Mutagenetix > Incidental Mutation

Incidental Mutation 'R9154:Nfx1'

695212

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

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.602) question?

Stock #

R9154 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

40970906-41025992 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 40990845 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 471 (C471S)

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: C471S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000030133
Gene: ENSMUSG00000028423
AA Change: C471S

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: C471S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000089203
Gene: ENSMUSG00000028423
AA Change: C471S

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: C471S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000095747
Gene: ENSMUSG00000028423
AA Change: C471S

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930590J08Rik	T	C	6: 91,926,926 (GRCm39)	V862A	probably benign	Het
A2m	A	T	6: 121,645,512 (GRCm39)	K1019M	probably damaging	Het
Acot6	G	T	12: 84,147,789 (GRCm39)	W15L	possibly damaging	Het
Adam32	CCAGCAGCAGCAGCAGCAG	CCAGCAGCAGCAGCAG	8: 25,438,769 (GRCm39)		probably benign	Het
Adnp	C	A	2: 168,026,580 (GRCm39)	Q238H	possibly damaging	Het
Akap7	T	C	10: 25,047,053 (GRCm39)	Y281C	probably damaging	Het
Ank1	A	G	8: 23,605,387 (GRCm39)	E1085G	probably damaging	Het
Arhgef38	A	T	3: 132,837,924 (GRCm39)	S669T	unknown	Het
Atp8b2	A	T	3: 89,865,927 (GRCm39)	S50R	possibly damaging	Het
Atp8b5	T	C	4: 43,372,630 (GRCm39)	I1090T	probably benign	Het
Ccdc198	A	T	14: 49,473,367 (GRCm39)	H129Q	probably benign	Het
Chrna4	G	A	2: 180,670,602 (GRCm39)	R385C	probably damaging	Het
Col4a1	T	A	8: 11,267,446 (GRCm39)	I1105F	probably damaging	Het
Crybg2	G	A	4: 133,792,620 (GRCm39)	R85Q	probably benign	Het
Cspg4	T	A	9: 56,798,287 (GRCm39)	L1434Q		Het
Cyp3a13	T	C	5: 137,919,758 (GRCm39)	N6S	probably benign	Het
Dnase2b	A	T	3: 146,299,326 (GRCm39)	Y42*	probably null	Het
F11r	A	G	1: 171,289,376 (GRCm39)	E233G	probably damaging	Het
Fip1l1	T	C	5: 74,747,703 (GRCm39)	I390T	possibly damaging	Het
Fiz1	G	A	7: 5,011,280 (GRCm39)	R413C	probably damaging	Het
Fus	G	A	7: 127,580,440 (GRCm39)	G450E	unknown	Het
Gm11569	C	A	11: 99,689,267 (GRCm39)	C144F	unknown	Het
Gm7298	A	T	6: 121,756,436 (GRCm39)	Y1027F	probably damaging	Het
Grik5	C	A	7: 24,758,403 (GRCm39)	W340L	probably damaging	Het
H1f2	A	G	13: 23,923,373 (GRCm39)	K181R	unknown	Het
Hectd4	G	A	5: 121,391,967 (GRCm39)	R77H		Het
Ift81	C	A	5: 122,689,122 (GRCm39)	V665L	probably benign	Het
Ints2	A	G	11: 86,125,524 (GRCm39)	F559L	probably damaging	Het
Kdm8	G	A	7: 125,054,296 (GRCm39)	V176I	probably benign	Het
Keap1	A	T	9: 21,142,121 (GRCm39)	Y584*	probably null	Het
Klra1	T	C	6: 130,357,607 (GRCm39)	T7A		Het
Lmo7	T	A	14: 102,122,743 (GRCm39)	W311R	probably damaging	Het
Lrp6	A	G	6: 134,518,855 (GRCm39)	V70A	probably damaging	Het
Luc7l3	A	T	11: 94,190,793 (GRCm39)	S174T	unknown	Het
Madd	T	C	2: 90,998,162 (GRCm39)	T653A	probably damaging	Het
Mlph	G	T	1: 90,855,716 (GRCm39)	G41V	probably damaging	Het
Mov10l1	A	G	15: 88,896,118 (GRCm39)	E654G	possibly damaging	Het
Mpp3	T	C	11: 101,911,328 (GRCm39)	I165V		Het
Mrgpra2a	T	G	7: 47,076,394 (GRCm39)	Y288S	probably damaging	Het
Mroh9	T	A	1: 162,890,030 (GRCm39)	M236L		Het
Muc5b	A	C	7: 141,417,974 (GRCm39)	K3640T	probably damaging	Het
Myh13	A	G	11: 67,253,318 (GRCm39)	I1485V	probably benign	Het
Nf2	A	T	11: 4,744,873 (GRCm39)	F285L	probably damaging	Het
Nsd1	C	T	13: 55,361,253 (GRCm39)	R74W	probably damaging	Het
Nudt16l1	A	T	16: 4,758,281 (GRCm39)	*212C	probably null	Het
Oaf	T	C	9: 43,133,992 (GRCm39)	Y243C	probably damaging	Het
Or51e1	T	C	7: 102,358,541 (GRCm39)	V25A	probably benign	Het
Or6c3	T	C	10: 129,308,690 (GRCm39)	I43T	probably benign	Het
Or7g30	T	A	9: 19,352,531 (GRCm39)	F107L	probably benign	Het
Or7h8	A	G	9: 20,124,173 (GRCm39)	H176R	possibly damaging	Het
Or8b36	T	A	9: 37,937,690 (GRCm39)	L196*	probably null	Het
Parp9	T	C	16: 35,768,543 (GRCm39)	I241T	probably damaging	Het
Phlpp2	G	T	8: 110,666,590 (GRCm39)	A1040S	possibly damaging	Het
Pon2	A	T	6: 5,265,391 (GRCm39)	V332E	possibly damaging	Het
Ptprc	A	G	1: 138,016,302 (GRCm39)	V544A	probably damaging	Het
Rfx6	A	G	10: 51,597,600 (GRCm39)	S446G	probably benign	Het
Rnf103	T	A	6: 71,487,099 (GRCm39)	C577S	probably benign	Het
Ros1	T	G	10: 51,922,301 (GRCm39)	E2278D	possibly damaging	Het
Rpl37	A	G	15: 5,147,109 (GRCm39)	S50G	probably benign	Het
Rrad	C	T	8: 105,355,343 (GRCm39)	V222M	possibly damaging	Het
Ryr1	T	C	7: 28,769,283 (GRCm39)	T2770A	probably benign	Het
Secisbp2l	G	A	2: 125,617,623 (GRCm39)	P18L	probably damaging	Het
Septin2	T	A	1: 93,429,310 (GRCm39)	W260R	probably damaging	Het
Slc35c2	A	G	2: 165,122,797 (GRCm39)	M117T	probably benign	Het
Slc44a5	A	G	3: 153,953,373 (GRCm39)	T252A	probably benign	Het
Speer4f2	T	A	5: 17,581,610 (GRCm39)	L184Q		Het
Sphkap	C	G	1: 83,234,982 (GRCm39)	V1615L	probably damaging	Het
Sult2a3	C	T	7: 13,806,981 (GRCm39)	V234I	probably benign	Het
Tanc1	T	C	2: 59,630,132 (GRCm39)	L704P	probably damaging	Het
Tas2r126	T	C	6: 42,412,174 (GRCm39)	S236P	probably benign	Het
Tnik	A	G	3: 28,704,235 (GRCm39)	I1020V	probably damaging	Het
Tomm5	T	C	4: 45,106,724 (GRCm39)	Q64R	unknown	Het
Ttll13	A	G	7: 79,897,182 (GRCm39)	E16G	probably benign	Het
Vmn1r21	C	A	6: 57,821,348 (GRCm39)	C32F	probably benign	Het
Vmn2r51	T	A	7: 9,839,480 (GRCm39)	D36V	probably damaging	Het
Vmn2r63	C	T	7: 42,576,413 (GRCm39)	D467N	probably damaging	Het
Vwce	A	G	19: 10,625,850 (GRCm39)	N454S	possibly damaging	Het
Wfdc1	A	C	8: 120,406,116 (GRCm39)	D77A		Het
Yme1l1	T	A	2: 23,077,815 (GRCm39)	I419N	probably damaging	Het
Zfp106	G	A	2: 120,364,812 (GRCm39)	Q555*	probably null	Het
Zfp773	A	C	7: 7,138,302 (GRCm39)	M111R	probably damaging	Het
Zmat3	G	A	3: 32,397,767 (GRCm39)	A165V	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
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
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'- AATTGGCTCTCCCGTTGCTG -3'
(R):5'- GCCGTAATAGTTAACAAGGCACG -3'

Sequencing Primer
(F):5'- GTTGCTGTGTTCACAATAGACCACAG -3'
(R):5'- CGAGACAGGACTCTGATTCTAGC -3'

Posted On

2022-01-20