Incidental Mutation 'R1102:Rfx3'
| ID |
98225 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rfx3
|
| Ensembl Gene |
ENSMUSG00000040929 |
| Gene Name |
regulatory factor X, 3 (influences HLA class II expression) |
| Synonyms |
MRFX3, C230093O12Rik |
| MMRRC Submission |
039175-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1102 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
27739121-27988566 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 27845000 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 43
(V43A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000134700
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000046898]
[ENSMUST00000165566]
[ENSMUST00000172907]
[ENSMUST00000173863]
[ENSMUST00000174420]
[ENSMUST00000174850]
|
| AlphaFold |
P48381 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000046898
AA Change: V43A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: V43A
| 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 benign
Transcript: ENSMUST00000165566
AA Change: V43A
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: V43A
| 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 benign
Transcript: ENSMUST00000172907
AA Change: V43A
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: V43A
| 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 benign
Transcript: ENSMUST00000173863
AA Change: V43A
PolyPhen 2
Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)
|
| SMART Domains |
Protein: ENSMUSP00000133367
Gene: ENSMUSG00000040929
AA Change: V43A
| 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 |
possibly damaging
Transcript: ENSMUST00000174420
AA Change: V43A
PolyPhen 2
Score 0.511 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000134700
Gene: ENSMUSG00000040929
AA Change: V43A
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RFX1_trans_act
|
1 |
70 |
3e-18 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000174850
AA Change: V43A
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: V43A
| 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 |
|
| Meta Mutation Damage Score |
0.1390 |
| Coding Region Coverage |
- 1x: 98.9%
- 3x: 98.0%
- 10x: 95.3%
- 20x: 88.8%
|
| Validation Efficiency |
98% (60/61) |
| 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: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700010I14Rik |
C |
T |
17: 9,211,460 (GRCm39) |
T203M |
probably damaging |
Het |
| Acy3 |
C |
T |
19: 4,037,850 (GRCm39) |
T119I |
probably damaging |
Het |
| Ccdc6 |
C |
A |
10: 70,023,636 (GRCm39) |
H400Q |
possibly damaging |
Het |
| Ccna1 |
T |
C |
3: 54,958,281 (GRCm39) |
D134G |
probably damaging |
Het |
| Cct2 |
A |
T |
10: 116,896,545 (GRCm39) |
|
probably null |
Het |
| Cd36 |
A |
G |
5: 18,019,211 (GRCm39) |
F170S |
possibly damaging |
Het |
| Cep350 |
G |
A |
1: 155,807,264 (GRCm39) |
P718S |
probably damaging |
Het |
| Cimip1 |
T |
A |
2: 173,364,516 (GRCm39) |
D20E |
probably damaging |
Het |
| Ctnna3 |
A |
T |
10: 64,421,774 (GRCm39) |
I523L |
probably benign |
Het |
| Dnah1 |
G |
T |
14: 31,018,414 (GRCm39) |
Y1405* |
probably null |
Het |
| Dnah8 |
T |
A |
17: 31,073,738 (GRCm39) |
|
probably null |
Het |
| Drd3 |
T |
C |
16: 43,582,846 (GRCm39) |
L113S |
probably damaging |
Het |
| Emsy |
T |
C |
7: 98,251,796 (GRCm39) |
T735A |
probably damaging |
Het |
| Epha5 |
A |
G |
5: 84,381,434 (GRCm39) |
|
probably benign |
Het |
| Ezhip |
GTCATCATCATCATC |
GTCATCATCATCATCATC |
X: 5,994,645 (GRCm39) |
|
probably benign |
Het |
| Fbxo10 |
A |
G |
4: 45,043,672 (GRCm39) |
L717P |
probably damaging |
Het |
| Galnt10 |
T |
C |
11: 57,671,871 (GRCm39) |
|
probably benign |
Het |
| Gle1 |
T |
G |
2: 29,834,066 (GRCm39) |
I437M |
possibly damaging |
Het |
| Gpr137b |
T |
C |
13: 13,539,616 (GRCm39) |
|
probably benign |
Het |
| Gsta1 |
T |
C |
9: 78,149,777 (GRCm39) |
F197L |
probably damaging |
Het |
| Icam1 |
G |
A |
9: 20,939,132 (GRCm39) |
V502M |
possibly damaging |
Het |
| Ido1 |
T |
A |
8: 25,083,156 (GRCm39) |
I90F |
probably damaging |
Het |
| Il4ra |
G |
A |
7: 125,173,889 (GRCm39) |
|
probably null |
Het |
| Med12l |
T |
A |
3: 59,152,257 (GRCm39) |
M1014K |
probably damaging |
Het |
| Mmp13 |
A |
G |
9: 7,272,952 (GRCm39) |
E104G |
possibly damaging |
Het |
| Mms19 |
T |
C |
19: 41,939,284 (GRCm39) |
E495G |
possibly damaging |
Het |
| Mrc2 |
A |
G |
11: 105,231,647 (GRCm39) |
I820V |
probably benign |
Het |
| Naip6 |
T |
C |
13: 100,440,923 (GRCm39) |
K286E |
possibly damaging |
Het |
| Ndrg1 |
T |
C |
15: 66,816,685 (GRCm39) |
Y110C |
probably damaging |
Het |
| Or1e1c |
G |
A |
11: 73,265,700 (GRCm39) |
V45I |
probably benign |
Het |
| Or4a78 |
A |
T |
2: 89,497,814 (GRCm39) |
C139S |
probably damaging |
Het |
| Or5b118 |
T |
C |
19: 13,448,771 (GRCm39) |
C146R |
probably damaging |
Het |
| Or5b3 |
G |
A |
19: 13,388,454 (GRCm39) |
V174M |
probably damaging |
Het |
| Oxtr |
C |
T |
6: 112,454,138 (GRCm39) |
R42Q |
probably benign |
Het |
| Pdzd4 |
G |
A |
X: 72,839,052 (GRCm39) |
R419C |
probably damaging |
Het |
| Pnpla7 |
G |
T |
2: 24,886,177 (GRCm39) |
M3I |
probably damaging |
Het |
| Popdc3 |
A |
G |
10: 45,192,642 (GRCm39) |
|
probably benign |
Het |
| Ppp5c |
A |
G |
7: 16,756,368 (GRCm39) |
F112S |
probably benign |
Het |
| Rbp3 |
A |
G |
14: 33,678,313 (GRCm39) |
T754A |
possibly damaging |
Het |
| Reep6 |
A |
G |
10: 80,171,080 (GRCm39) |
T319A |
probably benign |
Het |
| Rint1 |
A |
G |
5: 24,010,565 (GRCm39) |
|
probably benign |
Het |
| Sacm1l |
T |
G |
9: 123,411,363 (GRCm39) |
V384G |
probably damaging |
Het |
| Shox2 |
A |
T |
3: 66,885,628 (GRCm39) |
L149Q |
probably damaging |
Het |
| Sipa1 |
T |
C |
19: 5,702,782 (GRCm39) |
H805R |
probably benign |
Het |
| Skic2 |
T |
C |
17: 35,059,082 (GRCm39) |
D1095G |
probably benign |
Het |
| Slc5a3 |
G |
T |
16: 91,874,765 (GRCm39) |
W274L |
probably damaging |
Het |
| Spata31e4 |
A |
G |
13: 50,857,118 (GRCm39) |
T919A |
probably benign |
Het |
| Sptbn1 |
G |
T |
11: 30,070,785 (GRCm39) |
H1524Q |
possibly damaging |
Het |
| Ssr1 |
G |
T |
13: 38,171,591 (GRCm39) |
Q149K |
probably benign |
Het |
| Taf7l2 |
T |
C |
10: 115,949,299 (GRCm39) |
S76G |
probably damaging |
Het |
| Thsd7a |
T |
C |
6: 12,555,701 (GRCm39) |
D61G |
possibly damaging |
Het |
| Tmem245 |
T |
C |
4: 56,903,200 (GRCm39) |
|
probably benign |
Het |
| Tmem74 |
T |
C |
15: 43,730,186 (GRCm39) |
T286A |
probably benign |
Het |
| Tnc |
T |
C |
4: 63,938,705 (GRCm39) |
N45D |
probably benign |
Het |
| Trdmt1 |
T |
G |
2: 13,528,225 (GRCm39) |
|
probably benign |
Het |
| Uty |
A |
T |
Y: 1,174,741 (GRCm39) |
Y220N |
probably damaging |
Het |
| Vdr |
T |
C |
15: 97,757,002 (GRCm39) |
Y290C |
probably damaging |
Het |
| Vmn2r19 |
T |
A |
6: 123,313,132 (GRCm39) |
M734K |
probably benign |
Het |
| Vmn2r53 |
T |
C |
7: 12,332,410 (GRCm39) |
D413G |
possibly damaging |
Het |
| Vps45 |
A |
G |
3: 95,950,253 (GRCm39) |
|
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 |
|
|
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 |
|
|
R2960:Rfx3
|
UTSW |
19 |
27,878,211 (GRCm39) |
nonsense |
probably null |
|
|
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'- TCAGGGGAAATTGCTAAGGCACAC -3'
(R):5'- ACCACTTACCATGAACCTAATGCAATGT -3'
Sequencing Primer
(F):5'- TGCTAAGGCACACACAATTTG -3'
(R):5'- AGGCTTTTAAGGTCTACTAACCC -3'
|
| Posted On |
2014-01-05 |
Incidental Mutation