Incidental Mutation 'R5912:Rfx5'
| ID |
461046 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rfx5
|
| Ensembl Gene |
ENSMUSG00000005774 |
| Gene Name |
regulatory factor X, 5 (influences HLA class II expression) |
| Synonyms |
|
| MMRRC Submission |
044109-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.274)
|
| Stock # |
R5912 (G1)
|
| Quality Score |
221 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
94861355-94868685 bp(+) (GRCm39) |
| Type of Mutation |
unclassified |
| DNA Base Change (assembly) |
G to A
at 94866029 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000121157
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029772]
[ENSMUST00000107253]
[ENSMUST00000107254]
[ENSMUST00000107255]
[ENSMUST00000107260]
[ENSMUST00000132393]
[ENSMUST00000137088]
[ENSMUST00000145472]
[ENSMUST00000152869]
[ENSMUST00000142311]
[ENSMUST00000145031]
[ENSMUST00000147237]
[ENSMUST00000144132]
[ENSMUST00000140331]
|
| AlphaFold |
Q9JL61 |
| Predicted Effect |
unknown
Transcript: ENSMUST00000029772
AA Change: V443I
|
| SMART Domains |
Protein: ENSMUSP00000029772
Gene: ENSMUSG00000005774
AA Change: V443I
| 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 |
unknown
Transcript: ENSMUST00000107255
AA Change: V443I
|
| SMART Domains |
Protein: ENSMUSP00000102876
Gene: ENSMUSG00000005774
AA Change: V443I
| 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 |
unknown
Transcript: ENSMUST00000107260
AA Change: V443I
|
| SMART Domains |
Protein: ENSMUSP00000102881
Gene: ENSMUSG00000005774
AA Change: V443I
| 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 |
unknown
Transcript: ENSMUST00000137088
AA Change: V443I
|
| SMART Domains |
Protein: ENSMUSP00000117963
Gene: ENSMUSG00000005774
AA Change: V443I
| 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: ENSMUST00000145472
|
| 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 |
|
| 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: 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
|
| Meta Mutation Damage Score |
0.0744 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.2%
- 20x: 94.8%
|
| Validation Efficiency |
100% (52/52) |
| 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: 49 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 5031439G07Rik |
A |
T |
15: 84,839,897 (GRCm39) |
C166S |
possibly damaging |
Het |
| Ahnak |
T |
A |
19: 8,989,267 (GRCm39) |
M3517K |
probably damaging |
Het |
| Asap2 |
T |
C |
12: 21,256,344 (GRCm39) |
V214A |
probably damaging |
Het |
| Atp13a4 |
A |
G |
16: 29,275,389 (GRCm39) |
V365A |
probably benign |
Het |
| Bivm |
G |
T |
1: 44,165,573 (GRCm39) |
G8* |
probably null |
Het |
| Cc2d2a |
A |
C |
5: 43,877,772 (GRCm39) |
D1043A |
probably damaging |
Het |
| Cdh2 |
A |
C |
18: 16,773,507 (GRCm39) |
I331S |
possibly damaging |
Het |
| Clip3 |
A |
C |
7: 29,998,295 (GRCm39) |
D247A |
probably benign |
Het |
| Csf3r |
A |
T |
4: 125,923,753 (GRCm39) |
I88F |
probably damaging |
Het |
| Cyp2j13 |
A |
T |
4: 95,945,079 (GRCm39) |
N316K |
probably damaging |
Het |
| Dnah12 |
T |
A |
14: 26,491,965 (GRCm39) |
C1133* |
probably null |
Het |
| Glud1 |
G |
A |
14: 34,033,300 (GRCm39) |
|
probably null |
Het |
| Gm5805 |
A |
G |
15: 81,857,018 (GRCm39) |
|
noncoding transcript |
Het |
| Gsg1l2 |
G |
T |
11: 67,665,540 (GRCm39) |
|
probably null |
Het |
| Ikzf1 |
C |
A |
11: 11,698,464 (GRCm39) |
S105* |
probably null |
Het |
| Kif18b |
A |
G |
11: 102,803,817 (GRCm39) |
S448P |
probably benign |
Het |
| Klhl31 |
C |
A |
9: 77,563,012 (GRCm39) |
N592K |
probably damaging |
Het |
| Kmt2c |
A |
G |
5: 25,552,467 (GRCm39) |
F1239L |
possibly damaging |
Het |
| Lama5 |
A |
G |
2: 179,837,268 (GRCm39) |
Y1014H |
probably damaging |
Het |
| Macf1 |
A |
C |
4: 123,290,951 (GRCm39) |
L3980R |
probably damaging |
Het |
| Magi1 |
A |
T |
6: 93,685,126 (GRCm39) |
S524T |
possibly damaging |
Het |
| Nlrp4f |
A |
T |
13: 65,342,722 (GRCm39) |
Y308N |
probably damaging |
Het |
| Or1e33 |
A |
C |
11: 73,738,501 (GRCm39) |
I150R |
possibly damaging |
Het |
| Or3a1c |
A |
T |
11: 74,046,046 (GRCm39) |
E22V |
possibly damaging |
Het |
| Scn1b |
C |
T |
7: 30,817,228 (GRCm39) |
V165M |
probably damaging |
Het |
| Sema4c |
A |
C |
1: 36,593,469 (GRCm39) |
V41G |
possibly damaging |
Het |
| Serpini1 |
G |
T |
3: 75,523,914 (GRCm39) |
G174V |
probably benign |
Het |
| Sh2b1 |
T |
C |
7: 126,070,642 (GRCm39) |
E353G |
probably damaging |
Het |
| Slc7a6 |
G |
T |
8: 106,906,289 (GRCm39) |
V174L |
probably benign |
Het |
| Smg1 |
A |
T |
7: 117,753,809 (GRCm39) |
|
probably benign |
Het |
| Spag9 |
A |
G |
11: 93,935,251 (GRCm39) |
N21D |
probably damaging |
Het |
| Spdye4c |
C |
T |
2: 128,437,994 (GRCm39) |
R245* |
probably null |
Het |
| Sulf1 |
A |
G |
1: 12,856,976 (GRCm39) |
|
probably benign |
Het |
| Swt1 |
A |
G |
1: 151,287,160 (GRCm39) |
S111P |
probably damaging |
Het |
| Syne2 |
G |
A |
12: 75,955,721 (GRCm39) |
|
probably null |
Het |
| Tanc1 |
T |
C |
2: 59,622,030 (GRCm39) |
V383A |
possibly damaging |
Het |
| Tbc1d10b |
G |
T |
7: 126,799,033 (GRCm39) |
A491E |
probably damaging |
Het |
| Tek |
A |
G |
4: 94,686,877 (GRCm39) |
T132A |
probably damaging |
Het |
| Traf3 |
A |
G |
12: 111,221,783 (GRCm39) |
I290V |
probably benign |
Het |
| Traf5 |
A |
G |
1: 191,730,030 (GRCm39) |
|
probably benign |
Het |
| Ttn |
A |
T |
2: 76,640,687 (GRCm39) |
I13687N |
probably damaging |
Het |
| Unc5c |
A |
G |
3: 141,494,767 (GRCm39) |
D415G |
probably damaging |
Het |
| Ust |
A |
G |
10: 8,173,825 (GRCm39) |
Y227H |
probably benign |
Het |
| Vmn2r100 |
A |
G |
17: 19,752,071 (GRCm39) |
N705D |
probably damaging |
Het |
| Wnk2 |
T |
C |
13: 49,214,250 (GRCm39) |
E1444G |
probably damaging |
Het |
| Ylpm1 |
C |
T |
12: 85,087,660 (GRCm39) |
P1148L |
probably damaging |
Het |
| Zbtb5 |
A |
G |
4: 44,993,750 (GRCm39) |
S545P |
probably benign |
Het |
| Zfp710 |
A |
G |
7: 79,731,222 (GRCm39) |
D133G |
probably benign |
Het |
| Zfp866 |
A |
T |
8: 70,218,934 (GRCm39) |
C229S |
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 |
|
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'- TCCTACTTTGTCAGGGGCTG -3'
(R):5'- CAGGAGTAGCGTTTCTTTCCCC -3'
Sequencing Primer
(F):5'- ctaggtttgggccaggg -3'
(R):5'- CCTGGCTTCTTTCGAGGGC -3'
|
| Posted On |
2017-02-28 |
Incidental Mutation