Incidental Mutation 'R7186:Rfx5'
ID |
559280 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Rfx5
|
Ensembl Gene |
ENSMUSG00000005774 |
Gene Name |
regulatory factor X, 5 (influences HLA class II expression) |
Synonyms |
|
MMRRC Submission |
045271-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.242)
|
Stock # |
R7186 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
94861355-94868685 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
G to T
at 94865659 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Lysine to Asparagine
at position 319
(K319N)
|
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 benign
Transcript: ENSMUST00000029772
AA Change: K319N
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
SMART Domains |
Protein: ENSMUSP00000029772 Gene: ENSMUSG00000005774 AA Change: K319N
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 |
probably benign
Transcript: ENSMUST00000107255
AA Change: K319N
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
SMART Domains |
Protein: ENSMUSP00000102876 Gene: ENSMUSG00000005774 AA Change: K319N
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: ENSMUST00000107260
AA Change: K319N
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
SMART Domains |
Protein: ENSMUSP00000102881 Gene: ENSMUSG00000005774 AA Change: K319N
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 benign
Transcript: ENSMUST00000137088
AA Change: K319N
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
SMART Domains |
Protein: ENSMUSP00000117963 Gene: ENSMUSG00000005774 AA Change: K319N
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 |
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.1%
|
Validation Efficiency |
100% (67/67) |
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: 69 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
9930111J21Rik2 |
T |
A |
11: 48,910,100 (GRCm39) |
I778F |
possibly damaging |
Het |
Adam39 |
A |
T |
8: 41,279,349 (GRCm39) |
N580I |
probably damaging |
Het |
Adamts20 |
A |
G |
15: 94,220,689 (GRCm39) |
S1415P |
possibly damaging |
Het |
Adcy2 |
A |
G |
13: 68,816,758 (GRCm39) |
Y743H |
probably damaging |
Het |
Aldh1a3 |
A |
G |
7: 66,055,831 (GRCm39) |
V320A |
probably damaging |
Het |
Arid1a |
TGCCGCCGCCGCCGCCGCCGCCG |
TGCCGCCGCCGCCGCCGCCG |
4: 133,480,544 (GRCm39) |
|
|
Het |
Art5 |
G |
T |
7: 101,746,536 (GRCm39) |
R268S |
probably benign |
Het |
Bfar |
T |
C |
16: 13,510,371 (GRCm39) |
V238A |
probably benign |
Het |
Card6 |
TTGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGCGGATGAGAGGGCTTAGCATGGGAGGACTG |
TTGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGCGGATGAGAGGGCTTAGCATGGGAGGACTG |
15: 5,128,173 (GRCm39) |
|
probably benign |
Het |
Cdc23 |
G |
A |
18: 34,770,175 (GRCm39) |
T408I |
probably damaging |
Het |
Cdh24 |
G |
C |
14: 54,870,949 (GRCm39) |
P522A |
probably benign |
Het |
Clk4 |
T |
C |
11: 51,159,607 (GRCm39) |
V61A |
probably benign |
Het |
Clrn2 |
T |
C |
5: 45,611,115 (GRCm39) |
|
probably benign |
Het |
Cyp2j8 |
T |
C |
4: 96,363,787 (GRCm39) |
D292G |
probably benign |
Het |
Deaf1 |
T |
C |
7: 140,907,383 (GRCm39) |
E34G |
probably benign |
Het |
Elovl7 |
A |
G |
13: 108,408,382 (GRCm39) |
E127G |
probably damaging |
Het |
Flg |
A |
T |
3: 93,187,252 (GRCm39) |
R235* |
probably null |
Het |
Gbp3 |
G |
A |
3: 142,269,923 (GRCm39) |
V77M |
probably damaging |
Het |
Gda |
A |
T |
19: 21,372,569 (GRCm39) |
F450I |
probably benign |
Het |
Gipc1 |
A |
G |
8: 84,390,762 (GRCm39) |
E289G |
possibly damaging |
Het |
Gm4924 |
T |
C |
10: 82,214,778 (GRCm39) |
Y859H |
unknown |
Het |
Gpatch1 |
A |
T |
7: 34,994,738 (GRCm39) |
D509E |
possibly damaging |
Het |
Gpbp1 |
A |
G |
13: 111,577,233 (GRCm39) |
V219A |
possibly damaging |
Het |
Gpr107 |
A |
T |
2: 31,042,371 (GRCm39) |
M1L |
possibly damaging |
Het |
Heg1 |
T |
C |
16: 33,552,034 (GRCm39) |
F1003L |
probably damaging |
Het |
Hivep1 |
A |
G |
13: 42,309,814 (GRCm39) |
T685A |
probably benign |
Het |
Hpse |
T |
A |
5: 100,843,395 (GRCm39) |
D259V |
probably damaging |
Het |
Ido2 |
A |
T |
8: 25,040,826 (GRCm39) |
|
probably null |
Het |
Ighv14-1 |
T |
C |
12: 113,895,649 (GRCm39) |
D92G |
probably damaging |
Het |
Krt87 |
A |
T |
15: 101,385,083 (GRCm39) |
|
probably null |
Het |
Lsp1 |
T |
C |
7: 142,044,089 (GRCm39) |
V278A |
probably damaging |
Het |
Lurap1l |
C |
A |
4: 80,829,747 (GRCm39) |
S52R |
possibly damaging |
Het |
Luzp2 |
A |
G |
7: 54,485,577 (GRCm39) |
|
probably benign |
Het |
Micall1 |
A |
G |
15: 79,009,575 (GRCm39) |
E399G |
unknown |
Het |
Ncapd2 |
A |
G |
6: 125,163,119 (GRCm39) |
S130P |
possibly damaging |
Het |
Nrg2 |
A |
G |
18: 36,178,973 (GRCm39) |
V321A |
probably benign |
Het |
Nuf2 |
T |
C |
1: 169,352,954 (GRCm39) |
H17R |
probably damaging |
Het |
Numb |
A |
G |
12: 83,842,920 (GRCm39) |
W419R |
probably damaging |
Het |
Or4d2b |
G |
A |
11: 87,780,591 (GRCm39) |
L44F |
possibly damaging |
Het |
Or4f62 |
T |
A |
2: 111,986,507 (GRCm39) |
D70E |
probably damaging |
Het |
Or56a3b |
A |
G |
7: 104,771,473 (GRCm39) |
R270G |
probably benign |
Het |
Pde6a |
T |
A |
18: 61,353,678 (GRCm39) |
M1K |
probably null |
Het |
Pknox1 |
C |
T |
17: 31,822,172 (GRCm39) |
A313V |
probably damaging |
Het |
Ppp2ca |
T |
A |
11: 52,010,080 (GRCm39) |
N229K |
possibly damaging |
Het |
Ptgdr |
A |
T |
14: 45,096,401 (GRCm39) |
C104S |
probably damaging |
Het |
Ralgapa2 |
C |
A |
2: 146,230,406 (GRCm39) |
|
probably null |
Het |
Rnase10 |
A |
T |
14: 51,247,242 (GRCm39) |
T207S |
probably damaging |
Het |
Rreb1 |
A |
G |
13: 38,125,608 (GRCm39) |
T1305A |
probably benign |
Het |
Rrp12 |
C |
A |
19: 41,859,744 (GRCm39) |
|
probably null |
Het |
Rubcnl |
A |
C |
14: 75,269,453 (GRCm39) |
D37A |
possibly damaging |
Het |
Saxo5 |
T |
C |
8: 3,529,049 (GRCm39) |
F208S |
probably damaging |
Het |
Scn9a |
T |
C |
2: 66,364,567 (GRCm39) |
Y802C |
probably damaging |
Het |
Sec16a |
A |
T |
2: 26,330,715 (GRCm39) |
Y433* |
probably null |
Het |
Sgk3 |
T |
A |
1: 9,956,227 (GRCm39) |
V331D |
probably benign |
Het |
Sirt7 |
C |
T |
11: 120,511,311 (GRCm39) |
R280H |
probably benign |
Het |
Snx13 |
G |
C |
12: 35,142,912 (GRCm39) |
R252S |
probably damaging |
Het |
Stk32b |
G |
T |
5: 37,624,125 (GRCm39) |
D207E |
probably damaging |
Het |
Sult2a7 |
C |
T |
7: 14,203,978 (GRCm39) |
V262I |
not run |
Het |
Tcstv7b |
C |
T |
13: 120,702,587 (GRCm39) |
L128F |
probably damaging |
Het |
Tent5b |
T |
A |
4: 133,213,518 (GRCm39) |
F130I |
probably damaging |
Het |
Tmem33 |
G |
C |
5: 67,421,130 (GRCm39) |
V35L |
possibly damaging |
Het |
Uba1y |
A |
G |
Y: 825,537 (GRCm39) |
I300V |
probably benign |
Het |
Usp32 |
A |
T |
11: 84,942,060 (GRCm39) |
V344E |
probably benign |
Het |
Usp50 |
C |
T |
2: 126,625,218 (GRCm39) |
|
probably benign |
Het |
Vmn1r238 |
A |
C |
18: 3,122,661 (GRCm39) |
F251C |
probably damaging |
Het |
Vmn2r74 |
A |
T |
7: 85,601,150 (GRCm39) |
Y829* |
probably null |
Het |
Wars1 |
A |
G |
12: 108,846,982 (GRCm39) |
F141L |
probably damaging |
Het |
Zfp879 |
A |
G |
11: 50,724,621 (GRCm39) |
V145A |
probably benign |
Het |
Zfp934 |
A |
T |
13: 62,640,204 (GRCm39) |
V56D |
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 |
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'- GGCAGTGACCCTTCTACATC -3'
(R):5'- CCCCTGACAAAGTAGGAACAGG -3'
Sequencing Primer
(F):5'- ATTGTAAGCCAGCTGCCATG -3'
(R):5'- ACAGGTGGTAAGATCATGTTGATG -3'
|
Posted On |
2019-06-26 |