Incidental Mutation 'IGL02679:Rfx3'
| ID |
303290 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| 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 # |
IGL02679
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
19 |
| Chromosomal Location |
27739121-27988566 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 27827137 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Tyrosine
at position 150
(H150Y)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133461
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000046898]
[ENSMUST00000165566]
[ENSMUST00000172907]
[ENSMUST00000173863]
[ENSMUST00000174850]
|
| AlphaFold |
P48381 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000046898
AA Change: H150Y
PolyPhen 2
Score 0.281 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000038760
Gene: ENSMUSG00000040929
AA Change: H150Y
| 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: H150Y
PolyPhen 2
Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000126313
Gene: ENSMUSG00000040929
AA Change: H150Y
| 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 |
possibly damaging
Transcript: ENSMUST00000172907
AA Change: H150Y
PolyPhen 2
Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000134141
Gene: ENSMUSG00000040929
AA Change: H150Y
| 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: H150Y
PolyPhen 2
Score 0.109 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000133367
Gene: ENSMUSG00000040929
AA Change: H150Y
| 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: H150Y
PolyPhen 2
Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000133461
Gene: ENSMUSG00000040929
AA Change: H150Y
| 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 |
|
| 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: 47 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930442H23Rik |
T |
A |
10: 81,018,813 (GRCm39) |
|
probably benign |
Het |
| Adam5 |
A |
T |
8: 25,296,542 (GRCm39) |
Y302N |
probably damaging |
Het |
| Ankrd34c |
A |
T |
9: 89,612,132 (GRCm39) |
Y70N |
probably damaging |
Het |
| Asph |
G |
A |
4: 9,601,349 (GRCm39) |
P190S |
possibly damaging |
Het |
| Atp6v1h |
T |
C |
1: 5,194,525 (GRCm39) |
C235R |
probably damaging |
Het |
| Brwd1 |
A |
G |
16: 95,804,023 (GRCm39) |
L2049P |
probably benign |
Het |
| Capn2 |
T |
A |
1: 182,300,149 (GRCm39) |
I614F |
probably benign |
Het |
| Ccdc126 |
T |
A |
6: 49,310,995 (GRCm39) |
M1K |
probably null |
Het |
| Cdh9 |
T |
C |
15: 16,832,316 (GRCm39) |
I401T |
probably damaging |
Het |
| Cep57l1 |
T |
C |
10: 41,605,382 (GRCm39) |
E121G |
probably damaging |
Het |
| Cfap46 |
A |
G |
7: 139,194,386 (GRCm39) |
I2276T |
probably damaging |
Het |
| Cnnm3 |
T |
C |
1: 36,559,239 (GRCm39) |
S490P |
probably benign |
Het |
| D430041D05Rik |
C |
T |
2: 104,060,650 (GRCm39) |
V731I |
possibly damaging |
Het |
| Dynlt2b |
T |
C |
16: 32,244,125 (GRCm39) |
V107A |
possibly damaging |
Het |
| Fgf3 |
C |
A |
7: 144,394,487 (GRCm39) |
N100K |
probably damaging |
Het |
| Gas7 |
G |
A |
11: 67,566,553 (GRCm39) |
|
probably null |
Het |
| Gfm1 |
C |
T |
3: 67,382,100 (GRCm39) |
P725S |
possibly damaging |
Het |
| Gimap4 |
T |
A |
6: 48,667,429 (GRCm39) |
C61* |
probably null |
Het |
| Greb1 |
C |
T |
12: 16,758,724 (GRCm39) |
R664Q |
probably damaging |
Het |
| Kpnb1 |
T |
A |
11: 97,068,086 (GRCm39) |
I295F |
possibly damaging |
Het |
| Lamc3 |
A |
G |
2: 31,835,410 (GRCm39) |
E1577G |
probably benign |
Het |
| Lrrk1 |
C |
T |
7: 65,924,620 (GRCm39) |
V235M |
probably damaging |
Het |
| Meak7 |
A |
T |
8: 120,499,149 (GRCm39) |
D114E |
probably benign |
Het |
| Mipol1 |
T |
A |
12: 57,352,829 (GRCm39) |
V56E |
possibly damaging |
Het |
| Mycbp2 |
T |
C |
14: 103,442,621 (GRCm39) |
I1927V |
probably benign |
Het |
| Ncaph |
A |
T |
2: 126,966,784 (GRCm39) |
N223K |
possibly damaging |
Het |
| Nipbl |
A |
G |
15: 8,325,037 (GRCm39) |
M2542T |
probably benign |
Het |
| Nolc1 |
C |
A |
19: 46,071,468 (GRCm39) |
|
probably benign |
Het |
| Or10j5 |
G |
A |
1: 172,784,743 (GRCm39) |
C127Y |
probably damaging |
Het |
| Or51h1 |
A |
G |
7: 102,308,384 (GRCm39) |
M119V |
possibly damaging |
Het |
| Pkhd1l1 |
T |
C |
15: 44,393,441 (GRCm39) |
|
probably null |
Het |
| Ppat |
A |
T |
5: 77,067,316 (GRCm39) |
C306S |
probably benign |
Het |
| Ptpn13 |
A |
T |
5: 103,717,320 (GRCm39) |
M1821L |
possibly damaging |
Het |
| Rabl3 |
C |
T |
16: 37,362,287 (GRCm39) |
S42L |
probably damaging |
Het |
| Rbm12 |
C |
T |
2: 155,937,480 (GRCm39) |
|
probably benign |
Het |
| Rngtt |
A |
G |
4: 33,356,098 (GRCm39) |
M312V |
possibly damaging |
Het |
| Slc10a2 |
T |
A |
8: 5,148,499 (GRCm39) |
T149S |
probably damaging |
Het |
| Spata21 |
T |
C |
4: 140,838,576 (GRCm39) |
|
probably benign |
Het |
| Stx8 |
G |
T |
11: 67,860,598 (GRCm39) |
W6C |
probably damaging |
Het |
| Tcn2 |
T |
C |
11: 3,877,504 (GRCm39) |
E48G |
possibly damaging |
Het |
| Tecpr1 |
A |
T |
5: 144,143,364 (GRCm39) |
N670K |
probably benign |
Het |
| Tmem255b |
G |
A |
8: 13,507,055 (GRCm39) |
M240I |
probably benign |
Het |
| Ubr4 |
G |
A |
4: 139,186,445 (GRCm39) |
E651K |
probably damaging |
Het |
| Ubr5 |
T |
C |
15: 38,002,558 (GRCm39) |
T1498A |
probably benign |
Het |
| Vmn2r95 |
G |
A |
17: 18,664,116 (GRCm39) |
C445Y |
probably damaging |
Het |
| Zfp429 |
T |
A |
13: 67,547,855 (GRCm39) |
|
probably benign |
Het |
| Zfp804b |
T |
G |
5: 6,821,392 (GRCm39) |
D557A |
possibly 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 |
|
|
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 |
|
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 |
|
| Posted On |
2015-04-16 |
Incidental Mutation