	UTSW	19	27793672	missense	possibly damaging	0.71
R8995:Rfx3	UTSW	19	27806325	missense	probably benign	0.14
R9147:Rfx3	UTSW	19	27900807	missense	possibly damaging	0.84
R9148:Rfx3	UTSW	19	27900807	missense	possibly damaging	0.84
R9310:Rfx3	UTSW	19	27849929	missense	probably benign	0.00
Z1088:Rfx3	UTSW	19	27837450	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GTTAGAGTAAGCTGGAAAACTCTGC -3'
(R):5'- GAAAGCCTATGAGTCCTCCC -3'

Sequencing Primer
(F):5'- GGAAAACTCTGCTTTCCTGCTGTTAG -3'
(R):5'- CGTAGGGAGCACGGAGGTC -3'

Posted On

2019-05-15