Mutagenetix > Incidental Mutation

Incidental Mutation 'RF061:Rfx5'

605403

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?

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

Stock #

RF061 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

94861355-94868685 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 94863070 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Isoleucine at position 54 (K54I)

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: K54I

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

SMART Domains

Protein: ENSMUSP00000029772
Gene: ENSMUSG00000005774
AA Change: K54I

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: K54I

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000102874
Gene: ENSMUSG00000005774
AA Change: K54I

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000107254
AA Change: K54I

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000102875
Gene: ENSMUSG00000005774
AA Change: K54I

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000107255
AA Change: K54I

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

SMART Domains

Protein: ENSMUSP00000102876
Gene: ENSMUSG00000005774
AA Change: K54I

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: K54I

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

SMART Domains

Protein: ENSMUSP00000102881
Gene: ENSMUSG00000005774
AA Change: K54I

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 damaging
Transcript: ENSMUST00000132393
AA Change: K54I

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

SMART Domains

Protein: ENSMUSP00000117999
Gene: ENSMUSG00000005774
AA Change: K54I

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000137088
AA Change: K54I

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

SMART Domains

Protein: ENSMUSP00000117963
Gene: ENSMUSG00000005774
AA Change: K54I

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 damaging
Transcript: ENSMUST00000142311
AA Change: K54I

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

SMART Domains

Protein: ENSMUSP00000119704
Gene: ENSMUSG00000005774
AA Change: K54I

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 damaging
Transcript: ENSMUST00000145031
AA Change: K54I

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

SMART Domains

Protein: ENSMUSP00000118099
Gene: ENSMUSG00000005774
AA Change: K54I

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

Predicted Effect

probably benign
Transcript: ENSMUST00000145472

Predicted Effect

probably damaging
Transcript: ENSMUST00000147237
AA Change: K54I

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

SMART Domains

Protein: ENSMUSP00000118586
Gene: ENSMUSG00000005774
AA Change: K54I

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: K54I

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

SMART Domains

Protein: ENSMUSP00000121157
Gene: ENSMUSG00000005774
AA Change: K54I

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

Coding Region Coverage

1x: 99.8%
3x: 99.7%
10x: 99.3%
20x: 98.7%

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: 28 list
Gene	Ref	Var	Chr/Loc	Predicted Effect	Zygosity
2810004N23Rik	ACTT	ACTTACTT	8: 125,566,570 (GRCm39)	probably null	Het
Abi3bp	GCCCACGACCC	GCCCACGACCCACGACCC	16: 56,447,950 (GRCm39)	probably null	Het
Ankhd1	GGCGGC	GGCGGCCGCGGC	18: 36,693,974 (GRCm39)	probably benign	Het
Ankrd24	GAGGC	GAGGCGGAGGCATAGGC	10: 81,479,401 (GRCm39)	probably null	Het
Bpifb4	A	ACCTCCAC	2: 153,799,048 (GRCm39)	probably benign	Het
Chga	CAG	CAGAAG	12: 102,527,672 (GRCm39)	probably benign	Het
Chga	G	GCAC	12: 102,527,686 (GRCm39)	probably benign	Het
Cyb5r4	ACACTGCCCAGGGA	ACACTGCCCAGGGATGTGACAGACGCACTGCCCAGGGA	9: 86,922,488 (GRCm39)	probably benign	Het
Dnmt1	CAGTTCCTACCTCGTT	CAGTTCCTACCTCGTTTTGGGGGCGGAGCAAAGTTCCTACCTCGTT	9: 20,821,426 (GRCm39)	probably null	Het
Fbrsl1	GTGCTGGTGCGT	GTGCTGGTGCGTCTGCTGGTGCGT	5: 110,525,997 (GRCm39)	probably benign	Het
Gabre	GCTCCG	GCTCCGACTCCG	X: 71,313,654 (GRCm39)	probably benign	Het
Hsdl2	AG	AGCAGCAGCCACAGCTGCTG	4: 59,610,657 (GRCm39)	probably benign	Het
Il2	GGG	GGGGCTTGAAGTGGG	3: 37,179,990 (GRCm39)	probably benign	Het
Krtap28-10	CCACCACAGC	CCACCACAGCCACAGACACCACAGC	1: 83,020,002 (GRCm39)	probably benign	Het
Lrch1	GCTGGTGGT	G	14: 75,184,995 (GRCm39)	probably null	Het
Lrch1	GGTGGTGTTG	GG	14: 75,185,007 (GRCm39)	probably null	Het
Mamld1	AGC	AGCCGC	X: 70,162,456 (GRCm39)	probably benign	Het
Map1a	TGGCTCCAGCTCCAGCTCCAGCTCCAGCTCC	TGGCTCCAGCTCCAGCTCCAGCTCCAGCTCCGGCTCCAGCTCCAGCTCCAGCTCCAGCTCC	2: 121,136,768 (GRCm39)	probably benign	Het
Or10n7-ps1	GA	GATATA	9: 39,598,049 (GRCm39)	probably null	Het
Pdcd11	AGGAGGAGG	AG	19: 47,101,884 (GRCm39)	probably null	Het
Pknox2	ACACACACACACACACTCAC	ACAC	9: 36,820,905 (GRCm39)	probably benign	Het
Rps19	AAAAAAT	AAAAAATAAAAAT	7: 24,588,605 (GRCm39)	probably benign	Het
Rragd	CATGCCTTTCATTCTA	C	4: 32,995,150 (GRCm39)	probably benign	Het
Sbp	GACAACA	GACAACACAGATGCTAACAACA	17: 24,164,351 (GRCm39)	probably benign	Het
Stab2	CTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA	CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA	10: 86,702,622 (GRCm39)	probably benign	Het
Tfeb	CAG	CAGGAG	17: 48,097,017 (GRCm39)	probably benign	Het
Trim33	GGCCCCCGC	GGC	3: 103,187,533 (GRCm39)	probably benign	Het
Zfp598	ACAACCAC	ACAACCACAACCAC	17: 24,899,744 (GRCm39)	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
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
Z1176:Rfx5	UTSW	3	94,863,126 (GRCm39)	missense	probably benign	0.27

Predicted Primers

PCR Primer
(F):5'- AAGGTTGCCAGCACAGTGAG -3'
(R):5'- GGTTCTGAGCTATGCATCTCC -3'

Sequencing Primer
(F):5'- GCACCCAACCTCAAGTCATTTCTTAG -3'
(R):5'- TGTCGGATTTCCAGAAACTGAG -3'

Posted On

2019-12-04