Mutagenetix > Incidental Mutations

Incidental Mutation 'R0336:Rfx3'

34155

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

038545-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R0336 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

27761721-28011166 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 27806262 bp

Zygosity

Heterozygous

Amino Acid Change

Methionine to Threonine at position 428 (M428T)

Ref Sequence

ENSEMBL: ENSMUSP00000133461 (fasta)

Gene Model

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

Predicted Effect

probably benign
Transcript: ENSMUST00000046898
AA Change: M403T

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: M403T

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: M428T

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: M428T

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 benign
Transcript: ENSMUST00000172907
AA Change: M428T

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: M428T

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 benign
Transcript: ENSMUST00000174850
AA Change: M428T

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: M428T

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

0.1707

Coding Region Coverage

1x: 99.5%
3x: 99.0%
10x: 98.1%
20x: 97.1%

Validation Efficiency

98% (62/63)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	A	G	11: 9,298,481	I2743V	probably benign	Het
Adamts16	A	G	13: 70,791,794		probably benign	Het
Adgrb1	A	G	15: 74,587,149	I427V	probably benign	Het
Apopt1	T	C	12: 111,733,658		probably benign	Het
Arhgef1	T	A	7: 24,921,957	F510I	possibly damaging	Het
B3glct	A	G	5: 149,746,592	D342G	probably damaging	Het
Bcl2a1c	G	T	9: 114,330,285	V44F	probably damaging	Het
Brca1	A	G	11: 101,523,993	V1105A	probably benign	Het
Cep135	A	G	5: 76,601,502	H272R	probably benign	Het
Cog1	A	C	11: 113,662,250	H365P	probably benign	Het
Col12a1	A	T	9: 79,702,345	L293Q	probably damaging	Het
Col18a1	A	G	10: 77,058,736	L1493P	probably damaging	Het
Ctsh	A	G	9: 90,075,738	Y290C	probably damaging	Het
Dach1	C	T	14: 98,168,748	G188R	probably damaging	Het
Defb39	G	T	8: 19,052,969	H37N	possibly damaging	Het
Epha3	A	G	16: 63,566,648	I875T	probably damaging	Het
Fbrsl1	A	G	5: 110,447,951	S73P	probably damaging	Het
Fga	T	C	3: 83,030,857	S180P	probably damaging	Het
Fndc1	C	T	17: 7,765,107	R1329Q	unknown	Het
Fyn	C	A	10: 39,526,901	T223K	possibly damaging	Het
Galnt6	A	T	15: 100,699,206	S360T	probably damaging	Het
Gm10436	T	C	12: 88,178,191	I122V	probably benign	Het
Grsf1	C	A	5: 88,663,153	V336F	probably damaging	Het
Hip1	A	T	5: 135,428,613	Y720N	probably benign	Het
Hivep3	G	A	4: 120,103,847	E1700K	probably damaging	Het
Ifna6	T	C	4: 88,827,941	S176P	probably damaging	Het
Lilr4b	T	A	10: 51,481,293	L75Q	probably benign	Het
Lrig3	C	T	10: 125,966,705	T77I	probably benign	Het
Mpped1	C	T	15: 83,836,282	P135L	probably damaging	Het
Mss51	T	A	14: 20,483,186	I406F	possibly damaging	Het
Mybpc2	T	C	7: 44,505,616	N956D	probably damaging	Het
Olfr1197	T	C	2: 88,729,154	I148M	possibly damaging	Het
Podxl2	G	A	6: 88,849,595	T243I	probably benign	Het
Polr2a	C	T	11: 69,736,893	R1396Q	possibly damaging	Het
Pygm	C	T	19: 6,388,758	R205W	probably damaging	Het
Ric1	A	T	19: 29,587,793	T647S	probably damaging	Het
Rictor	G	A	15: 6,776,753		probably null	Het
Rnf38	A	T	4: 44,152,350		probably benign	Het
Slc6a21	T	A	7: 45,286,468	I41K	probably damaging	Het
St8sia4	T	A	1: 95,653,558	D153V	probably benign	Het
Stk33	T	C	7: 109,331,474	N226S	probably benign	Het
Strn3	A	G	12: 51,661,608		probably null	Het
Tlr6	G	T	5: 64,953,946	N539K	probably benign	Het
Tmem129	G	T	5: 33,655,602	P134Q	probably damaging	Het
Tmem94	A	G	11: 115,787,385	I145V	probably benign	Het
Trap1	A	C	16: 4,044,626	V596G	probably damaging	Het
Tspan2	A	G	3: 102,735,027	I11V	probably null	Het
Ttc23	A	T	7: 67,662,483	H46L	probably benign	Het
Txnip	T	A	3: 96,559,979	D292E	probably benign	Het
Vmn1r121	T	A	7: 21,098,462	I18F	possibly damaging	Het
Vmn1r61	G	A	7: 5,611,067	H83Y	probably benign	Het
Vmn1r82	T	C	7: 12,305,321	S174P	probably benign	Het
Vmn2r79	A	C	7: 87,002,079	T229P	probably benign	Het
Vps13b	T	G	15: 35,455,133	Y729*	probably null	Het
Wisp2	C	A	2: 163,832,322	A214D	probably damaging	Het
Xdh	C	T	17: 73,922,463	V332M	possibly damaging	Het
Xkr5	C	A	8: 18,940,636	R205L	possibly damaging	Het
Zc3h4	T	C	7: 16,435,178	S1071P	unknown	Het
Zc3h6	A	G	2: 129,015,412	H617R	possibly damaging	Het
Zfp597	A	G	16: 3,866,379	V171A	probably benign	Het
Zfp709	T	C	8: 71,890,605	F626S	probably damaging	Het
Zfp944	C	A	17: 22,339,028	D413Y	probably damaging	Het
Zfp979	A	C	4: 147,613,135	S372R	possibly 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
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
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
Z1088:Rfx3	UTSW	19	27837450	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGTCAGTTCCCCTTCACTGCAATG -3'
(R):5'- CCAGCCATATGACACCAGTGCAATG -3'

Sequencing Primer
(F):5'- TCACTGCAATGTCACTCTAAGC -3'
(R):5'- CACCAGTGCAATGATGGTATAGTTC -3'

Posted On

2013-05-09