Incidental Mutation 'R5401:Rfx1'
| ID |
429993 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rfx1
|
| Ensembl Gene |
ENSMUSG00000031706 |
| Gene Name |
regulatory factor X, 1 (influences HLA class II expression) |
| Synonyms |
|
| MMRRC Submission |
042972-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5401 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
84793463-84823621 bp(+) (GRCm39) |
| Type of Mutation |
splice site |
| DNA Base Change (assembly) |
C to A
at 84793005 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000096191
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000005600]
[ENSMUST00000098592]
[ENSMUST00000211046]
|
| AlphaFold |
P48377 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000005600
|
| SMART Domains |
Protein: ENSMUSP00000005600
Gene: ENSMUSG00000031706
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
11 |
47 |
N/A |
INTRINSIC |
|
low complexity region
|
53 |
67 |
N/A |
INTRINSIC |
|
low complexity region
|
73 |
92 |
N/A |
INTRINSIC |
|
Pfam:RFX1_trans_act
|
106 |
176 |
9.6e-9 |
PFAM |
|
Pfam:RFX1_trans_act
|
211 |
366 |
1.8e-59 |
PFAM |
|
Pfam:RFX_DNA_binding
|
420 |
498 |
2.5e-35 |
PFAM |
|
Blast:HisKA
|
705 |
768 |
3e-28 |
BLAST |
|
low complexity region
|
908 |
920 |
N/A |
INTRINSIC |
|
low complexity region
|
932 |
948 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000071067
|
| SMART Domains |
Protein: ENSMUSP00000065182
Gene: ENSMUSG00000056753
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
14 |
25 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000098592
|
| SMART Domains |
Protein: ENSMUSP00000096191
Gene: ENSMUSG00000074215
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
13 |
N/A |
INTRINSIC |
|
low complexity region
|
88 |
99 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000209362
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000210660
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000211046
|
| Meta Mutation Damage Score |
0.9755 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.7%
- 10x: 97.3%
- 20x: 95.4%
|
| Validation Efficiency |
97% (66/68) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the regulatory factor X (RFX) family of transcription factors, which are characterized by a winged-helix DNA-binding domain. The encoded transcription factor contains an N-terminal activation domain and a C-terminal repression domain, and may activate or repress target gene expression depending on cellular context. This transcription factor has been shown to regulate a wide variety of genes involved in immunity and cancer, including the MHC class II genes and genes that may be involved in cancer progression. This gene exhibits altered expression in glioblastoma and the autoimmune disease systemic lupus erythematosis (SLE). [provided by RefSeq, Jul 2016]
PHENOTYPE: Mice homozygous for a gene trap allele die prior to implantation. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 53 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700001J11Rik |
A |
G |
9: 39,962,338 (GRCm39) |
|
noncoding transcript |
Het |
| 1700025H01Rik |
G |
T |
16: 30,018,801 (GRCm39) |
|
noncoding transcript |
Het |
| 9330159F19Rik |
T |
C |
10: 29,101,136 (GRCm39) |
V503A |
probably benign |
Het |
| Acacb |
A |
G |
5: 114,347,914 (GRCm39) |
N995S |
possibly damaging |
Het |
| Anapc4 |
A |
G |
5: 53,020,991 (GRCm39) |
K630R |
probably benign |
Het |
| Ankrd13a |
A |
C |
5: 114,930,234 (GRCm39) |
Q206H |
probably damaging |
Het |
| Ano10 |
A |
T |
9: 122,090,356 (GRCm39) |
L319Q |
probably damaging |
Het |
| Camkk2 |
T |
A |
5: 122,884,398 (GRCm39) |
D341V |
probably damaging |
Het |
| Ccdc88a |
A |
G |
11: 29,413,279 (GRCm39) |
I606V |
probably benign |
Het |
| Cdv3 |
G |
T |
9: 103,242,316 (GRCm39) |
|
probably benign |
Het |
| Cep97 |
A |
G |
16: 55,745,315 (GRCm39) |
V155A |
probably benign |
Het |
| Cmya5 |
T |
C |
13: 93,228,476 (GRCm39) |
E2204G |
probably damaging |
Het |
| Cracr2b |
A |
G |
7: 141,046,136 (GRCm39) |
*395W |
probably null |
Het |
| Defa27 |
A |
G |
8: 21,805,710 (GRCm39) |
E50G |
possibly damaging |
Het |
| Dnah7a |
A |
G |
1: 53,670,812 (GRCm39) |
I480T |
probably benign |
Het |
| Ep400 |
C |
A |
5: 110,831,037 (GRCm39) |
D2210Y |
unknown |
Het |
| Fam170a |
T |
A |
18: 50,413,618 (GRCm39) |
S28T |
probably benign |
Het |
| Fancc |
C |
A |
13: 63,550,767 (GRCm39) |
K18N |
probably damaging |
Het |
| Flt4 |
AC |
ACC |
11: 49,541,861 (GRCm39) |
|
probably null |
Het |
| Fndc8 |
T |
G |
11: 82,788,676 (GRCm39) |
S169A |
possibly damaging |
Het |
| Get3 |
A |
T |
8: 85,745,173 (GRCm39) |
I298N |
possibly damaging |
Het |
| Herc1 |
T |
C |
9: 66,409,338 (GRCm39) |
Y4688H |
probably damaging |
Het |
| Ighv11-2 |
A |
T |
12: 114,011,959 (GRCm39) |
D85E |
possibly damaging |
Het |
| Kat14 |
T |
C |
2: 144,231,180 (GRCm39) |
F196L |
possibly damaging |
Het |
| Kctd19 |
C |
T |
8: 106,109,617 (GRCm39) |
V942I |
probably benign |
Het |
| Llgl1 |
A |
G |
11: 60,597,297 (GRCm39) |
S249G |
probably benign |
Het |
| Map1a |
T |
C |
2: 121,130,153 (GRCm39) |
V323A |
probably damaging |
Het |
| Or4m1 |
C |
A |
14: 50,557,566 (GRCm39) |
C242F |
probably damaging |
Het |
| Phf21a |
C |
A |
2: 92,182,097 (GRCm39) |
T342K |
possibly damaging |
Het |
| Piezo2 |
T |
A |
18: 63,217,811 (GRCm39) |
D1122V |
possibly damaging |
Het |
| Pklr |
A |
G |
3: 89,049,173 (GRCm39) |
Y173C |
probably damaging |
Het |
| Plcz1 |
G |
T |
6: 139,938,778 (GRCm39) |
|
probably null |
Het |
| Polr3a |
T |
C |
14: 24,505,009 (GRCm39) |
I1084V |
possibly damaging |
Het |
| Prom1 |
A |
T |
5: 44,158,147 (GRCm39) |
Y845N |
probably damaging |
Het |
| Qng1 |
C |
A |
13: 58,530,405 (GRCm39) |
A202S |
probably benign |
Het |
| Ret |
A |
T |
6: 118,158,936 (GRCm39) |
S159T |
probably benign |
Het |
| Scp2 |
A |
T |
4: 108,001,976 (GRCm39) |
|
probably null |
Het |
| Sh3bp5 |
C |
A |
14: 31,099,452 (GRCm39) |
R265L |
probably benign |
Het |
| Slc22a30 |
G |
A |
19: 8,321,757 (GRCm39) |
Q436* |
probably null |
Het |
| Smad5 |
T |
C |
13: 56,875,282 (GRCm39) |
F157L |
probably benign |
Het |
| Smarcc2 |
C |
A |
10: 128,301,373 (GRCm39) |
D210E |
probably damaging |
Het |
| Sptlc3 |
T |
C |
2: 139,478,643 (GRCm39) |
L534P |
possibly damaging |
Het |
| Srrm1 |
A |
G |
4: 135,051,380 (GRCm39) |
|
probably benign |
Het |
| Srsf11 |
C |
T |
3: 157,728,981 (GRCm39) |
|
probably benign |
Het |
| Sugct |
T |
A |
13: 17,032,455 (GRCm39) |
Q432H |
probably damaging |
Het |
| Tex9 |
A |
T |
9: 72,394,060 (GRCm39) |
|
probably null |
Het |
| Tsc1 |
C |
A |
2: 28,576,920 (GRCm39) |
S1073* |
probably null |
Het |
| Vmn1r72 |
T |
C |
7: 11,403,843 (GRCm39) |
S202G |
probably damaging |
Het |
| Vmn2r55 |
A |
G |
7: 12,385,871 (GRCm39) |
V703A |
probably benign |
Het |
| Vmn2r67 |
A |
T |
7: 84,785,765 (GRCm39) |
Y747N |
probably damaging |
Het |
| Zcchc4 |
A |
G |
5: 52,964,419 (GRCm39) |
I292V |
probably benign |
Het |
| Zfp998 |
T |
C |
13: 66,579,722 (GRCm39) |
R254G |
probably benign |
Het |
| Zswim2 |
C |
T |
2: 83,755,589 (GRCm39) |
G104E |
possibly damaging |
Het |
|
| Other mutations in Rfx1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01612:Rfx1
|
APN |
8 |
84,819,601 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
IGL01779:Rfx1
|
APN |
8 |
84,819,291 (GRCm39) |
splice site |
probably benign |
|
|
IGL02505:Rfx1
|
APN |
8 |
84,822,438 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
IGL02741:Rfx1
|
APN |
8 |
84,822,471 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R1565:Rfx1
|
UTSW |
8 |
84,800,575 (GRCm39) |
missense |
probably benign |
|
|
R1793:Rfx1
|
UTSW |
8 |
84,793,050 (GRCm39) |
unclassified |
probably benign |
|
|
R1808:Rfx1
|
UTSW |
8 |
84,821,677 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1971:Rfx1
|
UTSW |
8 |
84,822,126 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4542:Rfx1
|
UTSW |
8 |
84,816,866 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4690:Rfx1
|
UTSW |
8 |
84,809,374 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
R4995:Rfx1
|
UTSW |
8 |
84,806,743 (GRCm39) |
splice site |
probably null |
|
|
R5163:Rfx1
|
UTSW |
8 |
84,819,840 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5212:Rfx1
|
UTSW |
8 |
84,793,221 (GRCm39) |
unclassified |
probably benign |
|
|
R5227:Rfx1
|
UTSW |
8 |
84,800,687 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5431:Rfx1
|
UTSW |
8 |
84,809,349 (GRCm39) |
nonsense |
probably null |
|
|
R5584:Rfx1
|
UTSW |
8 |
84,814,706 (GRCm39) |
splice site |
probably null |
|
|
R5693:Rfx1
|
UTSW |
8 |
84,800,533 (GRCm39) |
missense |
unknown |
|
|
R6210:Rfx1
|
UTSW |
8 |
84,819,647 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6715:Rfx1
|
UTSW |
8 |
84,822,444 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R6920:Rfx1
|
UTSW |
8 |
84,822,117 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7131:Rfx1
|
UTSW |
8 |
84,821,708 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R7155:Rfx1
|
UTSW |
8 |
84,821,455 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7336:Rfx1
|
UTSW |
8 |
84,800,385 (GRCm39) |
start gained |
probably benign |
|
|
R7467:Rfx1
|
UTSW |
8 |
84,800,542 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R8105:Rfx1
|
UTSW |
8 |
84,814,505 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R8145:Rfx1
|
UTSW |
8 |
84,800,657 (GRCm39) |
missense |
probably benign |
0.06 |
|
R8261:Rfx1
|
UTSW |
8 |
84,819,479 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8263:Rfx1
|
UTSW |
8 |
84,821,483 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8443:Rfx1
|
UTSW |
8 |
84,806,515 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8680:Rfx1
|
UTSW |
8 |
84,818,084 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R9302:Rfx1
|
UTSW |
8 |
84,817,662 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
R9473:Rfx1
|
UTSW |
8 |
84,819,903 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R9766:Rfx1
|
UTSW |
8 |
84,814,376 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1177:Rfx1
|
UTSW |
8 |
84,816,906 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTCTCATTAAATGTCTGCTGGC -3'
(R):5'- AAAGTCGGCTCTCTGGTTGG -3'
Sequencing Primer
(F):5'- GGCCAGAGACCTTTTCACTG -3'
(R):5'- TCTGGTTGGACTAACGAGAGATC -3'
|
| Posted On |
2016-09-06 |
Incidental Mutation