Mutagenetix > Incidental Mutations

Incidental Mutation 'R4993:Rfx5'

384983

Institutional Source

Beutler Lab

Gene Symbol

Rfx5

Ensembl Gene

ENSMUSG00000005774

Gene Name

regulatory factor X, 5 (influences HLA class II expression)

Synonyms

MMRRC Submission

042587-MU

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.287) question?

Stock #

R4993 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

94954075-94961561 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 94955815 bp

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 73 (V73I)

Ref Sequence

ENSEMBL: ENSMUSP00000117963 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029772] [ENSMUST00000107253] [ENSMUST00000107254] [ENSMUST00000107255] [ENSMUST00000107260] [ENSMUST00000132393] [ENSMUST00000137088] [ENSMUST00000140331] [ENSMUST00000142311] [ENSMUST00000145031] [ENSMUST00000147237] [ENSMUST00000152869] [ENSMUST00000144132] [ENSMUST00000145472]

Predicted Effect

probably benign
Transcript: ENSMUST00000029772
AA Change: V73I

PolyPhen 2 Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000029772
Gene: ENSMUSG00000005774
AA Change: V73I

Domain	Start	End	E-Value	Type
Pfam:RFX_DNA_binding	84	169	7.2e-33	PFAM
RFX5_DNA_bdg	438	656	4.29e-130	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000107253
AA Change: V73I

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

SMART Domains

Protein: ENSMUSP00000102874
Gene: ENSMUSG00000005774
AA Change: V73I

Domain	Start	End	E-Value	Type
Pfam:RFX_DNA_binding	84	169	1.8e-33	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000107254
AA Change: V73I

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

SMART Domains

Protein: ENSMUSP00000102875
Gene: ENSMUSG00000005774
AA Change: V73I

Domain	Start	End	E-Value	Type
Pfam:RFX_DNA_binding	84	169	1.8e-33	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000107255
AA Change: V73I

PolyPhen 2 Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000102876
Gene: ENSMUSG00000005774
AA Change: V73I

Domain	Start	End	E-Value	Type
Pfam:RFX_DNA_binding	84	169	7.2e-33	PFAM
RFX5_DNA_bdg	438	656	4.29e-130	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000107260
AA Change: V73I

PolyPhen 2 Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000102881
Gene: ENSMUSG00000005774
AA Change: V73I

Domain	Start	End	E-Value	Type
Pfam:RFX_DNA_binding	88	167	5.3e-31	PFAM
RFX5_DNA_bdg	438	656	4.29e-130	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125186

Predicted Effect

probably benign
Transcript: ENSMUST00000132393
AA Change: V73I

PolyPhen 2 Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000117999
Gene: ENSMUSG00000005774
AA Change: V73I

Domain	Start	End	E-Value	Type
PDB:2KW3\|B	23	89	9e-40	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000137088
AA Change: V73I

PolyPhen 2 Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000117963
Gene: ENSMUSG00000005774
AA Change: V73I

Domain	Start	End	E-Value	Type
Pfam:RFX_DNA_binding	84	169	7.2e-33	PFAM
RFX5_DNA_bdg	438	656	4.29e-130	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140294

Predicted Effect

probably benign
Transcript: ENSMUST00000140331

Predicted Effect

probably benign
Transcript: ENSMUST00000142311
AA Change: V73I

PolyPhen 2 Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000119704
Gene: ENSMUSG00000005774
AA Change: V73I

Domain	Start	End	E-Value	Type
Pfam:RFX_DNA_binding	84	131	4.1e-10	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000145031
AA Change: V73I

PolyPhen 2 Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000118099
Gene: ENSMUSG00000005774
AA Change: V73I

Domain	Start	End	E-Value	Type
PDB:2KW3\|B	23	89	9e-40	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000147237
AA Change: V73I

PolyPhen 2 Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000118586
Gene: ENSMUSG00000005774
AA Change: V73I

Domain	Start	End	E-Value	Type
Pfam:RFX_DNA_binding	84	169	8.7e-34	PFAM
Pfam:Pox_D5	88	159	1e-7	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148803

Predicted Effect

probably benign
Transcript: ENSMUST00000152869
AA Change: V73I

PolyPhen 2 Score 0.274 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000121157
Gene: ENSMUSG00000005774
AA Change: V73I

Domain	Start	End	E-Value	Type
PDB:2KW3\|B	23	89	7e-40	PDB

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142708

Predicted Effect

probably benign
Transcript: ENSMUST00000144132

Predicted Effect

probably benign
Transcript: ENSMUST00000145472

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.0%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Homozygous null mice have absent or decreased expression of MHC-II complexes on antigen presenting cells, which leads to reduced numbers of CD4⁺ thymocytes and T cells. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930505A04Rik	C	T	11: 30,426,349	V173M	probably damaging	Het
9130008F23Rik	G	T	17: 40,880,161	Q126K	probably benign	Het
Abca15	C	A	7: 120,401,718	N1492K	probably damaging	Het
Afap1l2	C	T	19: 56,918,040	D402N	probably damaging	Het
Akap11	A	G	14: 78,512,968	F660L	probably damaging	Het
Bcl3	T	C	7: 19,820,177	T89A	probably benign	Het
Bub1b	T	C	2: 118,636,770	I858T	possibly damaging	Het
Cdk19	A	G	10: 40,476,218	D288G	possibly damaging	Het
Cyp2d34	T	A	15: 82,618,329	D202V	probably damaging	Het
Dip2c	T	G	13: 9,575,223	Y584*	probably null	Het
Dpf3	A	T	12: 83,331,861		probably null	Het
Drp2	G	A	X: 134,441,316	R567H	probably damaging	Homo
Emid1	G	T	11: 5,131,512	Q212K	probably benign	Het
Esm1	C	T	13: 113,213,399	Q118*	probably null	Het
Fahd2a	T	G	2: 127,436,364	I308L	probably benign	Het
Fam208a	T	A	14: 27,429,114	W16R	possibly damaging	Het
Fanci	T	C	7: 79,435,378	*851Q	probably null	Het
Fastkd1	C	A	2: 69,702,740	V428F	probably damaging	Het
Fat2	A	T	11: 55,283,092	I2265N	probably damaging	Het
Gale	C	A	4: 135,966,860	H191Q	probably damaging	Het
Ghsr	T	A	3: 27,372,254	V153E	possibly damaging	Het
Gm10696	C	T	3: 94,176,316	G63R	probably damaging	Het
Gpc6	A	G	14: 117,624,539	N289S	possibly damaging	Het
Hoxb6	A	T	11: 96,300,711	Y153F	probably damaging	Het
Ints3	T	C	3: 90,415,507	T139A	probably benign	Het
Irf2bp2	A	G	8: 126,592,671	S256P	probably benign	Het
Klf4	G	T	4: 55,530,640	P148Q	probably damaging	Het
Loxl1	T	G	9: 58,312,537	H117P	probably damaging	Het
Lpl	A	G	8: 68,895,793	K225E	probably benign	Het
Lrba	T	A	3: 86,360,037	V1678D	probably damaging	Het
Med1	A	T	11: 98,163,904	F398Y	probably damaging	Het
Mfap2	T	C	4: 141,015,578	*186Q	probably null	Het
Mfsd3	T	C	15: 76,701,982	L105P	probably damaging	Het
Mlxip	T	G	5: 123,395,294	I122S	probably damaging	Het
Mmrn2	A	T	14: 34,396,398	Y107F	probably damaging	Het
Mtg1	G	T	7: 140,140,283	D88Y	probably null	Het
Mutyh	T	A	4: 116,817,935	S426R	probably benign	Het
Myo16	C	T	8: 10,476,094	T878I	probably damaging	Het
Myo9a	T	A	9: 59,861,472	Y912*	probably null	Het
Ncor1	A	C	11: 62,343,341	I669R	probably damaging	Het
Ndufs1	T	C	1: 63,163,776	I210V	probably benign	Het
Nek9	A	G	12: 85,310,420	C657R	probably damaging	Het
Noct	C	T	3: 51,250,021	T260I	probably damaging	Het
Nr1h4	A	T	10: 89,498,180	M102K	probably benign	Het
Obscn	G	A	11: 59,124,761	R1054C	possibly damaging	Het
Olfr1124	T	A	2: 87,435,152	F222I	probably benign	Het
Olfr352	C	A	2: 36,869,988	Q141K	probably benign	Het
Olfr47	A	G	6: 43,236,456	M283V	possibly damaging	Het
Olfr501-ps1	G	A	7: 108,508,243	M62I	probably damaging	Het
Olfr615	T	A	7: 103,561,317	I280N	possibly damaging	Het
Olfr619	A	T	7: 103,603,656	M1L	probably benign	Het
Otol1	C	A	3: 70,018,878	Q129K	probably benign	Het
Otx1	A	T	11: 21,998,532		probably null	Het
Pcdhac2	C	A	18: 37,146,251	N761K	probably damaging	Het
Pde1c	A	T	6: 56,150,624	M452K	probably damaging	Het
Phkg2	T	C	7: 127,573,941	Y24H	probably damaging	Het
Pigr	G	A	1: 130,841,817	D122N	probably benign	Het
Prg4	C	T	1: 150,460,681	C97Y	probably damaging	Het
Ptdss1	T	C	13: 66,945,288	V64A	probably benign	Het
Ralgapa2	T	C	2: 146,447,311	K324E	probably damaging	Het
Riiad1	T	C	3: 94,472,863	T42A	probably benign	Het
Rims2	T	C	15: 39,454,445	V640A	possibly damaging	Het
Rnpep	G	T	1: 135,263,032	S592Y	possibly damaging	Het
Scap	T	C	9: 110,378,390	L431P	probably damaging	Het
Siglec1	T	A	2: 131,073,361	I1437F	possibly damaging	Het
Skint1	T	C	4: 112,028,333		probably null	Het
Slc44a1	A	G	4: 53,543,644	E396G	probably damaging	Het
Slc4a2	T	C	5: 24,434,869	F521S	probably damaging	Het
Smarcc1	T	A	9: 110,175,061	S394R	probably damaging	Het
Socs1	A	G	16: 10,784,685	S63P	probably benign	Het
Sun1	T	G	5: 139,225,333	S20A	possibly damaging	Het
Tac4	A	T	11: 95,265,242	K50*	probably null	Het
Tcaf2	A	G	6: 42,642,640	I151T	probably damaging	Het
Tcf4	T	C	18: 69,681,769	V587A	probably damaging	Het
Ttc37	T	A	13: 76,182,936	M1495K	probably damaging	Het
Ttn	T	A	2: 76,740,909	K24801*	probably null	Het
Tuba3b	G	T	6: 145,621,273	M413I	possibly damaging	Het
Ufl1	C	T	4: 25,267,832	A280T	possibly damaging	Het
Ugt2b5	T	A	5: 87,139,673	I212L	probably benign	Het
Umodl1	A	G	17: 30,986,485	T685A	probably benign	Het
Uqcrc1	T	A	9: 108,944,810	V183D	probably damaging	Het
Ush2a	A	G	1: 188,910,720	N4093S	probably benign	Het
Vmn1r167	C	T	7: 23,505,228	S121N	probably damaging	Het
Vmn1r47	A	G	6: 90,022,758	S291G	possibly damaging	Het
Vmn2r108	A	G	17: 20,481,187	V17A	probably benign	Het
Vmn2r58	T	A	7: 41,837,752	H573L	probably benign	Het
Xirp1	C	T	9: 120,018,792	V342I	probably damaging	Het
Zfp462	A	G	4: 55,051,204	M2226V	possibly damaging	Het
Zfp467	G	A	6: 48,439,029	H230Y	probably damaging	Het
Zfp595	T	A	13: 67,316,401	K599N	probably damaging	Het
Zfp819	C	A	7: 43,617,296	T401K	probably benign	Het

Other mutations in Rfx5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01459:Rfx5	APN	3	94957775	unclassified	probably benign
IGL01478:Rfx5	APN	3	94958440	missense	possibly damaging	0.88
IGL02061:Rfx5	APN	3	94958481	missense	probably benign	0.03
IGL02152:Rfx5	APN	3	94957182	missense	probably damaging	1.00
IGL03395:Rfx5	APN	3	94957802	nonsense	probably null
chip	UTSW	3	94956355	missense	probably damaging	1.00
nonplussed	UTSW	3	94958961	missense	unknown
shrunken	UTSW	3	94955143	missense	probably damaging	1.00
R0098:Rfx5	UTSW	3	94958368	missense	probably damaging	1.00
R0098:Rfx5	UTSW	3	94958368	missense	probably damaging	1.00
R0505:Rfx5	UTSW	3	94956355	missense	probably damaging	1.00
R0681:Rfx5	UTSW	3	94956355	missense	probably damaging	1.00
R1342:Rfx5	UTSW	3	94958412	missense	probably benign	0.09
R1460:Rfx5	UTSW	3	94956325	missense	probably damaging	1.00
R1466:Rfx5	UTSW	3	94956303	missense	probably damaging	1.00
R1466:Rfx5	UTSW	3	94956303	missense	probably damaging	1.00
R1972:Rfx5	UTSW	3	94957292	missense	probably damaging	1.00
R2173:Rfx5	UTSW	3	94956716	splice site	probably null
R4808:Rfx5	UTSW	3	94958280	missense	probably benign	0.03
R4996:Rfx5	UTSW	3	94955815	missense	probably benign	0.27
R5104:Rfx5	UTSW	3	94955140	missense	probably benign	0.35
R5912:Rfx5	UTSW	3	94958718	unclassified	probably benign
R7097:Rfx5	UTSW	3	94956539	missense	probably damaging	1.00
R7186:Rfx5	UTSW	3	94958348	missense	probably benign	0.01
R7194:Rfx5	UTSW	3	94955143	missense	probably damaging	1.00
R7202:Rfx5	UTSW	3	94958961	missense	unknown
R7203:Rfx5	UTSW	3	94958876	missense	unknown
R7374:Rfx5	UTSW	3	94958742	missense	unknown
R7375:Rfx5	UTSW	3	94958742	missense	unknown
RF061:Rfx5	UTSW	3	94955759	missense	probably damaging	1.00
Z1176:Rfx5	UTSW	3	94955815	missense	probably benign	0.27

Predicted Primers

PCR Primer
(F):5'- TTCTGACAACCTGACATCGAG -3'
(R):5'- GGTTCTGAGCTATGCATCTCC -3'

Sequencing Primer
(F):5'- ACATCGAGTCAGCTGGTATG -3'
(R):5'- TGTCGGATTTCCAGAAACTGAG -3'

Posted On

2016-05-10