Incidental Mutation 'R2089:Nfx1'
| ID |
231641 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nfx1
|
| Ensembl Gene |
ENSMUSG00000028423 |
| Gene Name |
nuclear transcription factor, X-box binding 1 |
| Synonyms |
Tex42, 3000003M19Rik, 1300017N15Rik, TEG-42 |
| MMRRC Submission |
040094-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.602)
|
| Stock # |
R2089 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
40970906-41025992 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 40977004 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 226
(V226A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000095747
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030133]
[ENSMUST00000091614]
[ENSMUST00000098143]
|
| AlphaFold |
B1AY10 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030133
AA Change: V226A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000030133
Gene: ENSMUSG00000028423
AA Change: V226A
| Domain | Start | End | E-Value | Type |
|---|
|
RING
|
352 |
402 |
3.91e-2 |
SMART |
|
ZnF_NFX
|
447 |
465 |
1.23e-3 |
SMART |
|
ZnF_NFX
|
500 |
519 |
6.16e-4 |
SMART |
|
ZnF_NFX
|
561 |
580 |
2e-3 |
SMART |
|
ZnF_NFX
|
626 |
649 |
5.45e-5 |
SMART |
|
ZnF_NFX
|
688 |
707 |
5.25e0 |
SMART |
|
ZnF_NFX
|
715 |
734 |
2.92e-5 |
SMART |
|
ZnF_NFX
|
772 |
791 |
5.25e0 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000091614
AA Change: V226A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000089203
Gene: ENSMUSG00000028423
AA Change: V226A
| Domain | Start | End | E-Value | Type |
|---|
|
RING
|
352 |
402 |
3.91e-2 |
SMART |
|
ZnF_NFX
|
447 |
465 |
1.23e-3 |
SMART |
|
ZnF_NFX
|
500 |
519 |
6.16e-4 |
SMART |
|
ZnF_NFX
|
561 |
580 |
2e-3 |
SMART |
|
ZnF_NFX
|
626 |
649 |
5.45e-5 |
SMART |
|
ZnF_NFX
|
688 |
707 |
5.25e0 |
SMART |
|
ZnF_NFX
|
715 |
734 |
2.92e-5 |
SMART |
|
ZnF_NFX
|
772 |
791 |
5.25e0 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000098143
AA Change: V226A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000095747
Gene: ENSMUSG00000028423
AA Change: V226A
| Domain | Start | End | E-Value | Type |
|---|
|
RING
|
352 |
402 |
3.91e-2 |
SMART |
|
ZnF_NFX
|
447 |
465 |
1.23e-3 |
SMART |
|
ZnF_NFX
|
500 |
519 |
6.16e-4 |
SMART |
|
ZnF_NFX
|
561 |
580 |
2e-3 |
SMART |
|
ZnF_NFX
|
626 |
649 |
5.45e-5 |
SMART |
|
ZnF_NFX
|
688 |
707 |
5.25e0 |
SMART |
|
ZnF_NFX
|
715 |
734 |
2.92e-5 |
SMART |
|
ZnF_NFX
|
772 |
791 |
5.25e0 |
SMART |
|
ZnF_NFX
|
826 |
848 |
7.7e-5 |
SMART |
|
ZnF_NFX
|
857 |
878 |
4.23e-2 |
SMART |
|
coiled coil region
|
930 |
956 |
N/A |
INTRINSIC |
|
R3H
|
977 |
1055 |
1.38e-22 |
SMART |
|
low complexity region
|
1070 |
1088 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.3%
|
| Validation Efficiency |
96% (51/53) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] MHC class II gene expression is controlled primarily at the transcriptional level by transcription factors that bind to the X and Y boxes, two highly conserved elements in the proximal promoter of MHC class II genes. The protein encoded by this gene is a transcriptional repressor capable of binding to the conserved X box motif of HLA-DRA and other MHC class II genes in vitro. The protein may play a role in regulating the duration of an inflammatory response by limiting the period in which class II MHC molecules are induced by IFN-gamma. Three alternative splice variants, each of which encodes a different isoform, have been identified. [provided by RefSeq, Jul 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4921504E06Rik |
G |
C |
2: 19,522,357 (GRCm39) |
N247K |
probably damaging |
Het |
| 4930402F06Rik |
T |
C |
2: 35,266,079 (GRCm39) |
K197R |
probably benign |
Het |
| Adgrl1 |
T |
C |
8: 84,661,093 (GRCm39) |
I862T |
probably damaging |
Het |
| Agbl1 |
G |
A |
7: 76,239,248 (GRCm39) |
V583M |
probably damaging |
Het |
| Apba2 |
T |
A |
7: 64,345,341 (GRCm39) |
V177D |
probably benign |
Het |
| Atg14 |
A |
T |
14: 47,780,352 (GRCm39) |
I474N |
probably damaging |
Het |
| Bicdl1 |
A |
G |
5: 115,862,638 (GRCm39) |
S206P |
probably damaging |
Het |
| Bltp1 |
C |
T |
3: 37,042,405 (GRCm39) |
T2797I |
probably damaging |
Het |
| Calhm3 |
T |
A |
19: 47,140,430 (GRCm39) |
D221V |
probably damaging |
Het |
| Ccdc93 |
T |
A |
1: 121,411,071 (GRCm39) |
|
probably null |
Het |
| Dab1 |
C |
T |
4: 104,588,948 (GRCm39) |
A524V |
probably benign |
Het |
| Dido1 |
A |
T |
2: 180,303,677 (GRCm39) |
V1409E |
probably benign |
Het |
| Dsc2 |
G |
A |
18: 20,166,351 (GRCm39) |
T760I |
possibly damaging |
Het |
| Etnk2 |
T |
G |
1: 133,304,791 (GRCm39) |
|
probably null |
Het |
| Gbp7 |
A |
T |
3: 142,240,383 (GRCm39) |
I34F |
probably damaging |
Het |
| Gbp7 |
A |
T |
3: 142,251,316 (GRCm39) |
|
probably benign |
Het |
| Gpr37 |
A |
G |
6: 25,689,062 (GRCm39) |
S12P |
possibly damaging |
Het |
| Grxcr1 |
T |
C |
5: 68,267,755 (GRCm39) |
I168T |
probably damaging |
Het |
| Hat1 |
T |
C |
2: 71,264,378 (GRCm39) |
V272A |
probably benign |
Het |
| Igkv8-30 |
A |
C |
6: 70,094,070 (GRCm39) |
C114G |
probably damaging |
Het |
| Lrrc4 |
T |
G |
6: 28,830,586 (GRCm39) |
D343A |
probably benign |
Het |
| Mars1 |
A |
G |
10: 127,135,154 (GRCm39) |
S646P |
probably damaging |
Het |
| Micu3 |
G |
A |
8: 40,761,413 (GRCm39) |
G108R |
probably benign |
Het |
| Mterf1b |
A |
T |
5: 4,247,057 (GRCm39) |
T233S |
possibly damaging |
Het |
| Myrf |
A |
T |
19: 10,201,964 (GRCm39) |
V171D |
possibly damaging |
Het |
| Nbas |
G |
A |
12: 13,411,046 (GRCm39) |
D897N |
probably benign |
Het |
| Nrros |
C |
T |
16: 31,962,975 (GRCm39) |
W311* |
probably null |
Het |
| Ntrk2 |
A |
G |
13: 59,007,115 (GRCm39) |
H239R |
possibly damaging |
Het |
| Or10g9 |
T |
C |
9: 39,912,500 (GRCm39) |
T8A |
probably benign |
Het |
| Pcdhb18 |
T |
C |
18: 37,623,653 (GRCm39) |
S328P |
probably damaging |
Het |
| Pigm |
T |
C |
1: 172,205,100 (GRCm39) |
Y279H |
probably damaging |
Het |
| Pik3cd |
A |
G |
4: 149,737,156 (GRCm39) |
L880P |
probably damaging |
Het |
| Plaat3 |
A |
G |
19: 7,556,474 (GRCm39) |
I92V |
probably damaging |
Het |
| Ptger4 |
T |
A |
15: 5,272,326 (GRCm39) |
I98F |
possibly damaging |
Het |
| Rasl11a |
T |
A |
5: 146,783,927 (GRCm39) |
I124N |
probably damaging |
Het |
| Rest |
A |
G |
5: 77,429,126 (GRCm39) |
K515R |
possibly damaging |
Het |
| Ryr1 |
A |
G |
7: 28,785,474 (GRCm39) |
L1746P |
probably damaging |
Het |
| Ryr2 |
G |
T |
13: 11,960,863 (GRCm39) |
T25K |
probably benign |
Het |
| Serpina3g |
A |
T |
12: 104,205,417 (GRCm39) |
D52V |
probably damaging |
Het |
| Skint6 |
T |
C |
4: 112,703,881 (GRCm39) |
N998S |
probably benign |
Het |
| Sntg1 |
T |
A |
1: 8,665,763 (GRCm39) |
T184S |
probably benign |
Het |
| Ssbp1 |
A |
G |
6: 40,453,433 (GRCm39) |
Y73C |
probably null |
Het |
| Suclg1 |
A |
G |
6: 73,241,259 (GRCm39) |
K193R |
probably benign |
Het |
| Tnrc18 |
A |
C |
5: 142,759,396 (GRCm39) |
S813R |
unknown |
Het |
| Tnrc6a |
T |
C |
7: 122,771,343 (GRCm39) |
|
probably null |
Het |
| Trap1 |
A |
C |
16: 3,863,903 (GRCm39) |
Y472* |
probably null |
Het |
| Trpm8 |
T |
C |
1: 88,271,048 (GRCm39) |
I446T |
probably damaging |
Het |
| Tti2 |
T |
C |
8: 31,644,294 (GRCm39) |
L297P |
probably damaging |
Het |
| Umodl1 |
A |
G |
17: 31,190,893 (GRCm39) |
M247V |
probably benign |
Het |
| Unc80 |
T |
A |
1: 66,710,874 (GRCm39) |
|
probably benign |
Het |
| Zfp174 |
A |
G |
16: 3,672,506 (GRCm39) |
R352G |
possibly damaging |
Het |
|
| Other mutations in Nfx1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01377:Nfx1
|
APN |
4 |
40,977,241 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01998:Nfx1
|
APN |
4 |
41,004,353 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02072:Nfx1
|
APN |
4 |
41,016,119 (GRCm39) |
missense |
probably benign |
|
|
IGL02170:Nfx1
|
APN |
4 |
41,018,019 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02188:Nfx1
|
APN |
4 |
40,993,827 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02502:Nfx1
|
APN |
4 |
40,976,345 (GRCm39) |
splice site |
probably benign |
|
|
IGL02674:Nfx1
|
APN |
4 |
40,999,717 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL03007:Nfx1
|
APN |
4 |
40,984,962 (GRCm39) |
missense |
probably benign |
0.02 |
|
IGL03092:Nfx1
|
APN |
4 |
41,024,851 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03303:Nfx1
|
APN |
4 |
41,004,323 (GRCm39) |
splice site |
probably benign |
|
|
K7371:Nfx1
|
UTSW |
4 |
40,976,803 (GRCm39) |
missense |
probably damaging |
1.00 |
|
PIT4498001:Nfx1
|
UTSW |
4 |
40,977,244 (GRCm39) |
missense |
probably benign |
|
|
R0032:Nfx1
|
UTSW |
4 |
41,015,321 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0032:Nfx1
|
UTSW |
4 |
41,015,321 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0069:Nfx1
|
UTSW |
4 |
40,986,688 (GRCm39) |
splice site |
probably benign |
|
|
R1056:Nfx1
|
UTSW |
4 |
41,003,057 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R1449:Nfx1
|
UTSW |
4 |
40,976,803 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1635:Nfx1
|
UTSW |
4 |
40,977,004 (GRCm39) |
missense |
probably benign |
|
|
R1636:Nfx1
|
UTSW |
4 |
41,016,072 (GRCm39) |
splice site |
probably null |
|
|
R1882:Nfx1
|
UTSW |
4 |
41,009,240 (GRCm39) |
missense |
possibly damaging |
0.55 |
|
R2091:Nfx1
|
UTSW |
4 |
40,977,004 (GRCm39) |
missense |
probably benign |
|
|
R2091:Nfx1
|
UTSW |
4 |
40,977,004 (GRCm39) |
missense |
probably benign |
|
|
R3792:Nfx1
|
UTSW |
4 |
41,004,357 (GRCm39) |
nonsense |
probably null |
|
|
R3793:Nfx1
|
UTSW |
4 |
41,004,357 (GRCm39) |
nonsense |
probably null |
|
|
R4668:Nfx1
|
UTSW |
4 |
40,976,367 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
R4678:Nfx1
|
UTSW |
4 |
41,012,070 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4894:Nfx1
|
UTSW |
4 |
40,996,877 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4972:Nfx1
|
UTSW |
4 |
40,976,375 (GRCm39) |
missense |
probably benign |
0.36 |
|
R5066:Nfx1
|
UTSW |
4 |
40,991,868 (GRCm39) |
missense |
probably benign |
|
|
R5389:Nfx1
|
UTSW |
4 |
40,985,000 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5429:Nfx1
|
UTSW |
4 |
41,004,343 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5643:Nfx1
|
UTSW |
4 |
40,984,973 (GRCm39) |
missense |
probably null |
1.00 |
|
R5644:Nfx1
|
UTSW |
4 |
40,984,973 (GRCm39) |
missense |
probably null |
1.00 |
|
R5915:Nfx1
|
UTSW |
4 |
40,977,285 (GRCm39) |
missense |
probably benign |
0.02 |
|
R6286:Nfx1
|
UTSW |
4 |
40,986,728 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6393:Nfx1
|
UTSW |
4 |
40,976,851 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R7409:Nfx1
|
UTSW |
4 |
41,021,830 (GRCm39) |
missense |
possibly damaging |
0.64 |
|
R7523:Nfx1
|
UTSW |
4 |
41,016,119 (GRCm39) |
missense |
probably benign |
|
|
R7916:Nfx1
|
UTSW |
4 |
40,977,142 (GRCm39) |
missense |
probably benign |
0.11 |
|
R8497:Nfx1
|
UTSW |
4 |
40,976,968 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
R8799:Nfx1
|
UTSW |
4 |
41,023,727 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9154:Nfx1
|
UTSW |
4 |
40,990,845 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9364:Nfx1
|
UTSW |
4 |
41,023,756 (GRCm39) |
missense |
probably benign |
0.31 |
|
R9497:Nfx1
|
UTSW |
4 |
40,994,104 (GRCm39) |
missense |
probably benign |
0.00 |
|
X0025:Nfx1
|
UTSW |
4 |
40,976,422 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGCACAGCTTACATACAACTATGG -3'
(R):5'- CGAAGACTTGCTGACAACTGC -3'
Sequencing Primer
(F):5'- GCTTACATACAACTATGGCAGAG -3'
(R):5'- AATTCCCAGTGTCACAGGCTG -3'
|
| Posted On |
2014-09-18 |
Incidental Mutation