Mutagenetix > Incidental Mutation

Incidental Mutation 'R9310:Rfx3'

705523

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

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9310 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

27739121-27988566 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 27827329 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Glycine at position 86 (S86G)

Ref Sequence

ENSEMBL: ENSMUSP00000038760 (fasta)

Gene Model

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

AlphaFold

P48381

Predicted Effect

probably benign
Transcript: ENSMUST00000046898
AA Change: S86G

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: S86G

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 benign
Transcript: ENSMUST00000165566
AA Change: S86G

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: S86G

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 benign
Transcript: ENSMUST00000172907
AA Change: S86G

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: S86G

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

possibly damaging
Transcript: ENSMUST00000173863
AA Change: S86G

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000133367
Gene: ENSMUSG00000040929
AA Change: S86G

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 benign
Transcript: ENSMUST00000174850
AA Change: S86G

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: S86G

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: 99.9%
10x: 99.6%
20x: 98.7%

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: 95 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700030J22Rik	T	C	8: 117,698,859 (GRCm39)	I83V	possibly damaging	Het
Abcf1	G	A	17: 36,272,621 (GRCm39)	A288V	probably null	Het
Acer1	A	T	17: 57,262,598 (GRCm39)	V184D	probably damaging	Het
Apoh	T	C	11: 108,298,307 (GRCm39)		probably null	Het
Arid1a	T	C	4: 133,413,625 (GRCm39)	Y959C	unknown	Het
Asb3	A	T	11: 30,978,962 (GRCm39)	H84L	probably benign	Het
Atxn1	A	C	13: 45,721,494 (GRCm39)	Y134D	probably damaging	Het
Btbd1	T	C	7: 81,478,985 (GRCm39)	Y52C	probably damaging	Het
Cabp2	A	G	19: 4,136,464 (GRCm39)	D170G	probably damaging	Het
Cacna1a	C	A	8: 85,263,046 (GRCm39)	A407E	probably damaging	Het
Cacna2d4	T	A	6: 119,248,914 (GRCm39)		probably null	Het
Cc2d2a	T	C	5: 43,852,488 (GRCm39)	F404S	probably damaging	Het
Cdh20	T	C	1: 104,875,061 (GRCm39)	M281T	probably damaging	Het
Cfap54	A	T	10: 92,798,177 (GRCm39)	M1694K	unknown	Het
Chd6	G	T	2: 160,881,181 (GRCm39)	T261K	probably damaging	Het
Cnksr1	T	C	4: 133,956,330 (GRCm39)	S585G	probably damaging	Het
Cntnap2	A	T	6: 45,978,281 (GRCm39)	Y312F	probably damaging	Het
Coa7	T	A	4: 108,195,510 (GRCm39)	Y146*	probably null	Het
Col28a1	T	C	6: 8,175,414 (GRCm39)	K145E	unknown	Het
Coq8b	T	A	7: 26,941,486 (GRCm39)	I221N	probably damaging	Het
Cpd	A	T	11: 76,705,607 (GRCm39)	L375*	probably null	Het
Dnah5	T	C	15: 28,448,579 (GRCm39)	F4214S	probably damaging	Het
Dnai3	C	T	3: 145,802,895 (GRCm39)		probably null	Het
Dock2	A	G	11: 34,244,139 (GRCm39)	F1067S	possibly damaging	Het
Dpp6	G	A	5: 27,836,439 (GRCm39)	A310T	probably damaging	Het
Dpp6	C	A	5: 27,930,642 (GRCm39)	L825I	probably benign	Het
Efcab5	A	G	11: 77,004,531 (GRCm39)	V929A	probably benign	Het
Ephx3	C	G	17: 32,408,290 (GRCm39)	D45H	probably benign	Het
Espl1	G	A	15: 102,205,285 (GRCm39)		probably null	Het
Firrm	A	G	1: 163,792,089 (GRCm39)	C610R	probably damaging	Het
Gm4847	T	C	1: 166,460,281 (GRCm39)	R402G	probably benign	Het
Grid1	T	C	14: 34,748,762 (GRCm39)	L194S	probably damaging	Het
Heatr1	A	T	13: 12,453,491 (GRCm39)	H2122L	probably benign	Het
Il17b	T	A	18: 61,825,334 (GRCm39)	C123*	probably null	Het
Il17rc	T	C	6: 113,451,210 (GRCm39)	L181P	probably damaging	Het
Inpp5e	T	A	2: 26,287,940 (GRCm39)	I619L	probably benign	Het
Itgax	C	A	7: 127,741,432 (GRCm39)	Y814*	probably null	Het
Marcks	C	T	10: 37,012,487 (GRCm39)	E183K	unknown	Het
Mefv	T	C	16: 3,533,252 (GRCm39)	T340A	probably benign	Het
Mical2	A	G	7: 111,950,920 (GRCm39)	K958R	probably benign	Het
Mrtfb	T	A	16: 13,218,954 (GRCm39)	D533E	probably benign	Het
Mtor	T	A	4: 148,553,834 (GRCm39)	L811Q	probably benign	Het
Myh4	A	G	11: 67,145,570 (GRCm39)	Y1351C	probably damaging	Het
Neb	T	C	2: 52,153,708 (GRCm39)	M2406V	probably benign	Het
Nebl	T	C	2: 17,353,678 (GRCm39)	T214A	probably benign	Het
Nlrx1	A	T	9: 44,164,705 (GRCm39)	I913N	probably damaging	Het
Npr2	G	T	4: 43,632,404 (GRCm39)	A74S	probably benign	Het
Or4c115	T	A	2: 88,928,257 (GRCm39)	S5C	probably damaging	Het
Or6b6	C	A	7: 106,570,678 (GRCm39)	C291F	probably damaging	Het
Or6c88	T	A	10: 129,406,687 (GRCm39)	N54K	probably benign	Het
Pard3b	G	T	1: 62,205,528 (GRCm39)	V441F	probably damaging	Het
Pcsk1	G	A	13: 75,238,191 (GRCm39)	R4K	probably benign	Het
Pisd	G	T	5: 32,894,784 (GRCm39)	N337K	possibly damaging	Het
Pml	T	C	9: 58,156,945 (GRCm39)	K10R	probably benign	Het
Prkci	T	C	3: 31,083,664 (GRCm39)	W132R	probably damaging	Het
Prrc2a	A	T	17: 35,374,975 (GRCm39)	M1225K	probably benign	Het
Prss23	T	C	7: 89,159,142 (GRCm39)	D309G	probably damaging	Het
Pxdn	G	A	12: 30,052,051 (GRCm39)	G743S	probably damaging	Het
Rab29	A	T	1: 131,799,860 (GRCm39)	E145V	probably damaging	Het
Rasef	C	T	4: 73,653,956 (GRCm39)		probably null	Het
Rcbtb1	T	G	14: 59,472,699 (GRCm39)	I496S	probably benign	Het
Rcor1	T	C	12: 111,066,393 (GRCm39)	Y228H		Het
Reep5	C	T	18: 34,490,222 (GRCm39)	V92I	probably damaging	Het
Rptn	T	A	3: 93,304,384 (GRCm39)	D572E	probably benign	Het
Rsl1	A	T	13: 67,324,510 (GRCm39)		probably null	Het
Sbf2	T	C	7: 109,914,292 (GRCm39)	E1630G	possibly damaging	Het
Sele	G	A	1: 163,876,975 (GRCm39)	V84I	probably benign	Het
Serpina1b	T	C	12: 103,698,756 (GRCm39)	D31G	probably benign	Het
Serpina3c	T	C	12: 104,115,813 (GRCm39)	I244V	probably benign	Het
Serpinb6e	A	G	13: 34,017,204 (GRCm39)	V272A	probably benign	Het
Serpinb9b	A	G	13: 33,219,523 (GRCm39)	D150G	probably benign	Het
Sgpp1	T	C	12: 75,769,374 (GRCm39)	T265A	probably benign	Het
Slc9a1	T	A	4: 133,143,681 (GRCm39)	M389K	probably damaging	Het
Slco3a1	A	T	7: 74,204,236 (GRCm39)	C35S	probably damaging	Het
Slco6d1	T	A	1: 98,427,619 (GRCm39)	V650E	possibly damaging	Het
Slit2	T	C	5: 48,349,568 (GRCm39)	V274A	possibly damaging	Het
Snd1	A	G	6: 28,795,936 (GRCm39)	E593G	probably null	Het
Spata2l	C	T	8: 123,960,873 (GRCm39)	V139M	probably benign	Het
Suco	T	C	1: 161,684,427 (GRCm39)	K231R	probably damaging	Het
Tenm3	C	A	8: 49,008,935 (GRCm39)		probably benign	Het
Tg	T	C	15: 66,699,118 (GRCm39)	S2415P	possibly damaging	Het
Traf6	C	A	2: 101,527,072 (GRCm39)	A274D	possibly damaging	Het
Usp14	A	G	18: 9,996,239 (GRCm39)	I447T	possibly damaging	Het
Usp32	G	A	11: 84,942,028 (GRCm39)	L355F	probably benign	Het
Vcpip1	T	C	1: 9,817,927 (GRCm39)	N152S	possibly damaging	Het
Vgf	A	G	5: 137,061,110 (GRCm39)	Q424R	probably benign	Het
Vmn2r84	A	T	10: 130,227,993 (GRCm39)	M81K	possibly damaging	Het
Washc5	G	A	15: 59,218,067 (GRCm39)	A732V	possibly damaging	Het
Xrcc3	T	G	12: 111,771,485 (GRCm39)	D213A	probably damaging	Het
Zeb2	T	C	2: 44,886,988 (GRCm39)	T690A	probably benign	Het
Zfat	G	A	15: 67,956,250 (GRCm39)	S1212L	probably damaging	Het
Zfp623	C	T	15: 75,819,949 (GRCm39)	L302F	probably damaging	Het
Zfp799	A	C	17: 33,039,733 (GRCm39)	C178G	possibly damaging	Het
Zfy1	T	C	Y: 727,634 (GRCm39)	E348G	unknown	Het
Zhx3	A	G	2: 160,621,393 (GRCm39)	W925R	possibly 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
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
Z1088:Rfx3	UTSW	19	27,814,850 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGTTCTCCATTGAATTGCCGATC -3'
(R):5'- GTGCTCCTATAGTGAGTATAACACTG -3'

Sequencing Primer
(F):5'- GATCAAATAGGTTCCTCCCGAGCTG -3'
(R):5'- CACTGTAGTACAAAACCAAGTTAAGG -3'

Posted On

2022-03-25