Incidental Mutation 'R1972:Rfx5'
ID |
221043 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Rfx5
|
Ensembl Gene |
ENSMUSG00000005774 |
Gene Name |
regulatory factor X, 5 (influences HLA class II expression) |
Synonyms |
|
MMRRC Submission |
039985-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.242)
|
Stock # |
R1972 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
94861355-94868685 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 94864603 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Leucine to Phenylalanine
at position 250
(L250F)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000117963
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029772]
[ENSMUST00000107253]
[ENSMUST00000107254]
[ENSMUST00000107255]
[ENSMUST00000107260]
[ENSMUST00000132393]
[ENSMUST00000137088]
[ENSMUST00000145472]
[ENSMUST00000147237]
[ENSMUST00000144132]
[ENSMUST00000140331]
[ENSMUST00000145031]
[ENSMUST00000152869]
[ENSMUST00000142311]
|
AlphaFold |
Q9JL61 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000029772
AA Change: L250F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000029772 Gene: ENSMUSG00000005774 AA Change: L250F
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: L250F
PolyPhen 2
Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
|
SMART Domains |
Protein: ENSMUSP00000102874 Gene: ENSMUSG00000005774 AA Change: L250F
Domain | Start | End | E-Value | Type |
Pfam:RFX_DNA_binding
|
84 |
169 |
1.8e-33 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000107254
AA Change: L250F
PolyPhen 2
Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
|
SMART Domains |
Protein: ENSMUSP00000102875 Gene: ENSMUSG00000005774 AA Change: L250F
Domain | Start | End | E-Value | Type |
Pfam:RFX_DNA_binding
|
84 |
169 |
1.8e-33 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000107255
AA Change: L250F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000102876 Gene: ENSMUSG00000005774 AA Change: L250F
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: L250F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000102881 Gene: ENSMUSG00000005774 AA Change: L250F
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 |
probably damaging
Transcript: ENSMUST00000137088
AA Change: L250F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000117963 Gene: ENSMUSG00000005774 AA Change: L250F
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: 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: ENSMUST00000144132
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000140331
|
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: 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: ENSMUST00000142311
|
SMART Domains |
Protein: ENSMUSP00000119704 Gene: ENSMUSG00000005774
Domain | Start | End | E-Value | Type |
Pfam:RFX_DNA_binding
|
84 |
131 |
4.1e-10 |
PFAM |
|
Meta Mutation Damage Score |
0.0826 |
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.2%
|
Validation Efficiency |
100% (77/77) |
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: 75 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adat1 |
A |
G |
8: 112,717,050 (GRCm39) |
|
probably benign |
Het |
Bbs2 |
A |
G |
8: 94,807,805 (GRCm39) |
|
probably benign |
Het |
Bcl9 |
A |
C |
3: 97,114,518 (GRCm39) |
D1035E |
probably damaging |
Het |
Bmpr2 |
A |
G |
1: 59,852,762 (GRCm39) |
E31G |
possibly damaging |
Het |
Borcs5 |
A |
G |
6: 134,687,137 (GRCm39) |
D164G |
probably damaging |
Het |
Cap2 |
A |
G |
13: 46,791,375 (GRCm39) |
R181G |
probably damaging |
Het |
Ccdc113 |
A |
T |
8: 96,264,874 (GRCm39) |
H128L |
probably benign |
Het |
Cdh20 |
G |
A |
1: 109,988,862 (GRCm39) |
V255I |
probably benign |
Het |
Chat |
C |
T |
14: 32,146,148 (GRCm39) |
V342I |
probably benign |
Het |
Chrm4 |
C |
T |
2: 91,757,838 (GRCm39) |
A82V |
probably benign |
Het |
Cyp2d22 |
A |
T |
15: 82,260,028 (GRCm39) |
M52K |
probably benign |
Het |
Dennd2c |
T |
C |
3: 103,039,014 (GRCm39) |
V54A |
probably benign |
Het |
Dgka |
C |
T |
10: 128,556,335 (GRCm39) |
G717D |
probably damaging |
Het |
Dnah1 |
C |
T |
14: 30,987,348 (GRCm39) |
W3550* |
probably null |
Het |
Eif2ak1 |
A |
G |
5: 143,821,532 (GRCm39) |
T283A |
probably benign |
Het |
Entrep2 |
A |
T |
7: 64,425,516 (GRCm39) |
I192N |
possibly damaging |
Het |
Fcgbp |
A |
T |
7: 27,793,617 (GRCm39) |
Y1173F |
probably benign |
Het |
Flt1 |
G |
A |
5: 147,591,903 (GRCm39) |
|
probably benign |
Het |
Gpr149 |
T |
C |
3: 62,438,216 (GRCm39) |
K647R |
probably benign |
Het |
Gsdma2 |
T |
C |
11: 98,541,744 (GRCm39) |
V157A |
probably benign |
Het |
Heatr4 |
T |
A |
12: 84,001,794 (GRCm39) |
I884F |
probably damaging |
Het |
Ift56 |
C |
A |
6: 38,387,738 (GRCm39) |
N396K |
probably benign |
Het |
Il17ra |
A |
G |
6: 120,459,177 (GRCm39) |
E776G |
probably benign |
Het |
Inpp5d |
T |
C |
1: 87,604,036 (GRCm39) |
S235P |
probably benign |
Het |
Iqgap3 |
T |
A |
3: 87,991,235 (GRCm39) |
|
probably null |
Het |
Isoc2a |
T |
A |
7: 4,895,086 (GRCm39) |
D171E |
probably damaging |
Het |
Itga10 |
C |
T |
3: 96,559,054 (GRCm39) |
|
probably benign |
Het |
Kcnk12 |
T |
C |
17: 88,104,560 (GRCm39) |
D108G |
possibly damaging |
Het |
Klra9 |
A |
T |
6: 130,159,345 (GRCm39) |
|
probably null |
Het |
Lgmn |
A |
G |
12: 102,362,080 (GRCm39) |
|
probably benign |
Het |
Morf4l1 |
A |
T |
9: 89,977,267 (GRCm39) |
|
probably benign |
Het |
Mthfr |
T |
C |
4: 148,136,384 (GRCm39) |
I380T |
probably damaging |
Het |
Mybpc1 |
T |
C |
10: 88,387,404 (GRCm39) |
I436V |
probably benign |
Het |
Naip5 |
A |
G |
13: 100,349,278 (GRCm39) |
V1350A |
probably damaging |
Het |
Neil2 |
A |
T |
14: 63,423,526 (GRCm39) |
C36S |
possibly damaging |
Het |
Nlrx1 |
A |
G |
9: 44,164,753 (GRCm39) |
V897A |
probably benign |
Het |
Nod2 |
A |
T |
8: 89,379,501 (GRCm39) |
M8L |
probably damaging |
Het |
Nop2 |
A |
G |
6: 125,111,602 (GRCm39) |
T112A |
probably benign |
Het |
Nrap |
T |
A |
19: 56,345,785 (GRCm39) |
T608S |
probably damaging |
Het |
Nuak2 |
A |
T |
1: 132,258,340 (GRCm39) |
H257L |
probably damaging |
Het |
Or10x1 |
T |
C |
1: 174,197,136 (GRCm39) |
F218L |
probably benign |
Het |
Or2ag12 |
T |
C |
7: 106,277,426 (GRCm39) |
D89G |
probably benign |
Het |
Or4c113 |
A |
T |
2: 88,884,891 (GRCm39) |
M293K |
probably benign |
Het |
Or52e8 |
T |
C |
7: 104,625,106 (GRCm39) |
I33V |
possibly damaging |
Het |
Or5ac25 |
A |
T |
16: 59,182,476 (GRCm39) |
V35D |
probably damaging |
Het |
Or5b119 |
T |
C |
19: 13,457,058 (GRCm39) |
N168S |
probably benign |
Het |
Or8b40 |
T |
A |
9: 38,027,863 (GRCm39) |
M257K |
possibly damaging |
Het |
Pde1a |
T |
C |
2: 79,696,065 (GRCm39) |
E358G |
probably damaging |
Het |
Pdlim1 |
A |
T |
19: 40,211,581 (GRCm39) |
S237R |
probably damaging |
Het |
Pithd1 |
T |
C |
4: 135,714,340 (GRCm39) |
D36G |
probably damaging |
Het |
Ppp2r3d |
A |
G |
9: 101,088,976 (GRCm39) |
F449S |
probably benign |
Het |
Prr11 |
G |
A |
11: 86,989,580 (GRCm39) |
R264C |
possibly damaging |
Het |
Rbm43 |
A |
T |
2: 51,815,548 (GRCm39) |
H224Q |
probably benign |
Het |
Rgs22 |
T |
A |
15: 36,103,982 (GRCm39) |
I160L |
probably benign |
Het |
Rorb |
T |
A |
19: 18,929,567 (GRCm39) |
Q393H |
probably damaging |
Het |
Rpl13a |
T |
A |
7: 44,775,419 (GRCm39) |
K368* |
probably null |
Het |
Scaf8 |
T |
G |
17: 3,219,646 (GRCm39) |
S276R |
unknown |
Het |
Scube2 |
A |
T |
7: 109,408,421 (GRCm39) |
N675K |
probably benign |
Het |
Sec22c |
A |
T |
9: 121,517,320 (GRCm39) |
M126K |
possibly damaging |
Het |
Serpinb11 |
T |
C |
1: 107,297,210 (GRCm39) |
F29L |
probably damaging |
Het |
Sis |
A |
G |
3: 72,828,337 (GRCm39) |
F1217S |
probably damaging |
Het |
Slc18a2 |
A |
G |
19: 59,263,085 (GRCm39) |
D294G |
possibly damaging |
Het |
Slc9c1 |
A |
G |
16: 45,413,835 (GRCm39) |
T988A |
possibly damaging |
Het |
Smndc1 |
A |
C |
19: 53,371,986 (GRCm39) |
|
probably null |
Het |
Sned1 |
G |
A |
1: 93,192,795 (GRCm39) |
G361S |
probably damaging |
Het |
Spatc1 |
A |
T |
15: 76,169,075 (GRCm39) |
|
probably null |
Het |
Stab2 |
A |
T |
10: 86,796,180 (GRCm39) |
C356S |
probably damaging |
Het |
Stk4 |
C |
T |
2: 163,942,448 (GRCm39) |
T360M |
probably benign |
Het |
Tbc1d30 |
A |
T |
10: 121,142,135 (GRCm39) |
|
probably null |
Het |
Tenm3 |
T |
C |
8: 48,681,626 (GRCm39) |
E2668G |
probably damaging |
Het |
Tigar |
A |
G |
6: 127,064,889 (GRCm39) |
V253A |
possibly damaging |
Het |
Tmc2 |
T |
A |
2: 130,056,584 (GRCm39) |
|
probably benign |
Het |
Ugt1a10 |
A |
T |
1: 87,983,769 (GRCm39) |
Y189F |
probably damaging |
Het |
Vmn2r82 |
A |
G |
10: 79,214,680 (GRCm39) |
D221G |
probably damaging |
Het |
Xkr5 |
C |
T |
8: 18,991,997 (GRCm39) |
V131M |
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 |
|
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 |
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 |
|
Predicted Primers |
PCR Primer
(F):5'- TCCGAATGAGCATGTTTCTCTC -3'
(R):5'- ATTCTGGAAGGCCTAGAGAGC -3'
Sequencing Primer
(F):5'- TCTCTACTCCAGCCAGAAATGGG -3'
(R):5'- GCCTAGAGAGCCGAGACG -3'
|
Posted On |
2014-08-25 |