Mutagenetix > Incidental Mutation

Incidental Mutation 'R1636:Nfx1'

173148

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

039672-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.592) question?

Stock #

R1636 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

40970906-41025992 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

T to G at 41016072 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000095747 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030133] [ENSMUST00000091614] [ENSMUST00000098143]

AlphaFold

B1AY10

Predicted Effect

probably benign
Transcript: ENSMUST00000030133

SMART Domains

Protein: ENSMUSP00000030133
Gene: ENSMUSG00000028423

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

SMART Domains

Protein: ENSMUSP00000089203
Gene: ENSMUSG00000028423

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 null
Transcript: ENSMUST00000098143

SMART Domains

Protein: ENSMUSP00000095747
Gene: ENSMUSG00000028423

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

0.9755

Coding Region Coverage

1x: 98.9%
3x: 97.8%
10x: 94.4%
20x: 86.1%

Validation Efficiency

96% (85/89)

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2m	C	A	6: 121,631,571 (GRCm39)	L623M	probably benign	Het
Abca7	A	G	10: 79,844,832 (GRCm39)	H1518R	probably benign	Het
Adam4	A	G	12: 81,466,464 (GRCm39)	L719S	probably damaging	Het
Adprm	T	C	11: 66,932,549 (GRCm39)	Y120C	possibly damaging	Het
Arhgap25	T	A	6: 87,472,923 (GRCm39)	Y78F	probably damaging	Het
Asap1	G	A	15: 63,995,761 (GRCm39)	P665L	probably damaging	Het
Bank1	T	C	3: 135,788,987 (GRCm39)	K637R	probably damaging	Het
Bcr	T	A	10: 74,966,898 (GRCm39)	L502M	probably damaging	Het
Brwd1	A	G	16: 95,860,841 (GRCm39)	L315P	probably damaging	Het
Btbd7	A	T	12: 102,760,110 (GRCm39)	Y613N	probably damaging	Het
Cdca7l	G	A	12: 117,840,663 (GRCm39)	R395H	probably damaging	Het
Cftr	T	A	6: 18,226,156 (GRCm39)	I368K	probably damaging	Het
D6Wsu163e	T	C	6: 126,923,564 (GRCm39)	V150A	possibly damaging	Het
Ddx52	A	G	11: 83,846,169 (GRCm39)	T470A	probably damaging	Het
Def6	A	G	17: 28,442,892 (GRCm39)	E316G	possibly damaging	Het
Dip2a	A	T	10: 76,157,412 (GRCm39)	N64K	probably benign	Het
Dlgap4	G	T	2: 156,587,997 (GRCm39)	E631*	probably null	Het
Dner	T	C	1: 84,563,051 (GRCm39)	K190E	possibly damaging	Het
Eif2b4	T	A	5: 31,349,610 (GRCm39)		probably null	Het
Eif3a	A	T	19: 60,770,343 (GRCm39)	D119E	possibly damaging	Het
Ercc2	C	T	7: 19,121,049 (GRCm39)	T276M	possibly damaging	Het
Exoc1	A	G	5: 76,715,965 (GRCm39)	K830R	probably benign	Het
F2r	G	T	13: 95,740,400 (GRCm39)	Y378*	probably null	Het
Fam186a	G	A	15: 99,839,539 (GRCm39)	T2235I	unknown	Het
Fmo3	T	G	1: 162,781,994 (GRCm39)	K453T	probably benign	Het
Fzd3	A	T	14: 65,490,555 (GRCm39)	D9E	probably benign	Het
Galns	A	G	8: 123,330,955 (GRCm39)		probably benign	Het
Gm1818	T	C	12: 48,602,550 (GRCm39)		noncoding transcript	Het
Gm9955	C	A	18: 24,842,287 (GRCm39)		probably benign	Het
Immp2l	T	C	12: 41,750,470 (GRCm39)	V113A	probably damaging	Het
Iyd	T	A	10: 3,495,588 (GRCm39)	M82K	possibly damaging	Het
Kif21a	A	T	15: 90,869,008 (GRCm39)		probably benign	Het
Lipf	A	G	19: 33,953,935 (GRCm39)	D342G	probably damaging	Het
Lmbrd1	C	A	1: 24,786,011 (GRCm39)	Y435*	probably null	Het
Mpped1	C	T	15: 83,676,191 (GRCm39)		probably benign	Het
Mtrf1l	A	G	10: 5,763,265 (GRCm39)	S355P	probably damaging	Het
Ndn	C	T	7: 61,998,256 (GRCm39)	P34L	probably benign	Het
Neo1	T	C	9: 58,820,560 (GRCm39)	S788G	probably damaging	Het
Nlrp4c	T	C	7: 6,069,737 (GRCm39)	V546A	possibly damaging	Het
Nwd2	G	A	5: 63,964,900 (GRCm39)	V1495M	probably damaging	Het
Oaf	T	A	9: 43,150,621 (GRCm39)	I84F	probably benign	Het
Obscn	A	G	11: 59,013,463 (GRCm39)	F1153S	probably damaging	Het
Ofcc1	A	T	13: 40,333,904 (GRCm39)	C396S	possibly damaging	Het
Omg	A	G	11: 79,393,166 (GRCm39)	S231P	probably benign	Het
Or51a7	T	G	7: 102,614,898 (GRCm39)	I197S	possibly damaging	Het
Or8g35	T	C	9: 39,381,215 (GRCm39)	D269G	probably benign	Het
Pdcl3	A	G	1: 39,034,016 (GRCm39)	T53A	possibly damaging	Het
Pik3r2	A	T	8: 71,224,542 (GRCm39)	H244Q	probably benign	Het
Pinx1	A	T	14: 64,103,586 (GRCm39)	H55L	probably damaging	Het
Pwwp2b	T	A	7: 138,834,758 (GRCm39)	H66Q	probably benign	Het
Rell2	A	G	18: 38,091,132 (GRCm39)	D99G	probably damaging	Het
Reln	G	A	5: 22,203,681 (GRCm39)	A1191V	probably damaging	Het
Rprm	T	C	2: 53,975,316 (GRCm39)	M1V	probably null	Het
Sav1	A	C	12: 70,031,269 (GRCm39)	H84Q	probably benign	Het
Scamp5	T	C	9: 57,358,692 (GRCm39)	D28G	possibly damaging	Het
Selenbp2	G	A	3: 94,604,122 (GRCm39)	G9D	probably damaging	Het
Sh3tc2	T	C	18: 62,122,792 (GRCm39)	W518R	probably damaging	Het
Slc10a6	A	T	5: 103,777,012 (GRCm39)	N29K	probably benign	Het
Spindoc	C	A	19: 7,351,922 (GRCm39)	D142Y	probably damaging	Het
Spink12	T	A	18: 44,240,795 (GRCm39)	D60E	probably benign	Het
Sugt1	A	G	14: 79,825,422 (GRCm39)	I23V	probably benign	Het
Syne2	T	C	12: 76,051,506 (GRCm39)	C4079R	probably benign	Het
Tex15	T	G	8: 34,066,415 (GRCm39)	Y1948*	probably null	Het
Thoc2l	T	A	5: 104,668,616 (GRCm39)	M1046K	probably damaging	Het
Tln2	T	C	9: 67,213,814 (GRCm39)	E321G	probably damaging	Het
Tmem198b	A	G	10: 128,638,065 (GRCm39)	L166P	probably damaging	Het
Tspear	T	A	10: 77,706,253 (GRCm39)	L341H	possibly damaging	Het
Ttn	T	A	2: 76,730,566 (GRCm39)		probably benign	Het
Unc13a	G	A	8: 72,106,034 (GRCm39)	T690I	probably damaging	Het
Ush2a	T	C	1: 188,198,373 (GRCm39)	I1479T	possibly damaging	Het
Vcan	G	A	13: 89,851,786 (GRCm39)	T1058I	possibly damaging	Het
Vmn1r84	T	C	7: 12,096,522 (GRCm39)	Q45R	probably benign	Het
Vmn2r111	T	C	17: 22,790,380 (GRCm39)	N209D	probably damaging	Het
Wbp1l	A	G	19: 46,632,883 (GRCm39)	Y40C	probably damaging	Het
Wdr72	A	T	9: 74,086,907 (GRCm39)	H625L	probably benign	Het
Zeb2	T	C	2: 44,892,623 (GRCm39)	Y195C	probably damaging	Het
Zkscan6	C	T	11: 65,705,256 (GRCm39)		probably benign	Het
Zmym6	C	A	4: 127,017,560 (GRCm39)	H1022N	probably 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
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
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'- CTTATGACCAAGACATGCGCCTCC -3'
(R):5'- GACATAGCTCAGTGGCAGCACATTC -3'

Sequencing Primer
(F):5'- CCAACGTGCCCATTGCTG -3'
(R):5'- GTGGCAGCACATTCATTAGC -3'

Posted On

2014-04-24