Incidental Mutation 'R1882:Nfx1'
| ID |
209165 |
| 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 |
039903-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.602)
|
| Stock # |
R1882 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
40970906-41025992 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 41009240 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 793
(T793A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000095747
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030133]
[ENSMUST00000091614]
[ENSMUST00000098143]
|
| AlphaFold |
B1AY10 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000030133
AA Change: T793A
PolyPhen 2
Score 0.549 (Sensitivity: 0.88; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000030133
Gene: ENSMUSG00000028423
AA Change: T793A
| 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 |
possibly damaging
Transcript: ENSMUST00000091614
AA Change: T793A
PolyPhen 2
Score 0.549 (Sensitivity: 0.88; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000089203
Gene: ENSMUSG00000028423
AA Change: T793A
| 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 |
possibly damaging
Transcript: ENSMUST00000098143
AA Change: T793A
PolyPhen 2
Score 0.549 (Sensitivity: 0.88; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000095747
Gene: ENSMUSG00000028423
AA Change: T793A
| 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000124595
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143798
|
| Meta Mutation Damage Score |
0.5842 |
| Coding Region Coverage |
- 1x: 97.4%
- 3x: 96.9%
- 10x: 95.6%
- 20x: 93.5%
|
| Validation Efficiency |
100% (59/59) |
| 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 |
|---|
| Abcc2 |
T |
C |
19: 43,786,945 (GRCm39) |
S189P |
probably benign |
Het |
| Adgrg3 |
G |
T |
8: 95,766,943 (GRCm39) |
V433F |
probably benign |
Het |
| Arhgap33 |
A |
T |
7: 30,222,234 (GRCm39) |
W1233R |
probably damaging |
Het |
| Brf2 |
T |
C |
8: 27,618,577 (GRCm39) |
D9G |
probably damaging |
Het |
| Btrc |
G |
A |
19: 45,515,839 (GRCm39) |
R562Q |
probably damaging |
Het |
| Cenpu |
T |
C |
8: 47,009,225 (GRCm39) |
F67L |
probably damaging |
Het |
| Chia1 |
T |
C |
3: 106,035,790 (GRCm39) |
M150T |
probably damaging |
Het |
| Cntln |
A |
G |
4: 85,019,072 (GRCm39) |
E1254G |
probably damaging |
Het |
| Creld1 |
G |
A |
6: 113,469,166 (GRCm39) |
C332Y |
probably damaging |
Het |
| Ctla2a |
A |
G |
13: 61,083,355 (GRCm39) |
|
probably benign |
Het |
| Dusp13b |
A |
T |
14: 21,785,043 (GRCm39) |
D223E |
probably benign |
Het |
| Ext1 |
C |
A |
15: 52,939,188 (GRCm39) |
L620F |
probably damaging |
Het |
| H2-DMb2 |
C |
T |
17: 34,366,834 (GRCm39) |
R89C |
probably damaging |
Het |
| Klhl32 |
A |
T |
4: 24,743,916 (GRCm39) |
L17* |
probably null |
Het |
| Lats2 |
C |
T |
14: 57,934,811 (GRCm39) |
V640M |
probably damaging |
Het |
| Lrig3 |
G |
A |
10: 125,845,694 (GRCm39) |
V708I |
possibly damaging |
Het |
| Mtcl1 |
T |
C |
17: 66,686,315 (GRCm39) |
T415A |
probably benign |
Het |
| Mynn |
A |
G |
3: 30,670,962 (GRCm39) |
*611W |
probably null |
Het |
| Nlrp4d |
T |
C |
7: 10,116,604 (GRCm39) |
|
noncoding transcript |
Het |
| Nos3 |
T |
C |
5: 24,573,818 (GRCm39) |
V194A |
probably damaging |
Het |
| Npc1l1 |
C |
T |
11: 6,167,473 (GRCm39) |
|
probably null |
Het |
| Nrg2 |
T |
C |
18: 36,154,150 (GRCm39) |
D589G |
probably damaging |
Het |
| Omg |
C |
T |
11: 79,392,545 (GRCm39) |
|
probably benign |
Het |
| Or10v9 |
T |
C |
19: 11,832,835 (GRCm39) |
T161A |
probably damaging |
Het |
| Or14j5 |
T |
C |
17: 38,161,839 (GRCm39) |
S119P |
probably damaging |
Het |
| Or2y17 |
A |
G |
11: 49,231,539 (GRCm39) |
Y60C |
probably damaging |
Het |
| Or8k16 |
T |
A |
2: 85,519,950 (GRCm39) |
M59K |
probably damaging |
Het |
| P2ry2 |
G |
T |
7: 100,648,058 (GRCm39) |
Y82* |
probably null |
Het |
| Pcdh1 |
T |
C |
18: 38,335,895 (GRCm39) |
T247A |
possibly damaging |
Het |
| Pecr |
A |
T |
1: 72,314,136 (GRCm39) |
|
probably null |
Het |
| Pgm3 |
A |
G |
9: 86,447,743 (GRCm39) |
Y167H |
possibly damaging |
Het |
| Pramel15 |
A |
T |
4: 144,103,485 (GRCm39) |
C214S |
probably benign |
Het |
| Prmt2 |
T |
C |
10: 76,058,302 (GRCm39) |
H169R |
probably benign |
Het |
| Rad51ap2 |
T |
A |
12: 11,506,251 (GRCm39) |
S58T |
possibly damaging |
Het |
| Rbpms2 |
ACTGCTGCTGCTGCTGC |
ACTGCTGCTGCTGCTGCTGC |
9: 65,558,948 (GRCm39) |
|
probably benign |
Het |
| Slc6a15 |
T |
C |
10: 103,230,925 (GRCm39) |
S217P |
probably benign |
Het |
| Slco1a8 |
C |
A |
6: 141,939,363 (GRCm39) |
|
probably null |
Het |
| Snx27 |
G |
A |
3: 94,426,416 (GRCm39) |
T361I |
probably damaging |
Het |
| St7l |
A |
G |
3: 104,775,363 (GRCm39) |
T80A |
probably damaging |
Het |
| Stk32b |
T |
A |
5: 37,689,031 (GRCm39) |
M98L |
possibly damaging |
Het |
| Tonsl |
C |
A |
15: 76,508,350 (GRCm39) |
A6S |
possibly damaging |
Het |
| Tpx2 |
A |
G |
2: 152,711,611 (GRCm39) |
R49G |
probably benign |
Het |
| Trmt2a |
A |
G |
16: 18,067,758 (GRCm39) |
K144E |
possibly damaging |
Het |
| Trpm7 |
A |
C |
2: 126,654,697 (GRCm39) |
L1414V |
probably benign |
Het |
| Ugdh |
T |
C |
5: 65,580,939 (GRCm39) |
K107E |
possibly damaging |
Het |
| Vamp3 |
A |
T |
4: 151,135,366 (GRCm39) |
|
probably benign |
Het |
| Vmn1r172 |
T |
C |
7: 23,359,651 (GRCm39) |
S179P |
probably damaging |
Het |
| Vmn1r28 |
A |
G |
6: 58,242,963 (GRCm39) |
M269V |
probably benign |
Het |
| Vmn2r94 |
T |
C |
17: 18,464,476 (GRCm39) |
T605A |
probably benign |
Het |
| Vwce |
A |
G |
19: 10,615,520 (GRCm39) |
T134A |
possibly damaging |
Het |
| Zfp277 |
T |
C |
12: 40,495,745 (GRCm39) |
E5G |
probably benign |
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 |
|
|
R2089:Nfx1
|
UTSW |
4 |
40,977,004 (GRCm39) |
missense |
probably benign |
|
|
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'- GTGACCATTTAGAGAAAGTCCTAAG -3'
(R):5'- TCTGGGCTGTAATCAGATTAAGATG -3'
Sequencing Primer
(F):5'- AGTCTGGAATTTGAAAGTCTGACGC -3'
(R):5'- TAAACTCAGGCTGTCAGTGC -3'
|
| Posted On |
2014-06-30 |
Incidental Mutation