Incidental Mutation 'R4894:Nfx1'
| ID |
377479 |
| 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 |
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.602)
|
| Stock # |
R4894 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
4 |
| Chromosomal Location |
40970906-41025992 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to G
at 40996877 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Alanine
at position 651
(S651A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000095747
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030133]
[ENSMUST00000091614]
[ENSMUST00000098143]
|
| AlphaFold |
B1AY10 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000030133
AA Change: S651A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000030133
Gene: ENSMUSG00000028423
AA Change: S651A
| 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 damaging
Transcript: ENSMUST00000091614
AA Change: S651A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000089203
Gene: ENSMUSG00000028423
AA Change: S651A
| 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 damaging
Transcript: ENSMUST00000098143
AA Change: S651A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000095747
Gene: ENSMUSG00000028423
AA Change: S651A
| 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: ENSMUST00000175121
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.4%
|
| Validation Efficiency |
|
| 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: 66 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgrf1 |
C |
A |
17: 43,609,975 (GRCm39) |
Y176* |
probably null |
Het |
| Akap13 |
T |
A |
7: 75,375,068 (GRCm39) |
M1900K |
possibly damaging |
Het |
| Ankrd36 |
A |
G |
11: 5,585,332 (GRCm39) |
E381G |
probably damaging |
Het |
| Ap3s1 |
T |
C |
18: 46,891,183 (GRCm39) |
|
probably null |
Het |
| Cacna1e |
G |
T |
1: 154,364,551 (GRCm39) |
S341* |
probably null |
Het |
| Camk1d |
G |
A |
2: 5,359,539 (GRCm39) |
S161L |
probably damaging |
Het |
| Cdh23 |
G |
T |
10: 60,173,630 (GRCm39) |
H1619Q |
probably benign |
Het |
| Chd7 |
T |
A |
4: 8,838,629 (GRCm39) |
I1276N |
probably damaging |
Het |
| Clca3a1 |
A |
G |
3: 144,719,662 (GRCm39) |
V436A |
probably damaging |
Het |
| Ctcfl |
G |
A |
2: 172,959,196 (GRCm39) |
P177S |
probably benign |
Het |
| Dab2ip |
A |
G |
2: 35,620,539 (GRCm39) |
|
probably benign |
Het |
| Dnah8 |
G |
A |
17: 30,967,542 (GRCm39) |
D2585N |
probably benign |
Het |
| Epc1 |
A |
T |
18: 6,449,011 (GRCm39) |
S495R |
probably benign |
Het |
| Espl1 |
A |
G |
15: 102,230,758 (GRCm39) |
|
probably null |
Het |
| Eya4 |
T |
C |
10: 22,985,753 (GRCm39) |
E583G |
possibly damaging |
Het |
| Fam111a |
C |
G |
19: 12,565,913 (GRCm39) |
T554R |
probably benign |
Het |
| Fbh1 |
A |
T |
2: 11,767,771 (GRCm39) |
I359N |
probably damaging |
Het |
| Fer1l6 |
T |
C |
15: 58,490,751 (GRCm39) |
C1023R |
probably damaging |
Het |
| Helz2 |
G |
C |
2: 180,877,940 (GRCm39) |
P953A |
probably benign |
Het |
| Ifi204 |
G |
T |
1: 173,587,808 (GRCm39) |
S117Y |
probably damaging |
Het |
| Ift70a1 |
T |
C |
2: 75,810,088 (GRCm39) |
*665W |
probably null |
Het |
| Igfn1 |
G |
A |
1: 135,882,520 (GRCm39) |
T2775M |
probably damaging |
Het |
| Igsf9 |
A |
G |
1: 172,325,634 (GRCm39) |
T1101A |
probably benign |
Het |
| Ipo13 |
A |
C |
4: 117,760,638 (GRCm39) |
I614S |
probably damaging |
Het |
| Ipo13 |
A |
G |
4: 117,761,687 (GRCm39) |
I476T |
possibly damaging |
Het |
| Kdm2b |
C |
A |
5: 123,079,030 (GRCm39) |
E308* |
probably null |
Het |
| Klhl20 |
A |
T |
1: 160,937,102 (GRCm39) |
M91K |
possibly damaging |
Het |
| Klrb1f |
T |
C |
6: 129,030,151 (GRCm39) |
F64L |
probably benign |
Het |
| Ldlrad3 |
C |
T |
2: 101,888,293 (GRCm39) |
C106Y |
probably damaging |
Het |
| Lilra6 |
T |
C |
7: 3,915,530 (GRCm39) |
T161A |
probably benign |
Het |
| Lrriq1 |
A |
T |
10: 102,997,613 (GRCm39) |
M1334K |
possibly damaging |
Het |
| Mepe |
C |
G |
5: 104,473,268 (GRCm39) |
P3R |
probably damaging |
Het |
| Mgat4e |
A |
G |
1: 134,468,856 (GRCm39) |
V396A |
probably benign |
Het |
| Or10ak13 |
A |
T |
4: 118,639,483 (GRCm39) |
C100S |
probably damaging |
Het |
| Or2w6 |
T |
C |
13: 21,843,352 (GRCm39) |
N47S |
probably damaging |
Het |
| Or4c109 |
T |
C |
2: 88,817,783 (GRCm39) |
I254M |
possibly damaging |
Het |
| Rag2 |
T |
C |
2: 101,460,022 (GRCm39) |
S111P |
probably damaging |
Het |
| Rai1 |
T |
A |
11: 60,077,572 (GRCm39) |
D545E |
probably damaging |
Het |
| Ralgps1 |
A |
G |
2: 33,033,115 (GRCm39) |
V498A |
possibly damaging |
Het |
| Rasal2 |
G |
A |
1: 157,020,374 (GRCm39) |
S205L |
probably damaging |
Het |
| Rec8 |
T |
C |
14: 55,862,787 (GRCm39) |
L582P |
probably damaging |
Het |
| Retn |
G |
A |
8: 3,707,358 (GRCm39) |
R106H |
probably damaging |
Het |
| Rnf112 |
A |
G |
11: 61,343,488 (GRCm39) |
L116P |
probably damaging |
Het |
| Rnf213 |
T |
C |
11: 119,372,066 (GRCm39) |
Y4885H |
probably damaging |
Het |
| Sacm1l |
A |
G |
9: 123,411,409 (GRCm39) |
I399M |
probably benign |
Het |
| Sez6 |
G |
T |
11: 77,866,086 (GRCm39) |
G738V |
probably damaging |
Het |
| Spata17 |
A |
G |
1: 186,872,643 (GRCm39) |
V56A |
probably benign |
Het |
| Spata31d1a |
A |
T |
13: 59,849,542 (GRCm39) |
V862D |
probably damaging |
Het |
| Sptb |
A |
G |
12: 76,671,768 (GRCm39) |
|
probably null |
Het |
| Srpk2 |
C |
A |
5: 23,750,527 (GRCm39) |
G59W |
probably damaging |
Het |
| Tyro3 |
T |
C |
2: 119,632,779 (GRCm39) |
S96P |
probably damaging |
Het |
| Ube2v1 |
A |
G |
2: 167,452,280 (GRCm39) |
S108P |
probably damaging |
Het |
| Usp2 |
C |
T |
9: 43,987,125 (GRCm39) |
S141L |
probably benign |
Het |
| Vamp5 |
T |
C |
6: 72,347,181 (GRCm39) |
D46G |
possibly damaging |
Het |
| Vmn1r23 |
T |
A |
6: 57,903,310 (GRCm39) |
Q156L |
probably benign |
Het |
| Vmn2r6 |
C |
T |
3: 64,454,829 (GRCm39) |
S490N |
probably benign |
Het |
| Vps39 |
A |
T |
2: 120,183,440 (GRCm39) |
I10N |
probably damaging |
Het |
| Vwf |
C |
T |
6: 125,622,897 (GRCm39) |
Q1755* |
probably null |
Het |
| Wdfy4 |
A |
T |
14: 32,877,717 (GRCm39) |
H82Q |
probably benign |
Het |
| Wdr24 |
T |
C |
17: 26,045,101 (GRCm39) |
Y279H |
probably damaging |
Het |
| Wdr72 |
A |
G |
9: 74,117,843 (GRCm39) |
T852A |
probably benign |
Het |
| Zfp1 |
T |
A |
8: 112,396,355 (GRCm39) |
C92* |
probably null |
Het |
| Zfp1004 |
T |
A |
2: 150,033,899 (GRCm39) |
C104* |
probably null |
Het |
| Zfp426 |
A |
T |
9: 20,386,369 (GRCm39) |
|
probably benign |
Het |
| Zfp442 |
C |
T |
2: 150,253,130 (GRCm39) |
|
probably null |
Het |
| Zfp74 |
T |
C |
7: 29,635,470 (GRCm39) |
|
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 |
|
|
R1882:Nfx1
|
UTSW |
4 |
41,009,240 (GRCm39) |
missense |
possibly damaging |
0.55 |
|
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 |
|
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'- AGCAGGCAACATGCTAGTGC -3'
(R):5'- CATGTGGCTAAATCACAGTAGTGC -3'
Sequencing Primer
(F):5'- GCAACATGCTAGTGCCCAGC -3'
(R):5'- AGTAGTGCTGTTTCTTTCTTCACATG -3'
|
| Posted On |
2016-03-17 |
Incidental Mutation