Incidental Mutation 'R1342:Rfx5'
| ID |
156388 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rfx5
|
| Ensembl Gene |
ENSMUSG00000005774 |
| Gene Name |
regulatory factor X, 5 (influences HLA class II expression) |
| Synonyms |
|
| MMRRC Submission |
039407-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.242)
|
| Stock # |
R1342 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
94861355-94868685 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 94865723 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 341
(I341V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000117963
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029772]
[ENSMUST00000107253]
[ENSMUST00000107254]
[ENSMUST00000107255]
[ENSMUST00000107260]
[ENSMUST00000132393]
[ENSMUST00000137088]
[ENSMUST00000144132]
[ENSMUST00000142311]
[ENSMUST00000147237]
[ENSMUST00000140331]
[ENSMUST00000145031]
[ENSMUST00000152869]
[ENSMUST00000145472]
|
| AlphaFold |
Q9JL61 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029772
AA Change: I341V
PolyPhen 2
Score 0.091 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000029772
Gene: ENSMUSG00000005774
AA Change: I341V
| 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: I341V
PolyPhen 2
Score 0.091 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000102876
Gene: ENSMUSG00000005774
AA Change: I341V
| 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: I341V
PolyPhen 2
Score 0.091 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000102881
Gene: ENSMUSG00000005774
AA Change: I341V
| 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 benign
Transcript: ENSMUST00000137088
AA Change: I341V
PolyPhen 2
Score 0.091 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000117963
Gene: ENSMUSG00000005774
AA Change: I341V
| 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: ENSMUST00000148803
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000140294
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000142708
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000144132
|
| 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: 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: 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: ENSMUST00000145472
|
| Meta Mutation Damage Score |
0.0673 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.1%
- 10x: 95.8%
- 20x: 91.6%
|
| Validation Efficiency |
100% (43/43) |
| 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: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Atp10a |
G |
T |
7: 58,465,894 (GRCm39) |
|
probably benign |
Het |
| B3gnt9 |
T |
C |
8: 105,980,956 (GRCm39) |
E144G |
probably null |
Het |
| Bcl9 |
G |
T |
3: 97,113,042 (GRCm39) |
Q1138K |
possibly damaging |
Het |
| C6 |
T |
C |
15: 4,769,231 (GRCm39) |
|
probably benign |
Het |
| Ccl4 |
A |
G |
11: 83,554,402 (GRCm39) |
|
probably benign |
Het |
| Cdc73 |
A |
G |
1: 143,578,230 (GRCm39) |
|
probably null |
Het |
| Cemip |
A |
T |
7: 83,593,283 (GRCm39) |
L1140* |
probably null |
Het |
| Chd4 |
C |
A |
6: 125,074,151 (GRCm39) |
P8Q |
probably benign |
Het |
| Col27a1 |
G |
A |
4: 63,175,351 (GRCm39) |
|
probably null |
Het |
| Col9a1 |
G |
A |
1: 24,262,701 (GRCm39) |
|
probably null |
Het |
| Colgalt1 |
C |
T |
8: 72,070,804 (GRCm39) |
T232I |
probably damaging |
Het |
| Dnah8 |
A |
G |
17: 30,939,974 (GRCm39) |
D1640G |
probably damaging |
Het |
| Dot1l |
T |
G |
10: 80,621,859 (GRCm39) |
C504G |
probably benign |
Het |
| Gm9892 |
T |
C |
8: 52,649,458 (GRCm39) |
T212A |
probably benign |
Het |
| Hjurp |
G |
A |
1: 88,205,090 (GRCm39) |
|
probably benign |
Het |
| Ifnar2 |
A |
G |
16: 91,200,809 (GRCm39) |
D350G |
possibly damaging |
Het |
| Ift172 |
T |
C |
5: 31,419,210 (GRCm39) |
I1144V |
probably benign |
Het |
| Ipo7 |
A |
T |
7: 109,629,011 (GRCm39) |
N94Y |
possibly damaging |
Het |
| Irag1 |
T |
A |
7: 110,487,252 (GRCm39) |
M699L |
probably benign |
Het |
| Mapkbp1 |
C |
A |
2: 119,829,015 (GRCm39) |
A57D |
possibly damaging |
Het |
| Mmd |
T |
A |
11: 90,167,676 (GRCm39) |
I235N |
probably benign |
Het |
| Naip2 |
T |
C |
13: 100,298,362 (GRCm39) |
E558G |
probably benign |
Het |
| Naip2 |
C |
T |
13: 100,298,368 (GRCm39) |
G556D |
probably benign |
Het |
| Palld |
A |
G |
8: 61,975,916 (GRCm39) |
|
probably null |
Het |
| Parp4 |
G |
A |
14: 56,827,854 (GRCm39) |
E202K |
probably damaging |
Het |
| Pclo |
C |
A |
5: 14,732,191 (GRCm39) |
|
probably benign |
Het |
| Pde8a |
T |
C |
7: 80,952,042 (GRCm39) |
|
probably null |
Het |
| Pdgfrb |
T |
A |
18: 61,198,952 (GRCm39) |
L370* |
probably null |
Het |
| Phf2 |
A |
T |
13: 48,957,953 (GRCm39) |
S1020R |
unknown |
Het |
| Pik3r4 |
T |
A |
9: 105,528,100 (GRCm39) |
|
probably null |
Het |
| Plxnb1 |
C |
A |
9: 108,929,720 (GRCm39) |
P192Q |
possibly damaging |
Het |
| Ppil3 |
A |
T |
1: 58,480,037 (GRCm39) |
I46N |
probably damaging |
Het |
| Prr14l |
A |
C |
5: 32,987,604 (GRCm39) |
C630W |
probably damaging |
Het |
| Ryr3 |
T |
C |
2: 112,581,148 (GRCm39) |
K2895E |
probably damaging |
Het |
| Slc5a12 |
T |
C |
2: 110,447,435 (GRCm39) |
|
probably null |
Het |
| Slc8a3 |
T |
C |
12: 81,362,790 (GRCm39) |
T10A |
probably damaging |
Het |
| Ss18 |
A |
G |
18: 14,769,595 (GRCm39) |
Y321H |
unknown |
Het |
| Sspo |
A |
G |
6: 48,438,569 (GRCm39) |
N1546D |
probably benign |
Het |
| Thbs4 |
G |
A |
13: 92,888,925 (GRCm39) |
L923F |
probably damaging |
Het |
| Ulk1 |
C |
T |
5: 110,937,223 (GRCm39) |
R691Q |
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 |
|
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 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTTTAGCCTCCTAAAGAGCAAGAAGCC -3'
(R):5'- TCGGGGAGAGTTCACAATAGCTGC -3'
Sequencing Primer
(F):5'- GCAAGAAGCCCGAGCTG -3'
(R):5'- cagaccagcccccagac -3'
|
| Posted On |
2014-02-11 |
Incidental Mutation