Mutagenetix > Incidental Mutation

Incidental Mutation 'R1466:Rfx5'

201150

Institutional Source

Beutler Lab

Gene Symbol

Rfx5

Ensembl Gene

ENSMUSG00000005774

Gene Name

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

Synonyms

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.160) question?

Stock #

R1466 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

94954075-94961561 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 94956303 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Asparagine at position 88 (Y88N)

Ref Sequence

ENSEMBL: ENSMUSP00000117963 (fasta)

Gene Model

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

AlphaFold

Q9JL61

Predicted Effect

probably damaging
Transcript: ENSMUST00000029772
AA Change: Y88N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000029772
Gene: ENSMUSG00000005774
AA Change: Y88N

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 damaging
Transcript: ENSMUST00000107253
AA Change: Y88N

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000102874
Gene: ENSMUSG00000005774
AA Change: Y88N

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000107254
AA Change: Y88N

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000102875
Gene: ENSMUSG00000005774
AA Change: Y88N

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000107255
AA Change: Y88N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000102876
Gene: ENSMUSG00000005774
AA Change: Y88N

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 damaging
Transcript: ENSMUST00000107260
AA Change: Y88N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000102881
Gene: ENSMUSG00000005774
AA Change: Y88N

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 damaging
Transcript: ENSMUST00000132393
AA Change: Y88N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000117999
Gene: ENSMUSG00000005774
AA Change: Y88N

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000137088
AA Change: Y88N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000117963
Gene: ENSMUSG00000005774
AA Change: Y88N

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

possibly damaging
Transcript: ENSMUST00000142311
AA Change: Y88N

PolyPhen 2 Score 0.893 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000119704
Gene: ENSMUSG00000005774
AA Change: Y88N

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142708

Predicted Effect

probably benign
Transcript: ENSMUST00000144132

Predicted Effect

possibly damaging
Transcript: ENSMUST00000145031
AA Change: Y88N

PolyPhen 2 Score 0.950 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000118099
Gene: ENSMUSG00000005774
AA Change: Y88N

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

Predicted Effect

probably benign
Transcript: ENSMUST00000145472

Predicted Effect

possibly damaging
Transcript: ENSMUST00000147237
AA Change: Y88N

PolyPhen 2 Score 0.872 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000118586
Gene: ENSMUSG00000005774
AA Change: Y88N

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

probably damaging
Transcript: ENSMUST00000152869
AA Change: Y88N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000121157
Gene: ENSMUSG00000005774
AA Change: Y88N

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148803

Coding Region Coverage

1x: 97.4%
3x: 96.7%
10x: 94.7%
20x: 90.4%

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: 134 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110012J17Rik	T	A	17: 66,380,435	D492V	probably damaging	Het
Abca13	T	C	11: 9,570,536		probably benign	Het
Abcg8	G	C	17: 84,686,727		probably benign	Het
Abhd15	C	T	11: 77,515,410	A71V	probably damaging	Het
AC167973.1	A	T	9: 43,265,352		noncoding transcript	Het
Adamts12	T	C	15: 11,311,359	F1234S	probably benign	Het
Ahnak	A	G	19: 9,015,875	D4841G	probably damaging	Het
Akap13	T	C	7: 75,729,049	S2095P	possibly damaging	Het
Ampd2	T	C	3: 108,080,337		probably null	Het
Arhgef17	G	T	7: 100,929,659	P694Q	possibly damaging	Het
Arrdc1	T	C	2: 24,925,795	I398V	probably benign	Het
Ash1l	T	C	3: 89,052,065	Y2250H	probably damaging	Het
Aspg	A	G	12: 112,121,852	N385D	probably benign	Het
Atxn3	G	A	12: 101,926,499	R319C	possibly damaging	Het
BC005561	T	A	5: 104,518,257	I215N	probably damaging	Het
Brca2	G	A	5: 150,552,258	A2478T	probably damaging	Het
Btrc	T	A	19: 45,513,382		probably benign	Het
C1s1	C	T	6: 124,531,131	C633Y	probably damaging	Het
C8g	C	T	2: 25,500,216	A6T	probably benign	Het
Capza2	T	C	6: 17,657,159		probably benign	Het
Cbl	A	T	9: 44,154,244	V706E	probably benign	Het
Ccdc84	A	T	9: 44,413,680		probably benign	Het
Cfhr1	C	T	1: 139,557,574	E45K	probably benign	Het
Chd7	G	A	4: 8,840,561		probably null	Het
Chek1	G	T	9: 36,725,857	A2E	probably damaging	Het
Clcn2	G	A	16: 20,712,552		probably benign	Het
Cndp2	G	A	18: 84,677,315		probably benign	Het
Cntnap1	C	A	11: 101,180,360	F366L	probably damaging	Het
Col5a1	G	T	2: 28,003,846		probably benign	Het
Corin	C	T	5: 72,302,790		probably null	Het
Crb2	T	C	2: 37,783,388	Y99H	probably damaging	Het
Csf3r	T	A	4: 126,031,932		probably benign	Het
Ctdspl2	G	A	2: 122,003,929	R332K	probably benign	Het
Ctnnbl1	C	T	2: 157,799,417		probably benign	Het
Cym	G	A	3: 107,213,458	T277I	probably damaging	Het
Cyp2d11	C	T	15: 82,391,735	C215Y	probably benign	Het
Dido1	G	A	2: 180,662,328	P1261L	probably damaging	Het
Dnah10	T	A	5: 124,763,096	Y1265N	probably benign	Het
Dtx3l	G	A	16: 35,932,728	L503F	probably damaging	Het
Eda	T	A	X: 100,392,392		probably benign	Homo
Efhb	A	G	17: 53,437,178	F462L	probably damaging	Het
Enpep	T	A	3: 129,319,448	T203S	probably damaging	Het
Exd1	G	A	2: 119,520,734		probably benign	Het
Fam184b	G	A	5: 45,580,509		probably benign	Het
Fam20b	T	C	1: 156,686,188		probably benign	Het
Fat3	A	C	9: 16,375,482	V915G	probably damaging	Het
Fbln7	A	G	2: 128,877,429	T49A	probably benign	Het
Fcho1	C	T	8: 71,712,560	A418T	probably benign	Het
Fgf14	T	A	14: 124,676,539	K60M	probably benign	Het
Galnt4	A	G	10: 99,108,709	R99G	probably benign	Het
Gimap4	C	A	6: 48,691,282	Q196K	probably benign	Het
Glcci1	C	T	6: 8,537,964	T6I	probably damaging	Het
Gm10110	A	T	14: 89,898,075		noncoding transcript	Het
Gm4884	A	G	7: 41,043,128	K174E	probably damaging	Het
Gm6583	C	T	5: 112,354,764	G358D	probably benign	Het
Grip2	A	T	6: 91,788,443	D19E	probably damaging	Het
Grk4	T	C	5: 34,694,750	S113P	probably benign	Het
Hectd3	G	A	4: 116,996,566	E220K	probably damaging	Het
Helz2	G	A	2: 181,236,297	P903S	probably damaging	Het
Hydin	T	A	8: 110,532,953	V2519E	possibly damaging	Het
Igf2r	A	T	17: 12,717,269		probably benign	Het
Ints11	G	A	4: 155,888,110		probably null	Het
Kif1a	A	G	1: 93,054,929	W718R	possibly damaging	Het
Kif1b	A	T	4: 149,223,252	Y839N	probably damaging	Het
Kif20b	T	A	19: 34,950,599	V1047D	probably benign	Het
Klhl23	T	C	2: 69,833,888	I527T	probably damaging	Het
Klra10	T	A	6: 130,279,315	R125S	probably damaging	Het
Klra10	T	C	6: 130,279,431	N87D	probably damaging	Het
Lars	G	A	18: 42,210,050	R1101C	probably damaging	Het
Lcn4	G	A	2: 26,668,576	P166L	probably damaging	Het
Letmd1	T	A	15: 100,472,542		probably null	Het
Lrrc27	A	G	7: 139,230,308		probably benign	Het
Map4k2	G	T	19: 6,341,917	W87L	probably damaging	Het
Mccc1	A	G	3: 35,974,286	V457A	probably benign	Het
Mdn1	T	A	4: 32,730,788	S2886T	probably benign	Het
Mgat4a	A	T	1: 37,464,406		probably benign	Het
Mmp1b	A	T	9: 7,384,779		probably benign	Het
Mroh2b	G	T	15: 4,925,684	D720Y	probably damaging	Het
Mrpl24	T	A	3: 87,921,928	Y21*	probably null	Het
Mrps35	C	T	6: 147,055,984	T169M	probably damaging	Het
Muc2	A	G	7: 141,748,974	Y457C	probably damaging	Het
Muc4	G	A	16: 32,753,595	G1157D	probably benign	Het
Myg1	T	A	15: 102,337,390	L275Q	probably damaging	Het
Naga	T	A	15: 82,334,788	M237L	probably null	Het
Nek1	C	T	8: 61,125,136		probably benign	Het
Oc90	T	A	15: 65,897,720	Y96F	probably damaging	Het
Olfr1029	T	A	2: 85,975,995	F251I	probably damaging	Het
Olfr103	A	T	17: 37,336,956	L92H	probably benign	Het
Olfr1253	C	T	2: 89,752,267	C187Y	probably damaging	Het
Olfr46	A	G	7: 140,610,969	I268V	probably benign	Het
Olfr522	A	G	7: 140,162,203	V249A	probably damaging	Het
Orc4	A	T	2: 48,909,494	C324S	possibly damaging	Het
Pald1	T	C	10: 61,348,525		probably benign	Het
Paox	A	G	7: 140,129,281		probably benign	Het
Pcdh10	T	G	3: 45,379,974	L241R	probably damaging	Het
Pdzrn4	T	C	15: 92,770,537	S857P	probably benign	Het
Plec	C	T	15: 76,185,908	E1000K	possibly damaging	Het
Plvap	A	T	8: 71,508,481	V149D	probably benign	Het
Ppef1	C	A	X: 160,625,674		probably null	Homo
Prkaa1	C	A	15: 5,178,798	P507T	probably benign	Het
Psmd2	A	G	16: 20,657,965		probably benign	Het
Ptch1	A	G	13: 63,524,969	Y804H	probably benign	Het
R3hdm2	A	G	10: 127,476,690	I434V	probably benign	Het
Rbm28	G	A	6: 29,155,017		probably benign	Het
Rnase2b	A	T	14: 51,162,839	K126*	probably null	Het
Rpl3l	A	G	17: 24,730,871	I15V	probably benign	Het
Saal1	G	T	7: 46,702,545		probably null	Het
Sbpl	A	C	17: 23,953,254	D230E	unknown	Het
Scn10a	T	C	9: 119,666,490	Y322C	probably damaging	Het
Sec16a	A	T	2: 26,431,157	Y1308N	probably damaging	Het
Sis	A	T	3: 72,932,060	D824E	possibly damaging	Het
Slc25a36	A	G	9: 97,080,355	F194L	probably damaging	Het
Slc27a4	T	A	2: 29,811,190	V331E	probably damaging	Het
Slc7a11	G	T	3: 50,381,073		probably null	Het
Slco4c1	A	T	1: 96,841,172	S322T	probably damaging	Het
Smarcc2	A	T	10: 128,474,245	T376S	probably damaging	Het
Srebf1	C	T	11: 60,200,702	R999H	probably benign	Het
St3gal3	A	C	4: 118,107,662	M1R	probably null	Het
Syp	A	T	X: 7,648,705		probably benign	Homo
Tas1r2	A	G	4: 139,669,411	D687G	probably damaging	Het
Tekt4	A	T	17: 25,472,074	Q118L	probably benign	Het
Tph2	T	C	10: 115,079,695	N480S	probably benign	Het
Tsc2	A	T	17: 24,608,973	M839K	probably damaging	Het
Ttc22	T	C	4: 106,622,780	F77S	probably damaging	Het
Uaca	C	T	9: 60,854,321	A205V	possibly damaging	Het
Ubp1	T	G	9: 113,944,835		probably benign	Het
Uhmk1	A	T	1: 170,208,653		probably null	Het
Usp17lc	A	G	7: 103,418,941	H481R	possibly damaging	Het
Vwa3a	A	G	7: 120,768,165	Y181C	probably damaging	Het
Wdr26	C	T	1: 181,185,934		probably benign	Het
Wfikkn2	G	A	11: 94,238,895	T140I	probably damaging	Het
Zfp704	G	T	3: 9,447,348	T288N	possibly damaging	Het
Zfp93	T	C	7: 24,276,096	V502A	probably damaging	Het
Zzef1	C	T	11: 72,924,679	P2942S	probably damaging	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
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
R4993:Rfx5	UTSW	3	94955815	missense	probably benign	0.27
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
R8919:Rfx5	UTSW	3	94957164	missense	probably damaging	1.00
R9562:Rfx5	UTSW	3	94959328	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'- GGACAACGACAAGCTGTACCTCTAC -3'
(R):5'- CTCTCGCAGTACTTTCTGAGTGAGC -3'

Sequencing Primer
(F):5'- acaccactctctgacctcc -3'
(R):5'- TTTCTGAGTGAGCAGAAGGG -3'

Posted On

2014-05-23