Incidental Mutation 'R6049:Rfx3'
| ID |
483481 |
| 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 |
044217-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6049 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
27739121-27988566 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 27779795 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Lysine
at position 481
(M481K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133461
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000046898]
[ENSMUST00000165566]
[ENSMUST00000172907]
[ENSMUST00000173863]
[ENSMUST00000174850]
|
| AlphaFold |
P48381 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000046898
AA Change: M456K
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: M456K
| 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 damaging
Transcript: ENSMUST00000165566
AA Change: M481K
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: M481K
| 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 |
noncoding transcript
Transcript: ENSMUST00000172498
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000172907
AA Change: M481K
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: M481K
| 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 |
possibly damaging
Transcript: ENSMUST00000173863
AA Change: N415K
PolyPhen 2
Score 0.883 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000133367
Gene: ENSMUSG00000040929
AA Change: N415K
| 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 damaging
Transcript: ENSMUST00000174850
AA Change: M481K
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: M481K
| 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 |
0.9209 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.1%
- 20x: 94.3%
|
| 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: 62 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4921539E11Rik |
G |
A |
4: 103,088,520 (GRCm39) |
H229Y |
probably benign |
Het |
| Aadacl2fm2 |
A |
C |
3: 59,659,570 (GRCm39) |
D341A |
probably damaging |
Het |
| Abcd2 |
A |
G |
15: 91,062,439 (GRCm39) |
F500L |
probably benign |
Het |
| Adgb |
A |
G |
10: 10,253,770 (GRCm39) |
L1190P |
probably damaging |
Het |
| Adgrv1 |
A |
G |
13: 81,545,473 (GRCm39) |
V5604A |
probably benign |
Het |
| Ank2 |
T |
A |
3: 126,736,669 (GRCm39) |
T3072S |
possibly damaging |
Het |
| Arhgap39 |
A |
G |
15: 76,611,601 (GRCm39) |
|
probably null |
Het |
| C6 |
T |
C |
15: 4,764,654 (GRCm39) |
C117R |
probably damaging |
Het |
| Cacna1a |
A |
G |
8: 85,365,475 (GRCm39) |
E2206G |
probably damaging |
Het |
| Cd2bp2 |
A |
T |
7: 126,793,007 (GRCm39) |
F338L |
probably damaging |
Het |
| Cemip2 |
A |
T |
19: 21,803,490 (GRCm39) |
Q841L |
probably benign |
Het |
| Cngb1 |
T |
C |
8: 95,997,470 (GRCm39) |
D575G |
probably damaging |
Het |
| Cplane2 |
T |
A |
4: 140,945,473 (GRCm39) |
V108D |
probably benign |
Het |
| Crat |
A |
G |
2: 30,293,553 (GRCm39) |
F63S |
probably damaging |
Het |
| Crybg3 |
T |
C |
16: 59,364,417 (GRCm39) |
T2402A |
probably benign |
Het |
| Ctsq |
A |
G |
13: 61,186,572 (GRCm39) |
|
probably null |
Het |
| Cux1 |
T |
C |
5: 136,361,564 (GRCm39) |
R248G |
probably damaging |
Het |
| D7Ertd443e |
T |
C |
7: 133,899,961 (GRCm39) |
H420R |
probably benign |
Het |
| Deup1 |
A |
G |
9: 15,472,552 (GRCm39) |
F587L |
possibly damaging |
Het |
| Dnah6 |
T |
C |
6: 73,063,149 (GRCm39) |
K2651R |
probably benign |
Het |
| Dnah7b |
A |
G |
1: 46,124,762 (GRCm39) |
I144V |
probably benign |
Het |
| Dnajc1 |
T |
C |
2: 18,236,511 (GRCm39) |
|
probably null |
Het |
| Fscb |
T |
C |
12: 64,521,094 (GRCm39) |
N124S |
possibly damaging |
Het |
| Gabbr2 |
A |
G |
4: 46,787,641 (GRCm39) |
Y341H |
probably damaging |
Het |
| Greb1 |
T |
A |
12: 16,731,395 (GRCm39) |
I1648F |
probably damaging |
Het |
| Hace1 |
A |
T |
10: 45,562,758 (GRCm39) |
N758Y |
probably damaging |
Het |
| Irs2 |
A |
C |
8: 11,056,805 (GRCm39) |
D542E |
probably benign |
Het |
| Kat6a |
T |
A |
8: 23,429,053 (GRCm39) |
H1469Q |
possibly damaging |
Het |
| Kif15 |
G |
A |
9: 122,840,687 (GRCm39) |
R36K |
probably damaging |
Het |
| Krt42 |
C |
T |
11: 100,157,886 (GRCm39) |
V193M |
probably damaging |
Het |
| Limch1 |
A |
T |
5: 67,188,203 (GRCm39) |
E878V |
probably benign |
Het |
| Med18 |
G |
T |
4: 132,187,024 (GRCm39) |
D158E |
probably benign |
Het |
| Med6 |
T |
C |
12: 81,638,097 (GRCm39) |
N38S |
probably damaging |
Het |
| Mup13 |
T |
C |
4: 61,183,596 (GRCm39) |
T76A |
probably benign |
Het |
| Nlrp4b |
T |
A |
7: 10,448,640 (GRCm39) |
L281* |
probably null |
Het |
| Or5h23 |
A |
T |
16: 58,906,509 (GRCm39) |
C112* |
probably null |
Het |
| Or7g28 |
C |
A |
9: 19,272,640 (GRCm39) |
G4* |
probably null |
Het |
| Or9r3 |
A |
T |
10: 129,948,481 (GRCm39) |
H59Q |
probably benign |
Het |
| Pde4d |
A |
T |
13: 109,169,119 (GRCm39) |
R54* |
probably null |
Het |
| Pdpk1 |
A |
T |
17: 24,317,109 (GRCm39) |
Y251* |
probably null |
Het |
| Pdzk1 |
A |
G |
3: 96,758,979 (GRCm39) |
E128G |
probably benign |
Het |
| Phf12 |
A |
G |
11: 77,918,996 (GRCm39) |
|
probably null |
Het |
| Pnliprp2 |
A |
G |
19: 58,748,884 (GRCm39) |
E63G |
possibly damaging |
Het |
| Prkcd |
T |
C |
14: 30,329,254 (GRCm39) |
E62G |
possibly damaging |
Het |
| Prl7b1 |
G |
T |
13: 27,790,161 (GRCm39) |
D77E |
probably benign |
Het |
| Rbck1 |
G |
T |
2: 152,165,094 (GRCm39) |
C85* |
probably null |
Het |
| Rmdn3 |
A |
G |
2: 118,983,906 (GRCm39) |
F159L |
probably damaging |
Het |
| Rpusd3 |
A |
C |
6: 113,394,802 (GRCm39) |
|
probably null |
Het |
| Ska1 |
T |
C |
18: 74,335,671 (GRCm39) |
T100A |
probably benign |
Het |
| Slc1a3 |
T |
C |
15: 8,675,177 (GRCm39) |
E276G |
probably damaging |
Het |
| Slc27a6 |
T |
A |
18: 58,731,732 (GRCm39) |
Y361N |
probably damaging |
Het |
| Smc1b |
A |
G |
15: 85,005,896 (GRCm39) |
L336S |
probably damaging |
Het |
| St7 |
A |
G |
6: 17,694,347 (GRCm39) |
D46G |
possibly damaging |
Het |
| Supt5 |
A |
G |
7: 28,014,622 (GRCm39) |
I1059T |
probably benign |
Het |
| Syne1 |
A |
T |
10: 5,297,926 (GRCm39) |
S1124T |
possibly damaging |
Het |
| Szt2 |
A |
G |
4: 118,260,185 (GRCm39) |
S54P |
probably damaging |
Het |
| Tanc2 |
G |
A |
11: 105,758,543 (GRCm39) |
R768Q |
probably damaging |
Het |
| Tbc1d7 |
A |
C |
13: 43,312,836 (GRCm39) |
M19R |
probably damaging |
Het |
| Tbpl2 |
T |
C |
2: 23,985,004 (GRCm39) |
N47D |
possibly damaging |
Het |
| Tgfbr3 |
C |
T |
5: 107,266,351 (GRCm39) |
A790T |
probably damaging |
Het |
| Tnr |
T |
C |
1: 159,740,324 (GRCm39) |
V1166A |
probably damaging |
Het |
| Ttn |
G |
A |
2: 76,676,654 (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 |
|
|
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 |
|
|
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 |
|
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'- TGAGTAACAGCTCTGAACGAC -3'
(R):5'- CGAGTCTAGTATTTTGAGACGCAC -3'
Sequencing Primer
(F):5'- CGACAGAATCCATATGCTAGTTCTGC -3'
(R):5'- CTTTTTCTGTCATTCAGGTG -3'
|
| Posted On |
2017-07-14 |
Incidental Mutation