Incidental Mutation 'R5899:Rfx3'
| ID |
457753 |
| 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 |
044098-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5899 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
27739121-27988566 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 27808165 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 193
(T193A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133367
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000046898]
[ENSMUST00000165566]
[ENSMUST00000172907]
[ENSMUST00000173863]
[ENSMUST00000174850]
|
| AlphaFold |
P48381 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000046898
AA Change: T168A
PolyPhen 2
Score 0.814 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: T168A
| 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 |
possibly damaging
Transcript: ENSMUST00000165566
AA Change: T193A
PolyPhen 2
Score 0.903 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: T193A
| 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 |
possibly damaging
Transcript: ENSMUST00000172907
AA Change: T193A
PolyPhen 2
Score 0.903 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: T193A
| 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 damaging
Transcript: ENSMUST00000173863
AA Change: T193A
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000133367
Gene: ENSMUSG00000040929
AA Change: T193A
| 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: ENSMUST00000174850
AA Change: T193A
PolyPhen 2
Score 0.903 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: T193A
| 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 |
0.1780 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.6%
- 20x: 92.5%
|
| Validation Efficiency |
93% (56/60) |
| 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: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ahi1 |
T |
C |
10: 20,876,465 (GRCm39) |
I792T |
probably benign |
Het |
| Anks1b |
T |
A |
10: 90,759,379 (GRCm39) |
|
probably null |
Het |
| Ano3 |
T |
G |
2: 110,693,232 (GRCm39) |
D122A |
probably benign |
Het |
| Atp12a |
T |
C |
14: 56,610,801 (GRCm39) |
V315A |
probably benign |
Het |
| B230104I21Rik |
G |
T |
4: 154,433,986 (GRCm39) |
G57* |
probably null |
Het |
| Bpifb2 |
A |
G |
2: 153,733,050 (GRCm39) |
K378E |
probably damaging |
Het |
| Cdk5rap2 |
T |
C |
4: 70,161,830 (GRCm39) |
|
probably benign |
Het |
| Ceacam23 |
A |
G |
7: 17,651,369 (GRCm39) |
D840G |
possibly damaging |
Het |
| Cflar |
A |
G |
1: 58,791,927 (GRCm39) |
D410G |
probably benign |
Het |
| Clcn6 |
A |
G |
4: 148,102,049 (GRCm39) |
V345A |
probably benign |
Het |
| Cnga1 |
C |
T |
5: 72,776,404 (GRCm39) |
V20I |
possibly damaging |
Het |
| Ddx50 |
T |
A |
10: 62,476,596 (GRCm39) |
K226* |
probably null |
Het |
| Dnah5 |
T |
C |
15: 28,448,513 (GRCm39) |
V4192A |
possibly damaging |
Het |
| Dnah8 |
G |
A |
17: 30,875,659 (GRCm39) |
D494N |
probably benign |
Het |
| Dock7 |
A |
T |
4: 98,879,660 (GRCm39) |
C965S |
probably benign |
Het |
| Dst |
C |
T |
1: 34,334,370 (GRCm39) |
A5083V |
probably damaging |
Het |
| E130208F15Rik |
T |
C |
7: 30,021,726 (GRCm39) |
Q10R |
probably damaging |
Het |
| Fbxw15 |
T |
C |
9: 109,384,741 (GRCm39) |
|
probably null |
Het |
| Fxr2 |
A |
G |
11: 69,543,511 (GRCm39) |
N671D |
probably damaging |
Het |
| Gbp7 |
A |
G |
3: 142,252,303 (GRCm39) |
T629A |
probably benign |
Het |
| Grm1 |
T |
C |
10: 10,565,092 (GRCm39) |
Y1072C |
probably benign |
Het |
| Hmcn2 |
A |
T |
2: 31,244,685 (GRCm39) |
E714V |
possibly damaging |
Het |
| Hsd17b13 |
T |
A |
5: 104,113,730 (GRCm39) |
E205D |
probably benign |
Het |
| Igf2bp3 |
A |
G |
6: 49,094,084 (GRCm39) |
|
probably benign |
Het |
| Il2ra |
A |
G |
2: 11,689,248 (GRCm39) |
H259R |
probably benign |
Het |
| Klk15 |
G |
T |
7: 43,588,247 (GRCm39) |
R185L |
probably benign |
Het |
| Map3k11 |
T |
G |
19: 5,745,937 (GRCm39) |
|
probably null |
Het |
| Morn3 |
A |
G |
5: 123,179,166 (GRCm39) |
W95R |
probably damaging |
Het |
| Nipbl |
A |
G |
15: 8,364,328 (GRCm39) |
|
probably null |
Het |
| Nrap |
A |
T |
19: 56,329,006 (GRCm39) |
V1145D |
possibly damaging |
Het |
| Or1e35 |
A |
G |
11: 73,797,755 (GRCm39) |
S188P |
probably damaging |
Het |
| Or2l13b |
C |
T |
16: 19,349,551 (GRCm39) |
G40R |
probably damaging |
Het |
| Or9k2 |
T |
A |
10: 129,998,542 (GRCm39) |
I218F |
probably benign |
Het |
| Pdcd11 |
A |
G |
19: 47,093,198 (GRCm39) |
N492S |
possibly damaging |
Het |
| Ptgfr |
C |
T |
3: 151,540,738 (GRCm39) |
V257I |
probably damaging |
Het |
| Racgap1 |
T |
C |
15: 99,521,509 (GRCm39) |
E549G |
possibly damaging |
Het |
| Rplp0 |
T |
A |
5: 115,699,489 (GRCm39) |
I149N |
probably benign |
Het |
| Samd7 |
T |
G |
3: 30,810,883 (GRCm39) |
I300S |
probably benign |
Het |
| Scpep1 |
A |
G |
11: 88,825,402 (GRCm39) |
|
probably null |
Het |
| Senp6 |
T |
C |
9: 80,049,352 (GRCm39) |
|
probably benign |
Het |
| Serpinb2 |
G |
T |
1: 107,447,446 (GRCm39) |
G78V |
probably damaging |
Het |
| Sesn1 |
T |
C |
10: 41,687,189 (GRCm39) |
S58P |
probably benign |
Het |
| Skic3 |
A |
G |
13: 76,259,938 (GRCm39) |
|
probably null |
Het |
| Spg11 |
T |
C |
2: 121,928,680 (GRCm39) |
D591G |
possibly damaging |
Het |
| Spire2 |
A |
C |
8: 124,080,833 (GRCm39) |
S26R |
probably damaging |
Het |
| Strip2 |
T |
A |
6: 29,956,957 (GRCm39) |
|
probably benign |
Het |
| Ttn |
G |
A |
2: 76,697,519 (GRCm39) |
|
probably benign |
Het |
| Vmn2r77 |
A |
G |
7: 86,460,924 (GRCm39) |
Y750C |
probably damaging |
Het |
| Wnt11 |
T |
A |
7: 98,488,383 (GRCm39) |
Y23* |
probably null |
Het |
| Zbp1 |
T |
A |
2: 173,052,340 (GRCm39) |
D272V |
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 |
|
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'- CAACACTGCTCTAATAGAATCAGAG -3'
(R):5'- TGATAACTGCTGTGATGTTTCCC -3'
Sequencing Primer
(F):5'- GAAGAACTAATTATGTCGACTGTCAG -3'
(R):5'- ATAACTGCTGTGATGTTTCCCATATC -3'
|
| Posted On |
2017-02-15 |
Incidental Mutation