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

Accession Numbers

Essential gene?

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

Stock #

R8919 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

94954075-94961561 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 94957164 bp (GRCm38)

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
1700061G19Rik	A	C	17: 56,882,218	I209L	probably benign	Het
Aadat	C	T	8: 60,540,124	T373I	possibly damaging	Het
Abca13	T	C	11: 9,291,653	L1172P	possibly damaging	Het
Abcg2	A	G	6: 58,684,341	Y459C	probably benign	Het
AC125199.3	T	C	16: 88,812,173	N4D	possibly damaging	Het
Acad8	A	G	9: 26,999,489	M3T	probably benign	Het
Adcyap1r1	C	T	6: 55,497,095	T472I	probably damaging	Het
Ank3	A	T	10: 70,004,841	K1890N	possibly damaging	Het
Asic1	G	A	15: 99,671,945	C49Y	probably benign	Het
Atp1a1	T	C	3: 101,591,231	N215S	probably damaging	Het
C87436	A	G	6: 86,445,792	Y116C	probably damaging	Het
Car5a	T	C	8: 121,944,780	D5G	probably benign	Het
Ccdc169	T	C	3: 55,150,947		probably null	Het
Ccdc93	A	G	1: 121,499,241	R586G	probably damaging	Het
Cep295	A	G	9: 15,326,711	V131A	probably damaging	Het
Cox5a	A	G	9: 57,529,046	D60G	possibly damaging	Het
Cpne6	A	T	14: 55,512,647	E78D	probably benign	Het
Cyp2u1	T	C	3: 131,295,465	E390G	probably damaging	Het
Dab2	C	A	15: 6,435,790	N707K		Het
Dock10	A	T	1: 80,505,430	D2101E	probably benign	Het
Duoxa2	G	A	2: 122,301,876		probably null	Het
Eif4a3	T	C	11: 119,299,932	D22G	probably benign	Het
Fam160a2	T	C	7: 105,388,270	T369A	possibly damaging	Het
Fubp3	A	G	2: 31,592,464		probably null	Het
Gm10330	A	G	12: 23,779,886	L98P	probably benign	Het
Gm5108	A	G	5: 67,976,956	*102W	probably null	Het
Gpr149	A	C	3: 62,531,057	S560A	probably damaging	Het
Haspin	T	C	11: 73,136,604	D553G	probably benign	Het
Hsf1	C	T	15: 76,497,851	H104Y	probably benign	Het
Ifi203	T	C	1: 173,928,928	T430A	unknown	Het
Itih2	G	A	2: 10,098,011	Q771*	probably null	Het
Kazald1	T	A	19: 45,076,956	L92Q	probably damaging	Het
Krt19	T	C	11: 100,141,154	E324G	probably damaging	Het
Lrrc28	A	T	7: 67,619,085	V79E	possibly damaging	Het
Ltn1	T	A	16: 87,381,493	Q1616L	probably damaging	Het
Mdc1	A	G	17: 35,847,951	K408E	probably benign	Het
Nalcn	A	T	14: 123,323,872	M738K	probably benign	Het
Ncoa4	T	C	14: 32,172,891	L125P	probably damaging	Het
Ncor2	G	T	5: 125,029,189	R810S		Het
Neb	C	T	2: 52,237,129	G348D		Het
Nfat5	T	A	8: 107,368,596	F1156L	probably damaging	Het
Oit3	G	A	10: 59,441,646	T13I	unknown	Het
Olfr1135	A	C	2: 87,672,223	L48W	probably damaging	Het
Olfr1404	T	C	1: 173,216,497	I282T	probably damaging	Het
Olfr490	A	G	7: 108,287,082	F15L	probably damaging	Het
Olfr552	T	A	7: 102,604,504	I50N	probably damaging	Het
Olfr785	G	T	10: 129,410,213	M282I	probably benign	Het
Opa1	A	C	16: 29,605,522	Q230P	probably damaging	Het
Papd7	G	T	13: 69,503,709	T531N	possibly damaging	Het
Parpbp	T	C	10: 88,110,327	H410R	probably null	Het
Pex5l	A	G	3: 32,953,184	V481A	probably damaging	Het
Plekhh3	C	A	11: 101,166,399	R344L	probably benign	Het
Prrc2b	T	C	2: 32,214,941	V1477A	probably benign	Het
Ptp4a2	G	A	4: 129,845,152	G94S	possibly damaging	Het
Ptprk	T	A	10: 28,483,207	Y598*	probably null	Het
Rnase2b	A	G	14: 51,162,890	T143A	possibly damaging	Het
Scn1a	A	G	2: 66,337,986	V92A	probably benign	Het
Shank2	C	A	7: 144,411,528	P958T	probably damaging	Het
Slc13a1	A	G	6: 24,108,195	I294T	probably damaging	Het
Slc4a8	A	T	15: 100,814,540	E1084D	probably benign	Het
Smurf1	T	A	5: 144,883,612	R549*	probably null	Het
Sprr2b	T	C	3: 92,317,725	C93R	unknown	Het
Tcn2	G	T	11: 3,923,569	S259Y	probably damaging	Het
Tex43	T	C	18: 56,592,465	F66L	probably damaging	Het
Tle1	A	G	4: 72,158,288	S168P	possibly damaging	Het
Tnfrsf1b	C	T	4: 145,223,580	G264D	probably damaging	Het
Tnks2	T	A	19: 36,845,688	N118K	probably damaging	Het
Topaz1	G	T	9: 122,797,865		probably benign	Het
Traf3ip1	A	G	1: 91,516,074		probably benign	Het
Ttk	A	G	9: 83,839,269	E69G	probably damaging	Het
Tulp3	T	C	6: 128,334,003	D87G	probably benign	Het
Usp38	C	T	8: 80,981,850	G1033D	probably damaging	Het
Usp44	T	A	10: 93,857,913	N707K	probably benign	Het
Vipas39	T	A	12: 87,259,084	R112*	probably null	Het
Vmn1r185	A	C	7: 26,611,781	S100A	probably damaging	Het
Vmn1r209	T	C	13: 22,806,053	M156V	probably benign	Het
Vmn1r3	G	A	4: 3,184,863	T148I	probably benign	Het
Wdr41	G	A	13: 95,015,112	R260H	probably benign	Het
Wdr90	G	A	17: 25,857,172	R104C		Het
Wnk2	A	T	13: 49,068,235	H1183Q	possibly damaging	Het
Zfp667	A	T	7: 6,305,257	H308L	possibly damaging	Het
Zfp952	A	G	17: 33,001,654	N18D	possibly 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
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
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'- TCAAATGGGTGGGACTGCAG -3'
(R):5'- TTCTGGAAGGCCTAGAGAGC -3'

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

Posted On

2021-08-02