Mutagenetix > Incidental Mutation

Incidental Mutation 'R8919:Rfx5'

679105

Institutional Source

Beutler Lab

Gene Symbol

Rfx5

Ensembl Gene

ENSMUSG00000005774

Gene Name

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

Synonyms

MMRRC Submission

068706-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.242) question?

Stock #

R8919 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

94861355-94868685 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 94864475 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Asparagine at position 207 (T207N)

Ref Sequence

ENSEMBL: ENSMUSP00000029772 (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: T207N

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

SMART Domains

Protein: ENSMUSP00000029772
Gene: ENSMUSG00000005774
AA Change: T207N

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: T207N

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

SMART Domains

Protein: ENSMUSP00000102874
Gene: ENSMUSG00000005774
AA Change: T207N

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000107254
AA Change: T207N

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

SMART Domains

Protein: ENSMUSP00000102875
Gene: ENSMUSG00000005774
AA Change: T207N

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000107255
AA Change: T207N

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

SMART Domains

Protein: ENSMUSP00000102876
Gene: ENSMUSG00000005774
AA Change: T207N

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: T207N

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

SMART Domains

Protein: ENSMUSP00000102881
Gene: ENSMUSG00000005774
AA Change: T207N

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

probably benign
Transcript: ENSMUST00000132393

SMART Domains

Protein: ENSMUSP00000117999
Gene: ENSMUSG00000005774

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000137088
AA Change: T207N

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

SMART Domains

Protein: ENSMUSP00000117963
Gene: ENSMUSG00000005774
AA Change: T207N

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: ENSMUST00000140331

Predicted Effect

probably benign
Transcript: ENSMUST00000142311

SMART Domains

Protein: ENSMUSP00000119704
Gene: ENSMUSG00000005774

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

Predicted Effect

probably benign
Transcript: ENSMUST00000144132

Predicted Effect

probably benign
Transcript: ENSMUST00000145031

SMART Domains

Protein: ENSMUSP00000118099
Gene: ENSMUSG00000005774

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

Predicted Effect

probably benign
Transcript: ENSMUST00000145472

Predicted Effect

probably benign
Transcript: ENSMUST00000147237

SMART Domains

Protein: ENSMUSP00000118586
Gene: ENSMUSG00000005774

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 benign
Transcript: ENSMUST00000152869

SMART Domains

Protein: ENSMUSP00000121157
Gene: ENSMUSG00000005774

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

Meta Mutation Damage Score

0.1679

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

99% (81/82)

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadat	C	T	8: 60,993,158 (GRCm39)	T373I	possibly damaging	Het
Abca13	T	C	11: 9,241,653 (GRCm39)	L1172P	possibly damaging	Het
Abcg2	A	G	6: 58,661,326 (GRCm39)	Y459C	probably benign	Het
AC125199.3	T	C	16: 88,609,061 (GRCm39)	N4D	possibly damaging	Het
Acad8	A	G	9: 26,910,785 (GRCm39)	M3T	probably benign	Het
Acsbg3	A	C	17: 57,189,218 (GRCm39)	I209L	probably benign	Het
Adcyap1r1	C	T	6: 55,474,080 (GRCm39)	T472I	probably damaging	Het
Ank3	A	T	10: 69,840,671 (GRCm39)	K1890N	possibly damaging	Het
Asic1	G	A	15: 99,569,826 (GRCm39)	C49Y	probably benign	Het
Atp1a1	T	C	3: 101,498,547 (GRCm39)	N215S	probably damaging	Het
C87436	A	G	6: 86,422,774 (GRCm39)	Y116C	probably damaging	Het
Car5a	T	C	8: 122,671,519 (GRCm39)	D5G	probably benign	Het
Ccdc169	T	C	3: 55,058,368 (GRCm39)		probably null	Het
Ccdc93	A	G	1: 121,426,970 (GRCm39)	R586G	probably damaging	Het
Cep295	A	G	9: 15,238,007 (GRCm39)	V131A	probably damaging	Het
Cox5a	A	G	9: 57,436,329 (GRCm39)	D60G	possibly damaging	Het
Cpne6	A	T	14: 55,750,104 (GRCm39)	E78D	probably benign	Het
Cyp2u1	T	C	3: 131,089,114 (GRCm39)	E390G	probably damaging	Het
Dab2	C	A	15: 6,465,271 (GRCm39)	N707K		Het
Dock10	A	T	1: 80,483,147 (GRCm39)	D2101E	probably benign	Het
Duoxa2	G	A	2: 122,132,357 (GRCm39)		probably null	Het
Eif4a3	T	C	11: 119,190,758 (GRCm39)	D22G	probably benign	Het
Fhip1b	T	C	7: 105,037,477 (GRCm39)	T369A	possibly damaging	Het
Fubp3	A	G	2: 31,482,476 (GRCm39)		probably null	Het
Gm10330	A	G	12: 23,829,887 (GRCm39)	L98P	probably benign	Het
Gm5108	A	G	5: 68,134,299 (GRCm39)	*102W	probably null	Het
Gpr149	A	C	3: 62,438,478 (GRCm39)	S560A	probably damaging	Het
Haspin	T	C	11: 73,027,430 (GRCm39)	D553G	probably benign	Het
Hsf1	C	T	15: 76,382,051 (GRCm39)	H104Y	probably benign	Het
Ifi203	T	C	1: 173,756,494 (GRCm39)	T430A	unknown	Het
Itih2	G	A	2: 10,102,822 (GRCm39)	Q771*	probably null	Het
Kazald1	T	A	19: 45,065,395 (GRCm39)	L92Q	probably damaging	Het
Krt19	T	C	11: 100,031,980 (GRCm39)	E324G	probably damaging	Het
Lrrc28	A	T	7: 67,268,833 (GRCm39)	V79E	possibly damaging	Het
Ltn1	T	A	16: 87,178,381 (GRCm39)	Q1616L	probably damaging	Het
Mdc1	A	G	17: 36,158,843 (GRCm39)	K408E	probably benign	Het
Nalcn	A	T	14: 123,561,284 (GRCm39)	M738K	probably benign	Het
Ncoa4	T	C	14: 31,894,848 (GRCm39)	L125P	probably damaging	Het
Ncor2	G	T	5: 125,106,253 (GRCm39)	R810S		Het
Neb	C	T	2: 52,127,141 (GRCm39)	G348D		Het
Nfat5	T	A	8: 108,095,228 (GRCm39)	F1156L	probably damaging	Het
Oit3	G	A	10: 59,277,468 (GRCm39)	T13I	unknown	Het
Opa1	A	C	16: 29,424,340 (GRCm39)	Q230P	probably damaging	Het
Or10j3b	T	C	1: 173,044,064 (GRCm39)	I282T	probably damaging	Het
Or52k2	T	A	7: 102,253,711 (GRCm39)	I50N	probably damaging	Het
Or5p66	A	G	7: 107,886,289 (GRCm39)	F15L	probably damaging	Het
Or5w12	A	C	2: 87,502,567 (GRCm39)	L48W	probably damaging	Het
Or6c5b	G	T	10: 129,246,082 (GRCm39)	M282I	probably benign	Het
Parpbp	T	C	10: 87,946,189 (GRCm39)	H410R	probably null	Het
Pex5l	A	G	3: 33,007,333 (GRCm39)	V481A	probably damaging	Het
Plekhh3	C	A	11: 101,057,225 (GRCm39)	R344L	probably benign	Het
Prrc2b	T	C	2: 32,104,953 (GRCm39)	V1477A	probably benign	Het
Ptp4a2	G	A	4: 129,738,945 (GRCm39)	G94S	possibly damaging	Het
Ptprk	T	A	10: 28,359,203 (GRCm39)	Y598*	probably null	Het
Rnase2b	A	G	14: 51,400,347 (GRCm39)	T143A	possibly damaging	Het
Scn1a	A	G	2: 66,168,330 (GRCm39)	V92A	probably benign	Het
Shank2	C	A	7: 143,965,265 (GRCm39)	P958T	probably damaging	Het
Slc13a1	A	G	6: 24,108,194 (GRCm39)	I294T	probably damaging	Het
Slc4a8	A	T	15: 100,712,421 (GRCm39)	E1084D	probably benign	Het
Smurf1	T	A	5: 144,820,422 (GRCm39)	R549*	probably null	Het
Spmip10	T	C	18: 56,725,537 (GRCm39)	F66L	probably damaging	Het
Sprr2b	T	C	3: 92,225,032 (GRCm39)	C93R	unknown	Het
Tcn2	G	T	11: 3,873,569 (GRCm39)	S259Y	probably damaging	Het
Tent4a	G	T	13: 69,651,828 (GRCm39)	T531N	possibly damaging	Het
Tle1	A	G	4: 72,076,525 (GRCm39)	S168P	possibly damaging	Het
Tnfrsf1b	C	T	4: 144,950,150 (GRCm39)	G264D	probably damaging	Het
Tnks2	T	A	19: 36,823,088 (GRCm39)	N118K	probably damaging	Het
Topaz1	G	T	9: 122,626,930 (GRCm39)		probably benign	Het
Traf3ip1	A	G	1: 91,443,796 (GRCm39)		probably benign	Het
Ttk	A	G	9: 83,721,322 (GRCm39)	E69G	probably damaging	Het
Tulp3	T	C	6: 128,310,966 (GRCm39)	D87G	probably benign	Het
Usp38	C	T	8: 81,708,479 (GRCm39)	G1033D	probably damaging	Het
Usp44	T	A	10: 93,693,775 (GRCm39)	N707K	probably benign	Het
Vipas39	T	A	12: 87,305,858 (GRCm39)	R112*	probably null	Het
Vmn1r185	A	C	7: 26,311,206 (GRCm39)	S100A	probably damaging	Het
Vmn1r209	T	C	13: 22,990,223 (GRCm39)	M156V	probably benign	Het
Vmn1r3	G	A	4: 3,184,863 (GRCm39)	T148I	probably benign	Het
Wdr41	G	A	13: 95,151,620 (GRCm39)	R260H	probably benign	Het
Wdr90	G	A	17: 26,076,146 (GRCm39)	R104C		Het
Wnk2	A	T	13: 49,221,711 (GRCm39)	H1183Q	possibly damaging	Het
Zfp667	A	T	7: 6,308,256 (GRCm39)	H308L	possibly damaging	Het
Zfp952	A	G	17: 33,220,628 (GRCm39)	N18D	possibly damaging	Het

Other mutations in Rfx5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01459:Rfx5	APN	3	94,865,086 (GRCm39)	unclassified	probably benign
IGL01478:Rfx5	APN	3	94,865,751 (GRCm39)	missense	possibly damaging	0.88
IGL02061:Rfx5	APN	3	94,865,792 (GRCm39)	missense	probably benign	0.03
IGL02152:Rfx5	APN	3	94,864,493 (GRCm39)	missense	probably damaging	1.00
IGL03395:Rfx5	APN	3	94,865,113 (GRCm39)	nonsense	probably null
chip	UTSW	3	94,863,666 (GRCm39)	missense	probably damaging	1.00
nonplussed	UTSW	3	94,866,272 (GRCm39)	missense	unknown
shrunken	UTSW	3	94,862,454 (GRCm39)	missense	probably damaging	1.00
R0098:Rfx5	UTSW	3	94,865,679 (GRCm39)	missense	probably damaging	1.00
R0098:Rfx5	UTSW	3	94,865,679 (GRCm39)	missense	probably damaging	1.00
R0505:Rfx5	UTSW	3	94,863,666 (GRCm39)	missense	probably damaging	1.00
R0681:Rfx5	UTSW	3	94,863,666 (GRCm39)	missense	probably damaging	1.00
R1342:Rfx5	UTSW	3	94,865,723 (GRCm39)	missense	probably benign	0.09
R1460:Rfx5	UTSW	3	94,863,636 (GRCm39)	missense	probably damaging	1.00
R1466:Rfx5	UTSW	3	94,863,614 (GRCm39)	missense	probably damaging	1.00
R1466:Rfx5	UTSW	3	94,863,614 (GRCm39)	missense	probably damaging	1.00
R1972:Rfx5	UTSW	3	94,864,603 (GRCm39)	missense	probably damaging	1.00
R2173:Rfx5	UTSW	3	94,864,027 (GRCm39)	splice site	probably null
R4808:Rfx5	UTSW	3	94,865,591 (GRCm39)	missense	probably benign	0.03
R4993:Rfx5	UTSW	3	94,863,126 (GRCm39)	missense	probably benign	0.27
R4996:Rfx5	UTSW	3	94,863,126 (GRCm39)	missense	probably benign	0.27
R5104:Rfx5	UTSW	3	94,862,451 (GRCm39)	missense	probably benign	0.35
R5912:Rfx5	UTSW	3	94,866,029 (GRCm39)	unclassified	probably benign
R7097:Rfx5	UTSW	3	94,863,850 (GRCm39)	missense	probably damaging	1.00
R7186:Rfx5	UTSW	3	94,865,659 (GRCm39)	missense	probably benign	0.01
R7194:Rfx5	UTSW	3	94,862,454 (GRCm39)	missense	probably damaging	1.00
R7202:Rfx5	UTSW	3	94,866,272 (GRCm39)	missense	unknown
R7203:Rfx5	UTSW	3	94,866,187 (GRCm39)	missense	unknown
R7374:Rfx5	UTSW	3	94,866,053 (GRCm39)	missense	unknown
R7375:Rfx5	UTSW	3	94,866,053 (GRCm39)	missense	unknown
R9562:Rfx5	UTSW	3	94,866,639 (GRCm39)	missense	unknown
RF061:Rfx5	UTSW	3	94,863,070 (GRCm39)	missense	probably damaging	1.00
Z1176:Rfx5	UTSW	3	94,863,126 (GRCm39)	missense	probably benign	0.27

Predicted Primers

PCR Primer
(F):5'- TCAAATGGGTGGGACTGCAG -3'
(R):5'- TTCTGGAAGGCCTAGAGAGC -3'

Sequencing Primer
(F):5'- AGGCTACTGCTGTCCTCAG -3'
(R):5'- CATAGTGAGACCCTGTGTACATC -3'

Posted On

2021-08-02