Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01478:Rfx5'

88522

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Rfx5

Ensembl Gene

ENSMUSG00000005774

Gene Name

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

Synonyms

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.274) question?

Stock #

IGL01478

Quality Score

Status

Chromosome

Chromosomal Location

94861355-94868685 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 94865751 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 350 (V350A)

Ref Sequence

ENSEMBL: ENSMUSP00000117963 (fasta)

Gene Model

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

AlphaFold

Q9JL61

Predicted Effect

possibly damaging
Transcript: ENSMUST00000029772
AA Change: V350A

PolyPhen 2 Score 0.883 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000029772
Gene: ENSMUSG00000005774
AA Change: V350A

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

possibly damaging
Transcript: ENSMUST00000107255
AA Change: V350A

PolyPhen 2 Score 0.883 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000102876
Gene: ENSMUSG00000005774
AA Change: V350A

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

possibly damaging
Transcript: ENSMUST00000107260
AA Change: V350A

PolyPhen 2 Score 0.883 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000102881
Gene: ENSMUSG00000005774
AA Change: V350A

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

SMART Domains

Protein: ENSMUSP00000117999
Gene: ENSMUSG00000005774

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000137088
AA Change: V350A

PolyPhen 2 Score 0.883 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000117963
Gene: ENSMUSG00000005774
AA Change: V350A

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

noncoding transcript
Transcript: ENSMUST00000142708

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148803

Predicted Effect

probably benign
Transcript: ENSMUST00000144132

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

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: 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: 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

Coding Region Coverage

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: 27 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930590J08Rik	A	G	6: 91,911,590 (GRCm39)	T613A	probably benign	Het
Cdh16	G	T	8: 105,341,120 (GRCm39)		probably benign	Het
Epn2	A	G	11: 61,413,912 (GRCm39)	S419P	probably benign	Het
Eral1	A	T	11: 77,966,558 (GRCm39)	V234D	probably damaging	Het
Fhad1	T	C	4: 141,678,949 (GRCm39)	K576E	possibly damaging	Het
Frmd4b	T	A	6: 97,305,254 (GRCm39)	D170V	probably damaging	Het
Gm4353	A	G	7: 115,682,975 (GRCm39)	V202A	possibly damaging	Het
Ighmbp2	A	G	19: 3,324,531 (GRCm39)	I245T	probably benign	Het
Igsf23	G	A	7: 19,672,161 (GRCm39)		probably benign	Het
Krt1	A	G	15: 101,754,721 (GRCm39)		probably benign	Het
Mapk8	A	G	14: 33,105,857 (GRCm39)	V371A	probably benign	Het
Mtrf1	T	G	14: 79,640,360 (GRCm39)		probably benign	Het
Myzap	A	G	9: 71,422,349 (GRCm39)		probably null	Het
Nsrp1	C	T	11: 76,941,478 (GRCm39)	V73I	probably benign	Het
Or1j15	T	A	2: 36,458,754 (GRCm39)	L48H	probably damaging	Het
Or52e18	A	G	7: 104,609,555 (GRCm39)	I128T	probably damaging	Het
Or8k39	A	T	2: 86,563,673 (GRCm39)	Y94*	probably null	Het
Pex6	C	T	17: 47,036,230 (GRCm39)	R976C	probably benign	Het
Ranbp9	G	A	13: 43,567,560 (GRCm39)	T546I	probably benign	Het
Rnf19b	A	G	4: 128,952,623 (GRCm39)	E187G	probably damaging	Het
Sbf1	A	G	15: 89,183,946 (GRCm39)	V1217A	probably damaging	Het
Sfmbt1	T	A	14: 30,533,478 (GRCm39)	D618E	probably damaging	Het
Sipa1l1	A	G	12: 82,493,672 (GRCm39)	E1697G	probably benign	Het
Syk	A	G	13: 52,778,784 (GRCm39)	Y290C	probably benign	Het
Trim69	T	C	2: 122,008,924 (GRCm39)	L328P	probably damaging	Het
Unc5c	T	A	3: 141,534,212 (GRCm39)	I911N	probably damaging	Het
Wdr5	T	C	2: 27,423,844 (GRCm39)	V294A	probably 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
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
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

Posted On

2013-11-18