Incidental Mutation 'R7815:Rfx3'
| ID |
601495 |
| 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 # |
R7815 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
19 |
| Chromosomal Location |
27739121-27988566 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 27803448 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Lysine
at position 265
(M265K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133367
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000046898]
[ENSMUST00000165566]
[ENSMUST00000172907]
[ENSMUST00000173863]
[ENSMUST00000174850]
|
| AlphaFold |
P48381 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000046898
AA Change: M254K
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: M254K
| 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: M279K
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: M279K
| 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: M279K
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: M279K
| 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 |
probably benign
Transcript: ENSMUST00000173863
AA Change: M265K
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000133367
Gene: ENSMUSG00000040929
AA Change: M265K
| 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 benign
Transcript: ENSMUST00000174850
AA Change: M279K
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: M279K
| 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: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 99.1%
|
| 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: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc2 |
A |
G |
19: 43,818,866 (GRCm39) |
D1285G |
probably benign |
Het |
| Abcc9 |
A |
G |
6: 142,598,331 (GRCm39) |
V669A |
probably damaging |
Het |
| Ajap1 |
C |
A |
4: 153,517,288 (GRCm39) |
G18C |
probably damaging |
Het |
| Alms1 |
G |
T |
6: 85,592,340 (GRCm39) |
M397I |
probably benign |
Het |
| Ampd2 |
A |
T |
3: 107,982,247 (GRCm39) |
M794K |
probably benign |
Het |
| Ankrd35 |
A |
T |
3: 96,592,117 (GRCm39) |
Q801L |
probably damaging |
Het |
| Casz1 |
A |
T |
4: 149,013,762 (GRCm39) |
I109F |
possibly damaging |
Het |
| Ces5a |
G |
A |
8: 94,247,623 (GRCm39) |
S297F |
possibly damaging |
Het |
| Col7a1 |
A |
G |
9: 108,798,633 (GRCm39) |
D1762G |
probably damaging |
Het |
| Dsp |
A |
T |
13: 38,375,446 (GRCm39) |
Y1077F |
probably benign |
Het |
| Eef2k |
A |
G |
7: 120,457,793 (GRCm39) |
N51D |
probably benign |
Het |
| Erbb4 |
A |
G |
1: 68,081,885 (GRCm39) |
Y1050H |
probably damaging |
Het |
| Fpgt |
A |
T |
3: 154,792,289 (GRCm39) |
S579R |
probably benign |
Het |
| Gabra4 |
T |
A |
5: 71,815,152 (GRCm39) |
M1L |
possibly damaging |
Het |
| Galk2 |
G |
A |
2: 125,817,321 (GRCm39) |
S370N |
probably damaging |
Het |
| Gpr155 |
T |
A |
2: 73,192,904 (GRCm39) |
T516S |
probably benign |
Het |
| Homez |
T |
C |
14: 55,095,675 (GRCm39) |
N11S |
probably benign |
Het |
| Hspg2 |
G |
A |
4: 137,239,775 (GRCm39) |
G494D |
probably damaging |
Het |
| Htr3b |
C |
T |
9: 48,856,833 (GRCm39) |
R215Q |
probably benign |
Het |
| Igfbp4 |
A |
G |
11: 98,932,654 (GRCm39) |
E111G |
probably benign |
Het |
| Igkv8-19 |
T |
C |
6: 70,318,420 (GRCm39) |
T5A |
probably benign |
Het |
| Insrr |
A |
G |
3: 87,716,002 (GRCm39) |
K566E |
probably damaging |
Het |
| Iqsec3 |
A |
G |
6: 121,450,317 (GRCm39) |
V69A |
probably benign |
Het |
| Kdm5d |
T |
C |
Y: 940,702 (GRCm39) |
V1071A |
probably damaging |
Het |
| Kif28 |
A |
G |
1: 179,563,548 (GRCm39) |
C143R |
probably damaging |
Het |
| Kpna6 |
T |
C |
4: 129,551,590 (GRCm39) |
M65V |
probably benign |
Het |
| L3mbtl3 |
T |
C |
10: 26,156,276 (GRCm39) |
S669G |
unknown |
Het |
| Man1a2 |
A |
T |
3: 100,563,495 (GRCm39) |
I50N |
probably damaging |
Het |
| Map3k11 |
A |
T |
19: 5,745,667 (GRCm39) |
M356L |
possibly damaging |
Het |
| Meioc |
A |
T |
11: 102,566,414 (GRCm39) |
N677Y |
probably damaging |
Het |
| Myom3 |
A |
T |
4: 135,528,674 (GRCm39) |
K1108M |
possibly damaging |
Het |
| Nav1 |
C |
T |
1: 135,512,377 (GRCm39) |
E228K |
possibly damaging |
Het |
| Ncapd3 |
G |
A |
9: 26,974,736 (GRCm39) |
W736* |
probably null |
Het |
| Nfkb1 |
T |
C |
3: 135,309,552 (GRCm39) |
D514G |
probably damaging |
Het |
| Nnt |
T |
A |
13: 119,494,111 (GRCm39) |
T657S |
possibly damaging |
Het |
| Or4k5 |
A |
G |
14: 50,386,253 (GRCm39) |
F26S |
probably benign |
Het |
| Or51b4 |
A |
G |
7: 103,530,992 (GRCm39) |
S153P |
probably benign |
Het |
| Oser1 |
A |
T |
2: 163,253,336 (GRCm39) |
S58T |
possibly damaging |
Het |
| Pcdha5 |
T |
A |
18: 37,094,556 (GRCm39) |
I355N |
possibly damaging |
Het |
| Pllp |
C |
G |
8: 95,402,804 (GRCm39) |
G99A |
probably damaging |
Het |
| Pram1 |
A |
G |
17: 33,861,106 (GRCm39) |
N509S |
probably benign |
Het |
| Prkd1 |
A |
C |
12: 50,472,300 (GRCm39) |
N204K |
probably damaging |
Het |
| Prss23 |
G |
A |
7: 89,159,253 (GRCm39) |
P272L |
probably damaging |
Het |
| Pxdn |
T |
C |
12: 30,055,824 (GRCm39) |
F1057L |
probably damaging |
Het |
| Rapgef5 |
T |
A |
12: 117,719,702 (GRCm39) |
S777R |
probably benign |
Het |
| Repin1 |
G |
T |
6: 48,574,279 (GRCm39) |
E403* |
probably null |
Het |
| S100a7a |
C |
A |
3: 90,565,119 (GRCm39) |
H105N |
probably benign |
Het |
| Serpinb3b |
T |
C |
1: 107,084,625 (GRCm39) |
D132G |
probably damaging |
Het |
| Sp7 |
T |
A |
15: 102,274,822 (GRCm39) |
|
probably benign |
Het |
| Tacstd2 |
A |
G |
6: 67,512,140 (GRCm39) |
F184S |
possibly damaging |
Het |
| Trdc |
C |
A |
14: 54,381,259 (GRCm39) |
|
probably benign |
Het |
| Trpa1 |
T |
A |
1: 14,974,486 (GRCm39) |
H232L |
probably benign |
Het |
| Trpc3 |
G |
T |
3: 36,709,294 (GRCm39) |
T394K |
probably benign |
Het |
| Tuba3b |
G |
A |
6: 145,566,847 (GRCm39) |
V363I |
possibly damaging |
Het |
| Tubb2a |
C |
A |
13: 34,258,962 (GRCm39) |
R276L |
probably benign |
Het |
| Ubap2l |
A |
T |
3: 89,951,071 (GRCm39) |
L72* |
probably null |
Het |
| Vps13a |
A |
T |
19: 16,702,936 (GRCm39) |
D672E |
probably damaging |
Het |
| Wdr26 |
A |
G |
1: 181,036,638 (GRCm39) |
V166A |
probably benign |
Het |
| Wwox |
T |
C |
8: 115,438,776 (GRCm39) |
S281P |
probably damaging |
Het |
| Xirp2 |
G |
A |
2: 67,339,756 (GRCm39) |
G666R |
probably damaging |
Het |
| Zfp131 |
T |
C |
13: 120,237,516 (GRCm39) |
K247E |
probably damaging |
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 |
|
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 |
|
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'- TCTATGCGGACCCAAAACACTG -3'
(R):5'- AAGGAGCTGTGCACCATGAG -3'
Sequencing Primer
(F):5'- TTGAGAGAGGGATCACTGGAATTC -3'
(R):5'- TTTTCTGCGTGAAGTTAATGGC -3'
|
| Posted On |
2019-12-03 |
Incidental Mutation