Incidental Mutation 'R2173:Rfx5'
| ID |
237605 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rfx5
|
| Ensembl Gene |
ENSMUSG00000005774 |
| Gene Name |
regulatory factor X, 5 (influences HLA class II expression) |
| Synonyms |
|
| MMRRC Submission |
040175-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.242)
|
| Stock # |
R2173 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
94861355-94868685 bp(+) (GRCm39) |
| Type of Mutation |
splice site (403 bp from exon) |
| DNA Base Change (assembly) |
A to G
at 94864027 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]
[ENSMUST00000147237]
[ENSMUST00000140331]
[ENSMUST00000144132]
[ENSMUST00000137088]
[ENSMUST00000142311]
[ENSMUST00000145031]
[ENSMUST00000152869]
[ENSMUST00000145472]
|
| AlphaFold |
Q9JL61 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029772
|
| SMART Domains |
Protein: ENSMUSP00000029772
Gene: ENSMUSG00000005774
| 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
|
| SMART Domains |
Protein: ENSMUSP00000102876
Gene: ENSMUSG00000005774
| 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
|
| SMART Domains |
Protein: ENSMUSP00000102881
Gene: ENSMUSG00000005774
| 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 null
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: 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 |
noncoding transcript
Transcript: ENSMUST00000142708
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000144132
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000137088
|
| SMART Domains |
Protein: ENSMUSP00000117963
Gene: ENSMUSG00000005774
| 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 |
probably null
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 null
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 null
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
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.6%
|
| Validation Efficiency |
97% (66/68) |
| 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: 64 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Alpk1 |
T |
A |
3: 127,477,239 (GRCm39) |
H273L |
probably damaging |
Het |
| Alpk3 |
A |
G |
7: 80,726,648 (GRCm39) |
Y111C |
probably damaging |
Het |
| Anapc2 |
T |
G |
2: 25,163,288 (GRCm39) |
V175G |
probably benign |
Het |
| Arhgap30 |
T |
C |
1: 171,235,335 (GRCm39) |
S570P |
probably damaging |
Het |
| AU040320 |
T |
C |
4: 126,686,069 (GRCm39) |
L215P |
probably benign |
Het |
| Ccdc59 |
A |
T |
10: 105,677,388 (GRCm39) |
K9M |
possibly damaging |
Het |
| Ccdc65 |
A |
G |
15: 98,618,914 (GRCm39) |
N298D |
probably benign |
Het |
| Cfap70 |
T |
A |
14: 20,458,630 (GRCm39) |
N727Y |
probably benign |
Het |
| Clcn7 |
A |
G |
17: 25,364,583 (GRCm39) |
H63R |
probably benign |
Het |
| Corin |
A |
T |
5: 72,661,422 (GRCm39) |
C24S |
probably benign |
Het |
| Cyp1a2 |
A |
G |
9: 57,584,798 (GRCm39) |
W419R |
probably damaging |
Het |
| Dlgap4 |
C |
A |
2: 156,604,732 (GRCm39) |
A256D |
probably damaging |
Het |
| Eif4enif1 |
A |
G |
11: 3,192,367 (GRCm39) |
|
probably null |
Het |
| Eri2 |
A |
G |
7: 119,385,766 (GRCm39) |
V245A |
possibly damaging |
Het |
| Erich6b |
T |
C |
14: 75,896,332 (GRCm39) |
F73L |
probably benign |
Het |
| Fam110a |
A |
G |
2: 151,812,429 (GRCm39) |
C114R |
probably damaging |
Het |
| Fam149a |
T |
C |
8: 45,806,991 (GRCm39) |
D288G |
probably damaging |
Het |
| Fam171a1 |
T |
A |
2: 3,226,656 (GRCm39) |
Y596* |
probably null |
Het |
| Fsd1 |
A |
G |
17: 56,298,223 (GRCm39) |
T183A |
possibly damaging |
Het |
| Fut10 |
T |
A |
8: 31,726,159 (GRCm39) |
Y305N |
probably damaging |
Het |
| Ganab |
A |
T |
19: 8,879,624 (GRCm39) |
|
probably benign |
Het |
| Gm9922 |
G |
T |
14: 101,967,012 (GRCm39) |
|
probably benign |
Het |
| Gp9 |
A |
G |
6: 87,756,035 (GRCm39) |
T17A |
probably benign |
Het |
| Gxylt2 |
T |
C |
6: 100,775,115 (GRCm39) |
Y345H |
probably damaging |
Het |
| Herc2 |
A |
G |
7: 55,835,699 (GRCm39) |
H3269R |
probably benign |
Het |
| Hpx |
A |
T |
7: 105,241,290 (GRCm39) |
S374T |
probably benign |
Het |
| Hspa5 |
T |
C |
2: 34,664,674 (GRCm39) |
V376A |
probably damaging |
Het |
| Hyi |
T |
C |
4: 118,219,381 (GRCm39) |
|
probably benign |
Het |
| Impdh2 |
G |
A |
9: 108,442,593 (GRCm39) |
|
probably null |
Het |
| Kremen2 |
A |
C |
17: 23,961,770 (GRCm39) |
W246G |
probably damaging |
Het |
| Krt87 |
A |
G |
15: 101,385,818 (GRCm39) |
V259A |
probably damaging |
Het |
| L3mbtl4 |
A |
T |
17: 68,894,188 (GRCm39) |
H398L |
probably damaging |
Het |
| Lama5 |
C |
A |
2: 179,838,035 (GRCm39) |
V894L |
probably benign |
Het |
| Maml2 |
A |
G |
9: 13,532,912 (GRCm39) |
|
probably benign |
Het |
| Nup153 |
A |
T |
13: 46,855,076 (GRCm39) |
|
probably benign |
Het |
| Or10g6 |
T |
G |
9: 39,934,550 (GRCm39) |
I287S |
probably damaging |
Het |
| Or2y15 |
G |
T |
11: 49,350,967 (GRCm39) |
V154L |
probably benign |
Het |
| Or5k14 |
A |
G |
16: 58,692,982 (GRCm39) |
F177S |
probably damaging |
Het |
| Or8b3b |
T |
C |
9: 38,584,240 (GRCm39) |
I180V |
probably benign |
Het |
| Or9r7 |
G |
A |
10: 129,962,372 (GRCm39) |
P185S |
probably benign |
Het |
| Otof |
C |
T |
5: 30,543,718 (GRCm39) |
R582H |
probably damaging |
Het |
| Otud4 |
T |
C |
8: 80,395,093 (GRCm39) |
S543P |
probably damaging |
Het |
| Pde6a |
A |
G |
18: 61,387,453 (GRCm39) |
D448G |
probably damaging |
Het |
| Phgdh |
A |
G |
3: 98,222,427 (GRCm39) |
V388A |
probably benign |
Het |
| Plin3 |
G |
T |
17: 56,586,891 (GRCm39) |
D385E |
possibly damaging |
Het |
| Polg |
G |
T |
7: 79,105,341 (GRCm39) |
D734E |
probably damaging |
Het |
| Pomt1 |
T |
C |
2: 32,140,912 (GRCm39) |
Y515H |
probably damaging |
Het |
| Prr35 |
A |
C |
17: 26,167,461 (GRCm39) |
H25Q |
probably damaging |
Het |
| Pwwp2a |
G |
A |
11: 43,573,313 (GRCm39) |
A132T |
probably benign |
Het |
| Rbm6 |
A |
T |
9: 107,729,390 (GRCm39) |
F419L |
possibly damaging |
Het |
| Rnf135 |
G |
A |
11: 80,080,066 (GRCm39) |
S119N |
probably benign |
Het |
| Scfd1 |
T |
A |
12: 51,433,862 (GRCm39) |
D51E |
probably benign |
Het |
| Smox |
A |
T |
2: 131,353,944 (GRCm39) |
E5D |
possibly damaging |
Het |
| Srpk2 |
T |
C |
5: 23,723,613 (GRCm39) |
|
probably null |
Het |
| Syne2 |
T |
A |
12: 76,147,763 (GRCm39) |
|
probably benign |
Het |
| Tcf20 |
A |
G |
15: 82,738,893 (GRCm39) |
S853P |
possibly damaging |
Het |
| Tmem131l |
A |
G |
3: 83,833,452 (GRCm39) |
F804L |
probably damaging |
Het |
| Ttll8 |
A |
G |
15: 88,798,800 (GRCm39) |
L645P |
probably damaging |
Het |
| Ubr3 |
T |
A |
2: 69,727,743 (GRCm39) |
H35Q |
probably benign |
Het |
| Uck1 |
GCCAACACC |
GCC |
2: 32,146,088 (GRCm39) |
|
probably benign |
Het |
| Vmn2r70 |
A |
T |
7: 85,214,290 (GRCm39) |
H287Q |
probably benign |
Het |
| Vps26a |
A |
T |
10: 62,304,171 (GRCm39) |
I150N |
probably damaging |
Het |
| Zfp605 |
G |
A |
5: 110,275,323 (GRCm39) |
R147H |
probably benign |
Het |
| Zfyve16 |
A |
G |
13: 92,631,596 (GRCm39) |
M1333T |
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 |
|
R1972:Rfx5
|
UTSW |
3 |
94,864,603 (GRCm39) |
missense |
probably damaging |
1.00 |
|
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'- GCTCACTCAGAAAGTACTGCG -3'
(R):5'- TTTCCCAGCCGTTAAAACAAG -3'
Sequencing Primer
(F):5'- GCCAACTTCGGTAAAATCATCAGAG -3'
(R):5'- AAGTCCTAAAAGCCTCTGTCTTTTAC -3'
|
| Posted On |
2014-10-02 |
Incidental Mutation