Mutagenetix > Incidental Mutation

Incidental Mutation 'R8995:Rfx3'

684702

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

068826-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8995 (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 A at 27783725 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Valine at position 382 (E382V)

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: E382V

PolyPhen 2 Score 0.144 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: E382V

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: E407V

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: E407V

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: E407V

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: E407V

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 damaging
Transcript: ENSMUST00000174850
AA Change: E407V

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: E407V

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: 99.4%
20x: 98.1%

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: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700018B08Rik	A	G	8: 122,257,764 (GRCm39)	*214R	probably null	Het
Acd	A	G	8: 106,427,131 (GRCm39)	L93P	probably damaging	Het
Adgrv1	GTT	GT	13: 81,553,457 (GRCm39)		probably null	Het
Aldh1b1	T	A	4: 45,803,413 (GRCm39)	M317K	possibly damaging	Het
Arfgap2	C	A	2: 91,103,929 (GRCm39)	Q342K	probably damaging	Het
Arhgef16	C	T	4: 154,371,495 (GRCm39)	E233K	probably damaging	Het
Asxl1	C	T	2: 153,235,886 (GRCm39)	R323C	probably damaging	Het
Bank1	G	T	3: 135,772,264 (GRCm39)	D656E	possibly damaging	Het
Bdh2	A	G	3: 135,000,989 (GRCm39)	M120V	probably damaging	Het
Bend7	A	G	2: 4,749,103 (GRCm39)	I73M	probably damaging	Het
Cd207	C	A	6: 83,652,891 (GRCm39)	D80Y	probably damaging	Het
Cdon	A	G	9: 35,398,093 (GRCm39)	T937A	probably damaging	Het
Cntn1	G	A	15: 92,132,347 (GRCm39)	V148M	probably damaging	Het
Csnk2a1-ps3	T	A	1: 156,352,873 (GRCm39)	V358E	probably benign	Het
Ddx50	A	G	10: 62,469,862 (GRCm39)	I375T	probably damaging	Het
Dhrs1	T	A	14: 55,977,396 (GRCm39)	T241S	probably benign	Het
Eef1b2	T	C	1: 63,217,629 (GRCm39)	Y79H	probably damaging	Het
Elmod2	A	G	8: 84,049,315 (GRCm39)	C84R	probably benign	Het
Exo1	A	G	1: 175,736,127 (GRCm39)	H837R	probably benign	Het
Fat3	T	C	9: 16,286,898 (GRCm39)	N875S	probably damaging	Het
Flvcr1	A	T	1: 190,743,817 (GRCm39)	L413Q	probably damaging	Het
Fras1	G	T	5: 96,860,415 (GRCm39)	V2154F	possibly damaging	Het
Golm2	A	C	2: 121,756,199 (GRCm39)	E409D	probably damaging	Het
Hectd4	G	A	5: 121,392,422 (GRCm39)	V229M	possibly damaging	Het
Ifitm6	A	T	7: 140,596,617 (GRCm39)	V52E	probably damaging	Het
Igkv4-58	A	G	6: 69,477,511 (GRCm39)	S29P	probably damaging	Het
Klc1	G	A	12: 111,743,344 (GRCm39)	A224T	probably damaging	Het
Knl1	T	C	2: 118,902,990 (GRCm39)	S1564P	probably benign	Het
Krt25	T	C	11: 99,207,382 (GRCm39)	D399G	probably benign	Het
Lamc1	T	C	1: 153,207,993 (GRCm39)	Q98R	probably benign	Het
Lpar1	T	A	4: 58,486,954 (GRCm39)	M106L	probably damaging	Het
Mpc1	A	G	17: 8,502,784 (GRCm39)	Y21C	probably benign	Het
Msr1	T	A	8: 40,042,460 (GRCm39)	I372F	possibly damaging	Het
Ndc80	T	C	17: 71,815,598 (GRCm39)	N396D	probably benign	Het
Nphp4	G	A	4: 152,623,345 (GRCm39)	R673H	probably damaging	Het
Nsd3	T	C	8: 26,131,169 (GRCm39)	F178S	probably damaging	Het
Or1p1b	A	T	11: 74,130,620 (GRCm39)	T77S	probably benign	Het
Or8g54	T	C	9: 39,707,313 (GRCm39)	I214T	possibly damaging	Het
Pcdhgb7	T	A	18: 37,885,230 (GRCm39)	F133L	probably damaging	Het
Pikfyve	A	G	1: 65,244,746 (GRCm39)		probably null	Het
Pld5	A	T	1: 175,791,580 (GRCm39)	D475E	probably benign	Het
Potefam3f	A	T	8: 20,479,025 (GRCm39)	H11L		Het
Prop1	G	A	11: 50,841,887 (GRCm39)	P173L	possibly damaging	Het
Rabepk	G	A	2: 34,689,842 (GRCm39)		probably benign	Het
Reln	A	G	5: 22,184,577 (GRCm39)	I1646T	probably benign	Het
Rexo1	A	T	10: 80,386,095 (GRCm39)	L321Q	probably damaging	Het
Rnf20	C	T	4: 49,648,437 (GRCm39)	T415I	possibly damaging	Het
Rpl10-ps3	T	A	9: 50,256,078 (GRCm39)	D55V	probably benign	Het
Sag	A	G	1: 87,733,052 (GRCm39)	T7A	probably benign	Het
Saysd1	G	A	14: 20,133,005 (GRCm39)	R51C	probably damaging	Het
Shprh	T	A	10: 11,040,574 (GRCm39)	Y682*	probably null	Het
Slc6a13	T	C	6: 121,302,012 (GRCm39)	I198T	probably damaging	Het
Slx9	G	A	10: 77,333,303 (GRCm39)	R121*	probably null	Het
Smyd5	C	A	6: 85,415,829 (GRCm39)	C101*	probably null	Het
Spata31d1d	A	G	13: 59,874,421 (GRCm39)	V1038A	probably benign	Het
Stat6	T	C	10: 127,494,511 (GRCm39)	S692P	probably benign	Het
Tbc1d9	A	T	8: 83,998,180 (GRCm39)	M1246L	probably benign	Het
Tmprss5	T	A	9: 49,025,894 (GRCm39)		probably null	Het
Trim12a	A	T	7: 103,953,532 (GRCm39)	M193K	probably benign	Het
Ube2t	T	A	1: 134,899,658 (GRCm39)	L102H	probably damaging	Het
Ubr1	G	A	2: 120,697,034 (GRCm39)	R1623W	probably damaging	Het
Ush2a	T	G	1: 188,176,850 (GRCm39)	M1338R	probably damaging	Het
Usp36	A	T	11: 118,175,825 (GRCm39)	L112Q	probably damaging	Het
Vmn1r53	A	G	6: 90,200,757 (GRCm39)	M189T	probably benign	Het
Vmn1r54	T	C	6: 90,246,668 (GRCm39)	V194A	probably benign	Het
Vmn2r33	A	G	7: 7,554,192 (GRCm39)	V787A	probably damaging	Het
Vps26a	A	G	10: 62,300,458 (GRCm39)	I236T	probably damaging	Het
Vwde	A	T	6: 13,195,996 (GRCm39)	L343Q	probably damaging	Het
Xdh	A	G	17: 74,205,369 (GRCm39)	V1032A	probably damaging	Het
Zan	A	G	5: 137,393,882 (GRCm39)	F4523S	unknown	Het
Zfand5	T	A	19: 21,254,387 (GRCm39)	V66E	probably benign	Het
Zfp658	T	A	7: 43,222,798 (GRCm39)	C358S	possibly damaging	Het
Zfp977	T	A	7: 42,232,072 (GRCm39)	R64W	probably damaging	Het
Zfp995	C	T	17: 22,099,172 (GRCm39)	S354N	probably benign	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
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'- AAGCATCCGTAGTTGTCTCC -3'
(R):5'- GCTAATGGACTACTATCCTATCTGC -3'

Sequencing Primer
(F):5'- CCATTTAACTTACTAGGAATGGGTC -3'
(R):5'- TTAATGTACATAAGTAGCCCTGGGG -3'

Posted On

2021-10-11