Incidental Mutation 'R5198:Rfx3'
| ID |
400529 |
| 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 |
042774-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5198 (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 27808176 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 189
(D189G)
|
| 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: D164G
PolyPhen 2
Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: D164G
| 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: D189G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: D189G
| 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: D189G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: D189G
| 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: D189G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000133367
Gene: ENSMUSG00000040929
AA Change: D189G
| 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: D189G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: D189G
| 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 |
0.8243 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.1%
|
| Validation Efficiency |
98% (54/55) |
| 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: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc9 |
A |
G |
6: 142,571,726 (GRCm39) |
V1121A |
probably benign |
Het |
| Adamtsl3 |
A |
C |
7: 82,261,006 (GRCm39) |
K1647Q |
possibly damaging |
Het |
| Adgrb1 |
A |
T |
15: 74,415,550 (GRCm39) |
Q710L |
probably null |
Het |
| Alox12 |
T |
C |
11: 70,145,243 (GRCm39) |
E110G |
probably damaging |
Het |
| Cep152 |
T |
A |
2: 125,429,544 (GRCm39) |
M738L |
probably benign |
Het |
| Cma2 |
T |
C |
14: 56,209,532 (GRCm39) |
V38A |
probably benign |
Het |
| Dlc1 |
C |
T |
8: 37,405,552 (GRCm39) |
G79D |
probably damaging |
Het |
| Dmpk |
C |
G |
7: 18,821,944 (GRCm39) |
L301V |
probably benign |
Het |
| Dus3l |
A |
G |
17: 57,076,574 (GRCm39) |
I585V |
probably benign |
Het |
| Etl4 |
A |
G |
2: 20,718,198 (GRCm39) |
Y313C |
probably damaging |
Het |
| Fbxw15 |
C |
A |
9: 109,387,242 (GRCm39) |
S251I |
probably benign |
Het |
| Gata4 |
G |
A |
14: 63,437,900 (GRCm39) |
S417L |
probably benign |
Het |
| Gdpd5 |
T |
A |
7: 99,087,515 (GRCm39) |
Y60N |
probably damaging |
Het |
| Gm17669 |
T |
C |
18: 67,695,626 (GRCm39) |
M57T |
probably benign |
Het |
| Gpr39 |
A |
T |
1: 125,605,173 (GRCm39) |
I34F |
probably benign |
Het |
| Iffo2 |
T |
A |
4: 139,302,528 (GRCm39) |
D90E |
probably benign |
Het |
| Il17c |
A |
G |
8: 123,149,108 (GRCm39) |
D84G |
possibly damaging |
Het |
| Itih3 |
T |
C |
14: 30,634,606 (GRCm39) |
T134A |
probably benign |
Het |
| Lama2 |
G |
A |
10: 27,222,999 (GRCm39) |
A429V |
probably damaging |
Het |
| Muc6 |
G |
T |
7: 141,218,685 (GRCm39) |
T1996N |
possibly damaging |
Het |
| Mug1 |
G |
A |
6: 121,851,521 (GRCm39) |
R806H |
probably damaging |
Het |
| Naaa |
G |
A |
5: 92,415,904 (GRCm39) |
R65* |
probably null |
Het |
| Nacc2 |
C |
T |
2: 25,950,346 (GRCm39) |
M463I |
probably benign |
Het |
| Nemf |
A |
G |
12: 69,402,821 (GRCm39) |
S72P |
probably damaging |
Het |
| Nudt7 |
G |
A |
8: 114,862,185 (GRCm39) |
|
probably null |
Het |
| Or4b1b |
T |
C |
2: 90,126,737 (GRCm39) |
Q156R |
probably damaging |
Het |
| Or52z15 |
T |
C |
7: 103,331,936 (GRCm39) |
S4P |
probably benign |
Het |
| Otx1 |
C |
A |
11: 21,947,037 (GRCm39) |
A91S |
probably damaging |
Het |
| Pacs1 |
T |
C |
19: 5,189,325 (GRCm39) |
D757G |
probably benign |
Het |
| Pkd2 |
A |
C |
5: 104,630,958 (GRCm39) |
I461L |
probably benign |
Het |
| Potegl |
G |
A |
2: 23,102,473 (GRCm39) |
C121Y |
probably damaging |
Het |
| Pramel5 |
T |
G |
4: 144,000,064 (GRCm39) |
|
probably benign |
Het |
| Ptgdr |
G |
C |
14: 45,096,300 (GRCm39) |
F137L |
probably damaging |
Het |
| Pum1 |
T |
A |
4: 130,507,190 (GRCm39) |
C1085* |
probably null |
Het |
| Rlf |
T |
A |
4: 121,005,750 (GRCm39) |
K1077* |
probably null |
Het |
| Slc25a30 |
C |
A |
14: 76,007,056 (GRCm39) |
D147Y |
probably benign |
Het |
| Smap2 |
T |
C |
4: 120,873,984 (GRCm39) |
E22G |
possibly damaging |
Het |
| Szt2 |
T |
C |
4: 118,245,519 (GRCm39) |
T1098A |
probably benign |
Het |
| Tbcc |
T |
C |
17: 47,201,788 (GRCm39) |
F58S |
probably damaging |
Het |
| Tekt3 |
G |
A |
11: 62,961,134 (GRCm39) |
R101H |
probably damaging |
Het |
| Vcan |
T |
A |
13: 89,838,991 (GRCm39) |
E2184D |
probably damaging |
Het |
| Vkorc1 |
T |
C |
7: 127,493,760 (GRCm39) |
E18G |
probably benign |
Het |
| Vmn1r68 |
T |
C |
7: 10,261,723 (GRCm39) |
H125R |
probably benign |
Het |
| Vmn2r63 |
C |
A |
7: 42,553,169 (GRCm39) |
V696L |
probably benign |
Het |
| Wdr59 |
G |
A |
8: 112,208,620 (GRCm39) |
H421Y |
probably benign |
Het |
| Xkr7 |
T |
C |
2: 152,896,873 (GRCm39) |
Y576H |
probably damaging |
Het |
| Zfp112 |
T |
C |
7: 23,824,281 (GRCm39) |
V83A |
possibly damaging |
Het |
| Zfp616 |
G |
A |
11: 73,974,336 (GRCm39) |
V293I |
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 |
|
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'- ACACTGCTCTAATAGAATCAGAGAG -3'
(R):5'- ACTGATAACTGCTGTGATGTTTCC -3'
Sequencing Primer
(F):5'- GTCGACTGTCAGTACTAACCTAGTG -3'
(R):5'- ATAACTGCTGTGATGTTTCCCATATC -3'
|
| Posted On |
2016-07-06 |
Incidental Mutation