Incidental Mutation 'R2960:Rfx3'
| ID |
255897 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rfx3
|
| Ensembl Gene |
ENSMUSG00000040929 |
| Gene Name |
regulatory factor X, 3 (influences HLA class II expression) |
| Synonyms |
MRFX3, C230093O12Rik |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R2960 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
19 |
| Chromosomal Location |
27739121-27988566 bp(-) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
G to A
at 27878211 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamine to Stop codon
at position 29
(Q29*)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133461
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000046898]
[ENSMUST00000165566]
[ENSMUST00000172907]
[ENSMUST00000173863]
[ENSMUST00000174420]
[ENSMUST00000174850]
|
| AlphaFold |
P48381 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000046898
AA Change: Q29*
|
| SMART Domains |
Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: Q29*
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX1_trans_act
|
1 |
140 |
6.3e-58 |
PFAM |
|
Pfam:RFX_DNA_binding
|
150 |
235 |
6.9e-41 |
PFAM |
|
low complexity region
|
274 |
283 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
326 |
414 |
1.39e-5 |
PROSPERO |
|
internal_repeat_1
|
439 |
527 |
1.39e-5 |
PROSPERO |
|
low complexity region
|
649 |
664 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000165566
AA Change: Q29*
|
| SMART Domains |
Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: Q29*
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX1_trans_act
|
4 |
138 |
9.7e-38 |
PFAM |
|
Pfam:RFX_DNA_binding
|
181 |
258 |
6.2e-36 |
PFAM |
|
low complexity region
|
299 |
308 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
351 |
439 |
1.82e-5 |
PROSPERO |
|
internal_repeat_1
|
464 |
552 |
1.82e-5 |
PROSPERO |
|
low complexity region
|
674 |
689 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000172907
AA Change: Q29*
|
| SMART Domains |
Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: Q29*
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX1_trans_act
|
1 |
140 |
9.4e-58 |
PFAM |
|
Pfam:RFX_DNA_binding
|
175 |
260 |
5.2e-41 |
PFAM |
|
low complexity region
|
299 |
308 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
351 |
439 |
1.82e-5 |
PROSPERO |
|
internal_repeat_1
|
464 |
552 |
1.82e-5 |
PROSPERO |
|
low complexity region
|
674 |
689 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173161
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000173863
AA Change: Q29*
|
| SMART Domains |
Protein: ENSMUSP00000133367
Gene: ENSMUSG00000040929
AA Change: Q29*
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX1_trans_act
|
1 |
140 |
3.3e-58 |
PFAM |
|
Pfam:RFX_DNA_binding
|
175 |
246 |
3.7e-24 |
PFAM |
|
low complexity region
|
285 |
294 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000174420
AA Change: Q29*
|
| SMART Domains |
Protein: ENSMUSP00000134700
Gene: ENSMUSG00000040929
AA Change: Q29*
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX1_trans_act
|
1 |
70 |
3e-18 |
PFAM |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000174850
AA Change: Q29*
|
| SMART Domains |
Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: Q29*
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX1_trans_act
|
1 |
140 |
9.4e-58 |
PFAM |
|
Pfam:RFX_DNA_binding
|
175 |
260 |
5.2e-41 |
PFAM |
|
low complexity region
|
299 |
308 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
351 |
439 |
1.82e-5 |
PROSPERO |
|
internal_repeat_1
|
464 |
552 |
1.82e-5 |
PROSPERO |
|
low complexity region
|
674 |
689 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.8%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X2, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. Multiple transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2013]
PHENOTYPE: Homozygous null mice display embryonic and perinatal lethality, impaired development of cilia on the embryonic node, abnormal left-right patterning, meso- and dextrocardia, and situs inversus in surviving adults. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 24 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Arl5c |
A |
G |
11: 97,885,902 (GRCm39) |
L33P |
probably damaging |
Het |
| Auh |
A |
T |
13: 52,993,610 (GRCm39) |
I268N |
probably damaging |
Het |
| Cimap2 |
A |
G |
4: 106,470,615 (GRCm39) |
S186P |
probably damaging |
Het |
| Defa25 |
A |
T |
8: 21,575,273 (GRCm39) |
H84L |
probably benign |
Het |
| Endou |
T |
C |
15: 97,611,687 (GRCm39) |
Y317C |
probably damaging |
Het |
| Fmn2 |
C |
T |
1: 174,437,385 (GRCm39) |
L1119F |
probably damaging |
Het |
| Glyat |
T |
A |
19: 12,617,214 (GRCm39) |
L22H |
probably damaging |
Het |
| Gpd2 |
C |
T |
2: 57,228,987 (GRCm39) |
R264* |
probably null |
Het |
| Grb7 |
C |
T |
11: 98,343,087 (GRCm39) |
T268I |
probably damaging |
Het |
| Ints15 |
A |
T |
5: 143,293,776 (GRCm39) |
F234I |
probably benign |
Het |
| Itfg2 |
G |
A |
6: 128,390,515 (GRCm39) |
A190V |
probably benign |
Het |
| Kirrel1 |
C |
T |
3: 86,996,458 (GRCm39) |
M380I |
probably null |
Het |
| Mdga2 |
G |
T |
12: 66,676,752 (GRCm39) |
Y513* |
probably null |
Het |
| Med8 |
A |
G |
4: 118,271,944 (GRCm39) |
T222A |
probably damaging |
Het |
| Nup43 |
T |
C |
10: 7,546,713 (GRCm39) |
V111A |
probably benign |
Het |
| Or9s14 |
A |
G |
1: 92,536,050 (GRCm39) |
I164V |
probably benign |
Het |
| Rfx8 |
A |
G |
1: 39,722,112 (GRCm39) |
V291A |
probably damaging |
Het |
| Scnn1a |
A |
G |
6: 125,299,256 (GRCm39) |
Y112C |
probably damaging |
Het |
| Tex11 |
C |
A |
X: 99,977,021 (GRCm39) |
A487S |
possibly damaging |
Het |
| Tmx3 |
T |
C |
18: 90,551,116 (GRCm39) |
V252A |
probably damaging |
Het |
| Vmn1r216 |
A |
G |
13: 23,284,103 (GRCm39) |
D262G |
probably benign |
Het |
| Vmn1r9 |
A |
G |
6: 57,048,657 (GRCm39) |
D244G |
possibly damaging |
Het |
| Xkr6 |
T |
A |
14: 63,844,586 (GRCm39) |
M203K |
possibly damaging |
Het |
| Zfr |
G |
A |
15: 12,162,319 (GRCm39) |
R823H |
probably benign |
Het |
|
| Other mutations in Rfx3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00548:Rfx3
|
APN |
19 |
27,783,586 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL00588:Rfx3
|
APN |
19 |
27,803,476 (GRCm39) |
nonsense |
probably null |
|
|
IGL01408:Rfx3
|
APN |
19 |
27,746,050 (GRCm39) |
missense |
probably benign |
0.04 |
|
IGL01937:Rfx3
|
APN |
19 |
27,808,129 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02668:Rfx3
|
APN |
19 |
27,793,014 (GRCm39) |
splice site |
probably benign |
|
|
IGL02679:Rfx3
|
APN |
19 |
27,827,137 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R0267:Rfx3
|
UTSW |
19 |
27,771,188 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0336:Rfx3
|
UTSW |
19 |
27,783,662 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0838:Rfx3
|
UTSW |
19 |
27,827,367 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R0967:Rfx3
|
UTSW |
19 |
27,783,751 (GRCm39) |
splice site |
probably benign |
|
|
R1102:Rfx3
|
UTSW |
19 |
27,845,000 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
R1507:Rfx3
|
UTSW |
19 |
27,745,913 (GRCm39) |
missense |
probably benign |
0.00 |
|
R2172:Rfx3
|
UTSW |
19 |
27,792,894 (GRCm39) |
nonsense |
probably null |
|
|
R2844:Rfx3
|
UTSW |
19 |
27,784,186 (GRCm39) |
splice site |
probably benign |
|
|
R4291:Rfx3
|
UTSW |
19 |
27,777,632 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4952:Rfx3
|
UTSW |
19 |
27,808,072 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5198:Rfx3
|
UTSW |
19 |
27,808,176 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5451:Rfx3
|
UTSW |
19 |
27,827,359 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5590:Rfx3
|
UTSW |
19 |
27,779,780 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5641:Rfx3
|
UTSW |
19 |
27,771,008 (GRCm39) |
splice site |
probably null |
|
|
R5663:Rfx3
|
UTSW |
19 |
27,771,017 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5899:Rfx3
|
UTSW |
19 |
27,808,165 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6049:Rfx3
|
UTSW |
19 |
27,779,795 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6368:Rfx3
|
UTSW |
19 |
27,746,009 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R7131:Rfx3
|
UTSW |
19 |
27,746,028 (GRCm39) |
nonsense |
probably null |
|
|
R7273:Rfx3
|
UTSW |
19 |
27,779,858 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7593:Rfx3
|
UTSW |
19 |
27,827,139 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7814:Rfx3
|
UTSW |
19 |
27,803,470 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7815:Rfx3
|
UTSW |
19 |
27,803,448 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8458:Rfx3
|
UTSW |
19 |
27,771,072 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R8995:Rfx3
|
UTSW |
19 |
27,783,725 (GRCm39) |
missense |
probably benign |
0.14 |
|
R9147:Rfx3
|
UTSW |
19 |
27,878,207 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R9148:Rfx3
|
UTSW |
19 |
27,878,207 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R9310:Rfx3
|
UTSW |
19 |
27,827,329 (GRCm39) |
missense |
probably benign |
0.00 |
|
Z1088:Rfx3
|
UTSW |
19 |
27,814,850 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TATCTCTACAGCCCAGCAAGG -3'
(R):5'- CCTCGTAATAGGATTTAAGAACTGC -3'
Sequencing Primer
(F):5'- TAACCAAGAGATGTCTGCTATCC -3'
(R):5'- GAACTGCAGTGACACTTATCATGC -3'
|
| Posted On |
2014-12-29 |
Incidental Mutation