Incidental Mutation 'R0098:Rfx5'
| ID |
64096 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rfx5
|
| Ensembl Gene |
ENSMUSG00000005774 |
| Gene Name |
regulatory factor X, 5 (influences HLA class II expression) |
| Synonyms |
|
| MMRRC Submission |
038384-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.274)
|
| Stock # |
R0098 (G1)
|
| Quality Score |
213 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
94861355-94868685 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 94865679 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Glutamic Acid
at position 326
(V326E)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000117963
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029772]
[ENSMUST00000107253]
[ENSMUST00000107254]
[ENSMUST00000107255]
[ENSMUST00000107260]
[ENSMUST00000132393]
[ENSMUST00000137088]
[ENSMUST00000144132]
[ENSMUST00000142311]
[ENSMUST00000145031]
[ENSMUST00000147237]
[ENSMUST00000140331]
[ENSMUST00000145472]
[ENSMUST00000152869]
|
| AlphaFold |
Q9JL61 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000029772
AA Change: V326E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000029772
Gene: ENSMUSG00000005774
AA Change: V326E
| 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 damaging
Transcript: ENSMUST00000107255
AA Change: V326E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000102876
Gene: ENSMUSG00000005774
AA Change: V326E
| 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: V326E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000102881
Gene: ENSMUSG00000005774
AA Change: V326E
| 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: V326E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000117963
Gene: ENSMUSG00000005774
AA Change: V326E
| 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: 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: ENSMUST00000140331
|
| 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 |
|
| Meta Mutation Damage Score |
0.1285 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.9%
- 10x: 97.8%
- 20x: 96.2%
|
| Validation Efficiency |
100% (54/54) |
| 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 |
|---|
| Acad9 |
T |
C |
3: 36,127,689 (GRCm39) |
I97T |
probably damaging |
Het |
| Acp3 |
C |
T |
9: 104,197,144 (GRCm39) |
|
probably null |
Het |
| Adam32 |
T |
A |
8: 25,404,405 (GRCm39) |
Y200F |
possibly damaging |
Het |
| Alpk2 |
A |
G |
18: 65,482,982 (GRCm39) |
L342S |
probably damaging |
Het |
| Arfgef3 |
A |
G |
10: 18,465,390 (GRCm39) |
V2151A |
probably damaging |
Het |
| Atm |
T |
C |
9: 53,429,869 (GRCm39) |
D389G |
probably benign |
Het |
| Atp10b |
A |
T |
11: 43,080,431 (GRCm39) |
S236C |
probably benign |
Het |
| B3gat1 |
C |
T |
9: 26,668,237 (GRCm39) |
R276C |
probably damaging |
Het |
| Cndp1 |
T |
A |
18: 84,646,949 (GRCm39) |
E246D |
probably damaging |
Het |
| Crebbp |
A |
G |
16: 3,909,792 (GRCm39) |
L1078P |
probably damaging |
Het |
| Cyp20a1 |
G |
T |
1: 60,426,413 (GRCm39) |
E452* |
probably null |
Het |
| Emb |
T |
C |
13: 117,404,034 (GRCm39) |
V262A |
probably damaging |
Het |
| Ephb1 |
C |
T |
9: 101,918,339 (GRCm39) |
R390H |
probably damaging |
Het |
| Faf1 |
T |
C |
4: 109,792,696 (GRCm39) |
L556S |
probably damaging |
Het |
| Fam237b |
T |
A |
5: 5,625,355 (GRCm39) |
L17Q |
possibly damaging |
Het |
| Fbf1 |
A |
T |
11: 116,038,945 (GRCm39) |
|
probably null |
Het |
| Gid8 |
T |
A |
2: 180,356,528 (GRCm39) |
I55N |
possibly damaging |
Het |
| Hexa |
T |
C |
9: 59,465,383 (GRCm39) |
Y213H |
probably damaging |
Het |
| Kalrn |
A |
T |
16: 33,795,989 (GRCm39) |
I1262K |
possibly damaging |
Het |
| Lrp1 |
C |
T |
10: 127,388,607 (GRCm39) |
V3281I |
probably benign |
Het |
| Lrp2 |
T |
C |
2: 69,305,756 (GRCm39) |
D2935G |
probably damaging |
Het |
| Lypd6 |
T |
A |
2: 50,080,792 (GRCm39) |
V160E |
probably benign |
Het |
| Muc19 |
C |
T |
15: 91,777,101 (GRCm39) |
|
noncoding transcript |
Het |
| Mybpc1 |
T |
C |
10: 88,365,426 (GRCm39) |
D899G |
probably benign |
Het |
| Myo18a |
A |
G |
11: 77,736,591 (GRCm39) |
E1564G |
probably damaging |
Het |
| Nrxn3 |
A |
G |
12: 89,226,971 (GRCm39) |
D202G |
probably damaging |
Het |
| Palld |
C |
A |
8: 61,978,120 (GRCm39) |
G890V |
probably damaging |
Het |
| Pcx |
C |
A |
19: 4,651,775 (GRCm39) |
|
probably benign |
Het |
| Plcg1 |
T |
C |
2: 160,573,920 (GRCm39) |
W62R |
probably damaging |
Het |
| Ppa2 |
C |
T |
3: 133,076,234 (GRCm39) |
|
probably benign |
Het |
| Ppp1r18 |
A |
G |
17: 36,178,888 (GRCm39) |
I254M |
probably benign |
Het |
| Prune2 |
A |
G |
19: 17,101,267 (GRCm39) |
E2257G |
possibly damaging |
Het |
| Rd3 |
A |
G |
1: 191,717,261 (GRCm39) |
M244V |
probably benign |
Het |
| Rgs3 |
G |
C |
4: 62,544,143 (GRCm39) |
R305P |
probably damaging |
Het |
| Rpp40 |
A |
G |
13: 36,082,970 (GRCm39) |
Y173H |
probably benign |
Het |
| Ryr3 |
T |
C |
2: 112,731,376 (GRCm39) |
N645D |
probably damaging |
Het |
| Sema3e |
T |
C |
5: 14,302,446 (GRCm39) |
V657A |
possibly damaging |
Het |
| Serpina3n |
T |
A |
12: 104,379,777 (GRCm39) |
V390E |
probably damaging |
Het |
| Shank1 |
A |
G |
7: 43,962,709 (GRCm39) |
Y141C |
unknown |
Het |
| Stat2 |
T |
A |
10: 128,119,131 (GRCm39) |
H428Q |
probably damaging |
Het |
| Stat5a |
A |
T |
11: 100,766,452 (GRCm39) |
Q378L |
probably damaging |
Het |
| Tfrc |
G |
T |
16: 32,442,244 (GRCm39) |
V490F |
probably damaging |
Het |
| Tnnt1 |
T |
C |
7: 4,512,044 (GRCm39) |
N155S |
probably damaging |
Het |
| Topaz1 |
T |
C |
9: 122,619,188 (GRCm39) |
Y1262H |
possibly damaging |
Het |
| Ubxn8 |
T |
C |
8: 34,125,393 (GRCm39) |
|
probably benign |
Het |
| Unk |
A |
G |
11: 115,940,995 (GRCm39) |
Y252C |
probably damaging |
Het |
| Vmn2r66 |
A |
C |
7: 84,654,965 (GRCm39) |
M448R |
probably damaging |
Het |
| Zfp386 |
T |
A |
12: 116,022,834 (GRCm39) |
L184* |
probably null |
Het |
| Zfp985 |
T |
C |
4: 147,661,566 (GRCm39) |
S4P |
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 |
|
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 |
|
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'- AATGGACCCTCCTGGCAGTGAC -3'
(R):5'- GCCCCTGACAAAGTAGGAACAGGTG -3'
Sequencing Primer
(F):5'- tgagccatttctccagcc -3'
(R):5'- GAACAGGTGGTAAGATCATGTTG -3'
|
| Posted On |
2013-08-06 |
Incidental Mutation