Mutagenetix > Incidental Mutations

Incidental Mutation 'R7273:Rfx3'

565427

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 #

R7273 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

27761721-28011166 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 27802458 bp

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glutamine at position 435 (R435Q)

Ref Sequence

ENSEMBL: ENSMUSP00000038760 (fasta)

Gene Model

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000046898
AA Change: R435Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: R435Q

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 damaging
Transcript: ENSMUST00000165566
AA Change: R460Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: R460Q

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 damaging
Transcript: ENSMUST00000172907
AA Change: R460Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: R460Q

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

silent
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 damaging
Transcript: ENSMUST00000174850
AA Change: R460Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: R460Q

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: 99.8%
20x: 99.3%

Validation Efficiency

100% (49/49)

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: 47 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Apol10a	A	T	15: 77,488,868	I235F	probably damaging	Het
Aspn	A	T	13: 49,558,876	E222D	probably benign	Het
Cfap221	A	T	1: 119,954,218	V280D	possibly damaging	Het
Chrd	G	A	16: 20,741,566	R922Q	probably benign	Het
Cnga4	T	A	7: 105,406,965	V361E	probably damaging	Het
Col15a1	T	A	4: 47,284,467		probably null	Het
Col6a4	A	G	9: 106,000,457	V2107A	possibly damaging	Het
Eea1	G	T	10: 95,989,631	V63F	probably benign	Het
Eml1	A	G	12: 108,538,173	H797R	possibly damaging	Het
Gm4858	G	T	3: 93,074,168	M90I	probably damaging	Het
Gm4869	T	A	5: 140,476,012	V523E	probably damaging	Het
Il1r2	A	G	1: 40,112,007	T141A	probably benign	Het
Il6st	T	C	13: 112,495,298	V457A	probably benign	Het
Lrrc56	T	C	7: 141,209,665	C532R	probably benign	Het
Lrrn4	T	C	2: 132,879,829	S23G	unknown	Het
Mapk8ip3	A	T	17: 24,906,174	D498E	probably benign	Het
Mcam	T	C	9: 44,140,944	F584S	possibly damaging	Het
Mdga1	A	T	17: 29,969,938	D50E	unknown	Het
Mfsd7a	T	C	5: 108,441,991	D515G	probably benign	Het
Mga	T	C	2: 119,935,214	S1320P	probably damaging	Het
Muc5b	G	A	7: 141,851,570	G905D	unknown	Het
Ncor2	T	C	5: 125,023,623	N1297S		Het
Nisch	A	G	14: 31,174,407	V946A	unknown	Het
Npc1l1	A	G	11: 6,218,320	F957S	probably damaging	Het
Nuggc	A	G	14: 65,619,608	N402S	probably damaging	Het
Nup210l	A	G	3: 90,118,547	T159A	probably benign	Het
Olfr981	A	T	9: 40,022,665	I91F	probably benign	Het
Otud1	A	G	2: 19,659,062	D334G	probably damaging	Het
Pclo	T	C	5: 14,681,594	V3370A	unknown	Het
Prdm16	A	G	4: 154,345,453	L353P	probably damaging	Het
Prepl	A	C	17: 85,081,992	V128G	probably benign	Het
Pum1	T	C	4: 130,751,480	V568A	probably damaging	Het
Rab10	G	T	12: 3,256,891	S101R	probably benign	Het
Rnf213	A	T	11: 119,431,756		probably null	Het
Sema5a	A	G	15: 32,417,462	D26G	probably benign	Het
Smim4	G	T	14: 31,124,598	R55S	probably damaging	Het
Spata31d1b	G	A	13: 59,717,632	V865I	probably benign	Het
Sycp3	A	T	10: 88,469,566	Q176H	probably damaging	Het
Tmprss11d	A	T	5: 86,337,239	V102D	probably damaging	Het
Top1mt	A	G	15: 75,664,082	V457A	probably benign	Het
Tubal3	T	A	13: 3,930,675	I129N	probably damaging	Het
Ubr3	G	A	2: 69,979,333	D1217N	probably damaging	Het
Uggt1	A	G	1: 36,162,221	I1146T	probably damaging	Het
Umod	T	C	7: 119,477,027	Q172R	probably benign	Het
Zdbf2	C	T	1: 63,303,404	A314V	possibly damaging	Het
Zfp787	A	T	7: 6,133,040	C71S	possibly damaging	Het
Zhx2	C	T	15: 57,823,428	A731V	probably benign	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
R7131:Rfx3	UTSW	19	27768628	nonsense	probably null
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
Z1088:Rfx3	UTSW	19	27837450	missense	probably damaging	1.00

Predicted Primers

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

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

Posted On

2019-06-26