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

MRFX3, C230093O12Rik

MMRRC Submission

045216-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7131 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

27739121-27988566 bp(-) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

T to A at 27746028 bp (GRCm39)

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
Aadacl4fm4	A	G	4: 144,396,637 (GRCm39)	V365A	probably damaging	Het
Abca13	A	G	11: 9,241,893 (GRCm39)	N1252S	probably benign	Het
Abcc3	A	T	11: 94,255,857 (GRCm39)	F543I	probably damaging	Het
Adam15	T	A	3: 89,254,287 (GRCm39)	Q170L	possibly damaging	Het
Aldoc	A	G	11: 78,215,282 (GRCm39)	I19V	possibly damaging	Het
Aoc1l1	T	A	6: 48,953,306 (GRCm39)	Y410*	probably null	Het
Atrip	T	C	9: 108,889,488 (GRCm39)	I711M	probably benign	Het
Brwd1	A	C	16: 95,867,698 (GRCm39)	L149R	probably damaging	Het
Capn9	A	T	8: 125,303,017 (GRCm39)	D45V	probably damaging	Het
Card9	G	A	2: 26,248,847 (GRCm39)	R101C	probably damaging	Het
Ccdc87	A	G	19: 4,891,785 (GRCm39)	E759G	probably damaging	Het
Ccn1	T	C	3: 145,354,536 (GRCm39)	D125G	probably damaging	Het
Cep250	T	C	2: 155,806,997 (GRCm39)	M193T	probably damaging	Het
Cfap54	T	C	10: 92,656,966 (GRCm39)	K3029E	probably benign	Het
Chrna9	G	A	5: 66,134,484 (GRCm39)	G445D	possibly damaging	Het
Cluap1	C	T	16: 3,758,639 (GRCm39)	S367L	probably benign	Het
Col5a1	A	G	2: 27,819,498 (GRCm39)	D200G	unknown	Het
Crhr2	T	C	6: 55,069,112 (GRCm39)	N388D		Het
Cyp2b23	A	G	7: 26,380,838 (GRCm39)	L129P	probably benign	Het
Dctd	A	G	8: 48,565,075 (GRCm39)	S67G	probably benign	Het
Dhtkd1	C	G	2: 5,908,881 (GRCm39)	V738L	probably benign	Het
Dnah17	C	T	11: 117,970,484 (GRCm39)	D2173N	probably benign	Het
Dnah7c	G	T	1: 46,720,932 (GRCm39)	A2819S	probably benign	Het
Dnai7	A	T	6: 145,123,132 (GRCm39)	L578Q	probably null	Het
Dot1l	A	G	10: 80,628,175 (GRCm39)	H1071R	unknown	Het
Dync2h1	T	A	9: 7,075,786 (GRCm39)	D3027V	probably damaging	Het
Efl1	A	G	7: 82,307,272 (GRCm39)	Y56C	probably damaging	Het
Eif4e1b	A	T	13: 54,931,913 (GRCm39)	R29W	probably null	Het
Evc2	A	G	5: 37,567,602 (GRCm39)	R860G	probably damaging	Het
Fbxl12	G	A	9: 20,555,679 (GRCm39)		probably benign	Het
Fibp	T	A	19: 5,511,519 (GRCm39)	I129N	probably damaging	Het
Folh1	G	T	7: 86,375,320 (GRCm39)	H555Q	probably damaging	Het
Gcnt4	A	T	13: 97,083,027 (GRCm39)	T108S	probably damaging	Het
H1f7	T	A	15: 98,154,250 (GRCm39)	K300*	probably null	Het
Hecw2	A	T	1: 53,904,280 (GRCm39)	V1156E	probably damaging	Het
Herc3	C	G	6: 58,864,409 (GRCm39)	A681G	probably damaging	Het
Igkv13-84	T	A	6: 68,916,764 (GRCm39)	C20*	probably null	Het
Iho1	A	T	9: 108,294,619 (GRCm39)	D98E	probably benign	Het
Iqca1l	A	G	5: 24,753,954 (GRCm39)	V435A	possibly damaging	Het
Ivd	C	A	2: 118,700,255 (GRCm39)	T94K	probably damaging	Het
Kank2	C	T	9: 21,705,975 (GRCm39)	A348T	probably benign	Het
Kcnma1	T	C	14: 23,417,562 (GRCm39)	Y889C	probably damaging	Het
Kif13b	T	C	14: 65,010,517 (GRCm39)	V1272A	probably damaging	Het
Kmt2d	GCTGCTGCT	GCTGCTGCTCCTGCTGCT	15: 98,747,497 (GRCm39)		probably benign	Het
Kmt5b	T	A	19: 3,865,412 (GRCm39)	D825E	probably benign	Het
Krt39	C	T	11: 99,411,697 (GRCm39)	A130T	probably benign	Het
Krtap4-9	C	T	11: 99,676,283 (GRCm39)	T68I	unknown	Het
Lmbr1l	A	T	15: 98,804,204 (GRCm39)	V365E	probably benign	Het
Lonp1	C	T	17: 56,924,814 (GRCm39)	R531Q	probably damaging	Het
Mecom	T	A	3: 30,035,094 (GRCm39)	H194L	probably damaging	Het
Mlx	C	T	11: 100,980,068 (GRCm39)	H188Y	probably damaging	Het
Mrps10	T	C	17: 47,685,940 (GRCm39)	S77P	probably damaging	Het
Mst1	A	G	9: 107,962,130 (GRCm39)	E716G	probably null	Het
Mttp	C	T	3: 137,821,893 (GRCm39)	V210I	probably benign	Het
Mug2	T	C	6: 122,052,206 (GRCm39)	V988A	probably damaging	Het
Ndufb6	A	G	4: 40,279,336 (GRCm39)	M1T	probably null	Het
Neurog1	A	T	13: 56,399,563 (GRCm39)	N61K	probably benign	Het
Nlrp14	A	G	7: 106,784,021 (GRCm39)	D581G	possibly damaging	Het
Nlrp4a	C	A	7: 26,149,258 (GRCm39)	N288K	probably benign	Het
Notch3	T	A	17: 32,363,191 (GRCm39)	H1264L	probably benign	Het
Or1e25	A	T	11: 73,493,562 (GRCm39)	D52V	possibly damaging	Het
Or1e34	A	T	11: 73,778,780 (GRCm39)	C139*	probably null	Het
Or3a1c	A	G	11: 74,046,606 (GRCm39)	M209V	probably benign	Het
Patl2	A	T	2: 121,952,263 (GRCm39)		probably null	Het
Pfkfb4	A	G	9: 108,836,370 (GRCm39)	T133A	probably benign	Het
Pla2g4f	T	C	2: 120,135,035 (GRCm39)	E471G	probably null	Het
Postn	T	C	3: 54,270,056 (GRCm39)	V45A	probably damaging	Het
Ppan	T	A	9: 20,802,450 (GRCm39)	V257E	possibly damaging	Het
Ptcra	C	G	17: 47,074,522 (GRCm39)	A7P	probably damaging	Het
Ptprd	C	T	4: 75,984,577 (GRCm39)	R523H	probably damaging	Het
Pycr3	A	T	15: 75,790,544 (GRCm39)	I105N	possibly damaging	Het
Rfx1	C	A	8: 84,821,708 (GRCm39)	Q815K	probably damaging	Het
Ryr2	A	T	13: 11,655,213 (GRCm39)	D3661E	possibly damaging	Het
Ryr2	A	G	13: 11,683,697 (GRCm39)		probably null	Het
Sec23ip	T	A	7: 128,381,364 (GRCm39)	S974T	probably damaging	Het
Semp2l2a	A	T	8: 13,886,982 (GRCm39)	W370R	probably damaging	Het
Setbp1	A	G	18: 79,130,175 (GRCm39)	F19S	probably benign	Het
Setd1a	AAGCAGCAGCAGCAGCAGCAG	AAGCAGCAGCAGCAGCAG	7: 127,395,590 (GRCm39)		probably benign	Het
Sh3pxd2b	A	G	11: 32,372,072 (GRCm39)	K413R	probably damaging	Het
Slc39a12	T	C	2: 14,454,614 (GRCm39)	V544A	probably damaging	Het
Slc6a7	T	C	18: 61,135,274 (GRCm39)	Y418C	probably damaging	Het
Snx19	T	G	9: 30,339,189 (GRCm39)	I109S	probably damaging	Het
Spart	T	C	3: 55,029,220 (GRCm39)		probably null	Het
Sptbn2	A	T	19: 4,799,488 (GRCm39)	Q2097L	probably null	Het
Syne1	T	C	10: 5,178,221 (GRCm39)	K4751R	probably damaging	Het
Tigit	C	A	16: 43,482,615 (GRCm39)	G40C	probably damaging	Het
Tmem181a	T	A	17: 6,348,247 (GRCm39)	I264K	probably damaging	Het
Tom1	T	A	8: 75,783,877 (GRCm39)	I287N	possibly damaging	Het
Top2a	G	A	11: 98,895,008 (GRCm39)	P864L	possibly damaging	Het
Trmt44	A	T	5: 35,728,410 (GRCm39)	V290E	probably damaging	Het
Try4	T	C	6: 41,281,337 (GRCm39)	I93T	probably benign	Het
Usp24	T	A	4: 106,239,500 (GRCm39)	H1147Q	possibly damaging	Het
Uspl1	A	T	5: 149,130,745 (GRCm39)	R109S	probably benign	Het
Vav3	T	A	3: 109,571,662 (GRCm39)	F755I	probably damaging	Het
Vezt	A	T	10: 93,806,409 (GRCm39)	Y667*	probably null	Het
Vmn1r231	T	A	17: 21,110,140 (GRCm39)	L258F	possibly damaging	Het
Zfp207	T	C	11: 80,286,354 (GRCm39)	M489T	unknown	Het
Zfp462	A	G	4: 55,009,380 (GRCm39)	T449A	probably benign	Het
Zfp956	C	A	6: 47,932,781 (GRCm39)	Q19K	probably benign	Het
Zkscan8	A	T	13: 21,709,443 (GRCm39)	W152R	probably damaging	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
R5590:Rfx3	UTSW	19	27,779,780 (GRCm39)	critical splice donor site	probably null
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
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'- GTTAGAGTAAGCTGGAAAACTCTGC -3'
(R):5'- GAAAGCCTATGAGTCCTCCC -3'

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

Posted On

2019-05-15