Mutagenetix > Incidental Mutation

Incidental Mutation 'R7202:Rfx5'

560354

Institutional Source

Beutler Lab

Gene Symbol

Rfx5

Ensembl Gene

ENSMUSG00000005774

Gene Name

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

Synonyms

MMRRC Submission

045280-MU

Accession Numbers

Essential gene?

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

Stock #

R7202 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

94861355-94868685 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 94866272 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Serine at position 524 (A524S)

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

unknown
Transcript: ENSMUST00000029772
AA Change: A524S

SMART Domains

Protein: ENSMUSP00000029772
Gene: ENSMUSG00000005774
AA Change: A524S

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

SMART Domains

Protein: ENSMUSP00000102874
Gene: ENSMUSG00000005774

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

Predicted Effect

probably benign
Transcript: ENSMUST00000107254

SMART Domains

Protein: ENSMUSP00000102875
Gene: ENSMUSG00000005774

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

Predicted Effect

unknown
Transcript: ENSMUST00000107255
AA Change: A524S

SMART Domains

Protein: ENSMUSP00000102876
Gene: ENSMUSG00000005774
AA Change: A524S

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

unknown
Transcript: ENSMUST00000107260
AA Change: A524S

SMART Domains

Protein: ENSMUSP00000102881
Gene: ENSMUSG00000005774
AA Change: A524S

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

unknown
Transcript: ENSMUST00000137088
AA Change: A524S

SMART Domains

Protein: ENSMUSP00000117963
Gene: ENSMUSG00000005774
AA Change: A524S

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

0.0869

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

Validation Efficiency

99% (74/75)

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: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca14	T	C	7: 119,917,236 (GRCm39)	I1467T	probably damaging	Het
Abtb3	A	G	10: 85,223,629 (GRCm39)	E146G	unknown	Het
Adgrf3	T	A	5: 30,409,378 (GRCm39)	K38*	probably null	Het
Ahdc1	T	A	4: 132,789,198 (GRCm39)	C146*	probably null	Het
Ahnak	A	T	19: 8,995,163 (GRCm39)	K5482N	probably damaging	Het
Arhgap23	C	T	11: 97,342,819 (GRCm39)	A367V	possibly damaging	Het
Arvcf	T	C	16: 18,223,948 (GRCm39)	S960P	probably damaging	Het
Asb14	C	A	14: 26,622,394 (GRCm39)	P74Q	probably benign	Het
Atad5	T	C	11: 79,980,601 (GRCm39)	V2A	probably damaging	Het
Baz2a	A	G	10: 127,954,428 (GRCm39)	I691M	possibly damaging	Het
Brca2	A	G	5: 150,455,819 (GRCm39)	T187A	probably benign	Het
Calr4	T	A	4: 109,101,254 (GRCm39)	N152K	possibly damaging	Het
Ccnb2	C	T	9: 70,318,128 (GRCm39)	A215T	probably damaging	Het
Cdh16	C	T	8: 105,340,780 (GRCm39)	D140N	unknown	Het
Ces1g	T	C	8: 94,029,595 (GRCm39)	T546A	probably benign	Het
Cfap74	G	T	4: 155,510,654 (GRCm39)		probably null	Het
Cfap91	T	C	16: 38,155,959 (GRCm39)	Y88C	probably benign	Het
Col5a1	G	T	2: 27,842,390 (GRCm39)	D422Y	unknown	Het
Cyp2c66	A	T	19: 39,130,348 (GRCm39)	Y61F	probably damaging	Het
Dnah12	G	A	14: 26,500,869 (GRCm39)		probably null	Het
Dnah6	A	G	6: 73,158,688 (GRCm39)		probably null	Het
Dop1a	T	G	9: 86,386,220 (GRCm39)		probably null	Het
Fam163a	A	G	1: 155,954,834 (GRCm39)	F106L	probably damaging	Het
Gfy	T	C	7: 44,827,596 (GRCm39)	T167A	probably benign	Het
Gm6525	A	T	3: 84,082,341 (GRCm39)	R87S	probably benign	Het
Gramd1c	C	A	16: 43,879,584 (GRCm39)	A19S	possibly damaging	Het
Herc2	T	C	7: 55,781,034 (GRCm39)	V1233A	probably damaging	Het
Hibch	G	A	1: 52,892,874 (GRCm39)		probably null	Het
Ibsp	A	T	5: 104,450,027 (GRCm39)	S9C	probably benign	Het
Il17ra	A	G	6: 120,452,572 (GRCm39)	I252V	probably benign	Het
Ino80	A	T	2: 119,204,918 (GRCm39)	M1536K	probably benign	Het
Ipo11	A	T	13: 107,012,078 (GRCm39)	L568Q	probably damaging	Het
Kcnu1	T	G	8: 26,409,609 (GRCm39)		probably null	Het
Kdm5b	T	G	1: 134,552,497 (GRCm39)	S1158A	probably benign	Het
Kmt2a	T	C	9: 44,759,012 (GRCm39)	T946A	probably benign	Het
Kmt2e	A	T	5: 23,697,292 (GRCm39)		probably benign	Het
Krba1	G	A	6: 48,389,261 (GRCm39)	V594M	probably damaging	Het
Lamb1	T	C	12: 31,374,314 (GRCm39)	L1559P	probably damaging	Het
Lig1	C	T	7: 13,025,175 (GRCm39)	P227S	probably benign	Het
Lims2	T	A	18: 32,090,017 (GRCm39)	D255E	probably benign	Het
Marchf3	C	T	18: 56,909,161 (GRCm39)	C208Y	probably benign	Het
Mei1	A	G	15: 81,976,843 (GRCm39)	E142G		Het
Melk	G	T	4: 44,351,106 (GRCm39)	R549L	probably benign	Het
Muc6	AGGCGCAGAAACCCTGGC	AGGC	7: 141,214,363 (GRCm39)		probably null	Het
Myorg	T	C	4: 41,498,268 (GRCm39)	Y454C	probably damaging	Het
Nae1	T	C	8: 105,250,215 (GRCm39)	Y226C	possibly damaging	Het
Nap1l1	T	C	10: 111,326,964 (GRCm39)	F175S	probably damaging	Het
Ndn	T	C	7: 61,998,709 (GRCm39)	L185P	probably damaging	Het
Ndst3	T	A	3: 123,465,388 (GRCm39)	I195F	possibly damaging	Het
Ndufaf1	A	T	2: 119,488,907 (GRCm39)	S206T	probably benign	Het
Nek10	C	A	14: 14,836,171 (GRCm38)	H131N	probably benign	Het
Obsl1	T	A	1: 75,466,360 (GRCm39)	D1456V	possibly damaging	Het
Or10a2	A	G	7: 106,673,448 (GRCm39)	N138D	probably benign	Het
Or10ak7	C	T	4: 118,791,215 (GRCm39)	V277I	probably benign	Het
Or52s6	T	A	7: 103,092,292 (GRCm39)	T13S	probably benign	Het
Otog	C	T	7: 45,937,474 (GRCm39)	L1728F	probably damaging	Het
Pcx	A	T	19: 4,652,361 (GRCm39)	M150L	possibly damaging	Het
Pole	A	G	5: 110,444,973 (GRCm39)	D443G	possibly damaging	Het
Prr14	G	T	7: 127,075,648 (GRCm39)	R552L	probably damaging	Het
Rasgrf1	T	G	9: 89,899,125 (GRCm39)	S1156A	possibly damaging	Het
Rfc4	T	A	16: 22,946,359 (GRCm39)		probably benign	Het
Ryr3	G	A	2: 112,596,664 (GRCm39)	P2497S	probably damaging	Het
Scg3	T	C	9: 75,590,992 (GRCm39)	T6A	probably benign	Het
Slc26a9	A	T	1: 131,690,526 (GRCm39)	D510V	possibly damaging	Het
Stpg3	A	G	2: 25,104,586 (GRCm39)	F10L	probably damaging	Het
Tmc5	T	A	7: 118,239,179 (GRCm39)	H357Q	possibly damaging	Het
Tmem40	A	T	6: 115,707,420 (GRCm39)	L253H	probably damaging	Het
Tmie	A	G	9: 110,696,632 (GRCm39)	V83A	probably damaging	Het
Uck2	A	T	1: 167,054,084 (GRCm39)	I218N	probably damaging	Het
Vtn	A	G	11: 78,391,626 (GRCm39)	D310G	possibly damaging	Het
Wdr49	A	T	3: 75,240,580 (GRCm39)	S430T	probably benign	Het
Wtip	A	G	7: 33,832,087 (GRCm39)	V133A	probably benign	Het
Zbtb9	T	A	17: 27,193,666 (GRCm39)	V357E	probably damaging	Het
Zfp953	G	A	13: 67,491,706 (GRCm39)	T82M	probably benign	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
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
R8919:Rfx5	UTSW	3	94,864,475 (GRCm39)	missense	probably damaging	1.00
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'- ATCCAAGACCTCATGACAAGGG -3'
(R):5'- GCTTCTTTGGCTTCCTGGGAAC -3'

Sequencing Primer
(F):5'- CCTCATGACAAGGGTATCAAAAG -3'
(R):5'- TTTGGAAACAGCACCATCTTGC -3'

Posted On

2019-06-26