Mutagenetix > Incidental Mutation

Incidental Mutation 'R5254:Nfia'

399319

Institutional Source

Beutler Lab

Gene Symbol

Nfia

Ensembl Gene

ENSMUSG00000028565

Gene Name

nuclear factor I/A

Synonyms

9430022M17Rik, NF1-A, 1110047K16Rik, NF1A

MMRRC Submission

042825-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5254 (G1)

Quality Score

205

Status

Validated

Chromosome

Chromosomal Location

97772734-98118874 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 98014297 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 262 (M262K)

Ref Sequence

ENSEMBL: ENSMUSP00000102677 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000052018] [ENSMUST00000075448] [ENSMUST00000092532] [ENSMUST00000107057] [ENSMUST00000107062]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000052018
AA Change: M240K

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000099856
Gene: ENSMUSG00000028565
AA Change: M240K

Domain	Start	End	E-Value	Type
Pfam:NfI_DNAbd_pre-N	3	46	1.6e-31	PFAM
DWA	67	175	2.4e-21	SMART
Pfam:CTF_NFI	192	487	7.3e-150	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000075448
AA Change: M262K

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000074899
Gene: ENSMUSG00000028565
AA Change: M262K

Domain	Start	End	E-Value	Type
Pfam:NfI_DNAbd_pre-N	6	46	5.6e-30	PFAM
DWA	67	175	2.4e-21	SMART
low complexity region	186	201	N/A	INTRINSIC
Pfam:CTF_NFI	214	508	1.8e-135	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000092532
AA Change: M262K

PolyPhen 2 Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000130032
Gene: ENSMUSG00000028565
AA Change: M262K

Domain	Start	End	E-Value	Type
Pfam:NfI_DNAbd_pre-N	3	46	1.2e-30	PFAM
DWA	67	175	2.4e-21	SMART
low complexity region	186	201	N/A	INTRINSIC
Pfam:CTF_NFI	214	318	4.1e-48	PFAM
Pfam:CTF_NFI	315	466	1.5e-78	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000107057

SMART Domains

Protein: ENSMUSP00000102672
Gene: ENSMUSG00000028565

Domain	Start	End	E-Value	Type
Pfam:NfI_DNAbd_pre-N	3	46	1.2e-31	PFAM
DWA	67	175	2.4e-21	SMART
Pfam:CTF_NFI	180	380	7.8e-96	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000107062
AA Change: M262K

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000102677
Gene: ENSMUSG00000028565
AA Change: M262K

Domain	Start	End	E-Value	Type
Pfam:NfI_DNAbd_pre-N	3	46	1.7e-31	PFAM
DWA	67	175	2.4e-21	SMART
low complexity region	186	201	N/A	INTRINSIC
Pfam:CTF_NFI	214	494	6.2e-128	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133011

Predicted Effect

unknown
Transcript: ENSMUST00000148930
AA Change: M92K

SMART Domains

Protein: ENSMUSP00000122641
Gene: ENSMUSG00000028565
AA Change: M92K

Domain	Start	End	E-Value	Type
low complexity region	19	30	N/A	INTRINSIC
Pfam:CTF_NFI	45	274	1.5e-102	PFAM

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.6%

Validation Efficiency

98% (82/84)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the NF1 (nuclear factor 1) family of transcription factors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
PHENOTYPE: Homozygous null mice display perinatal lethality, hydrocephalus, agenesis of the corpus callosum and hippocampal commissure. Fertility is surviving homozygotes is compromised. A decrease in the number of heterozygous animals is associated with a maternal effect. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abhd8	G	T	8: 71,458,398	C296*	probably null	Het
Adam11	T	A	11: 102,774,272	Y413*	probably null	Het
Ankhd1	A	G	18: 36,656,715	I907V	probably benign	Het
Arrdc5	A	G	17: 56,297,897	I130T	probably benign	Het
Asic5	T	A	3: 82,020,987	I419K	probably damaging	Het
Atp4a	A	T	7: 30,715,530	E248V	probably damaging	Het
Avil	C	A	10: 127,011,761	V154L	probably benign	Het
Bclaf1	T	A	10: 20,323,536	H226Q	possibly damaging	Het
Cald1	A	G	6: 34,746,416		probably benign	Het
Cd200r4	A	C	16: 44,832,090	D27A	possibly damaging	Het
Cdsn	T	A	17: 35,552,202	M1K	probably null	Het
Cfap46	T	A	7: 139,678,514	H281L	possibly damaging	Het
Chaf1a	T	C	17: 56,062,606	F533L	probably benign	Het
Chil4	T	A	3: 106,219,452	I5F	probably benign	Het
Ctu2	A	T	8: 122,476,588	R48W	probably damaging	Het
Daam1	A	T	12: 71,946,576	H373L	unknown	Het
Dcaf10	T	A	4: 45,370,415	Y328N	possibly damaging	Het
Dst	A	T	1: 34,177,931	K1151*	probably null	Het
Ect2	T	C	3: 27,130,070	D503G	probably damaging	Het
Epm2a	C	A	10: 11,457,345	D307E	probably benign	Het
Exph5	A	T	9: 53,337,930	D73V	probably damaging	Het
Fam20b	C	T	1: 156,705,740	G102D	probably damaging	Het
Fat2	T	C	11: 55,281,175	N2904S	probably damaging	Het
Flt3	T	A	5: 147,375,690	Q147L	possibly damaging	Het
Fndc11	A	G	2: 181,222,163	T254A	possibly damaging	Het
Galnt15	C	T	14: 32,058,287	R514*	probably null	Het
Gbgt1	A	G	2: 28,505,208	D286G	probably damaging	Het
Ggt1	T	A	10: 75,579,198		probably null	Het
Gm26526	A	T	7: 39,589,234		noncoding transcript	Het
H2-K1	T	C	17: 33,997,462	T237A	probably damaging	Het
Igf1r	T	A	7: 68,207,319	S1010T	probably damaging	Het
Il21	T	C	3: 37,227,735	T87A	possibly damaging	Het
Kmt2b	G	A	7: 30,569,175	R2010C	probably damaging	Het
Kmt2c	G	A	5: 25,314,594	P2173S	probably benign	Het
Krt1	A	T	15: 101,846,368	S512T	unknown	Het
Krtap16-1	G	A	11: 99,985,598	R327*	probably null	Het
Lama1	T	A	17: 67,756,716	I745N	probably benign	Het
Lrrk1	T	A	7: 66,307,107	N372I	probably benign	Het
Lyst	A	T	13: 13,683,070	E2481D	probably benign	Het
Map2k1	A	T	9: 64,187,745		probably benign	Het
Mbip	A	G	12: 56,337,443	V215A	probably damaging	Het
Mdc1	T	A	17: 35,847,922	V398D	probably benign	Het
Mog	T	G	17: 37,012,372	I225L	probably benign	Het
Mrgprx3-ps	T	A	7: 47,309,436		noncoding transcript	Het
Muc5b	C	T	7: 141,864,540	S3741L	probably benign	Het
Myo5a	A	T	9: 75,130,120	I202F	probably damaging	Het
Myo5b	A	T	18: 74,700,606	I818F	possibly damaging	Het
Nisch	C	T	14: 31,206,567		probably null	Het
Nkd1	A	G	8: 88,589,194	D64G	probably damaging	Het
Nt5c2	T	A	19: 46,893,560	K284*	probably null	Het
Olfr1052	A	T	2: 86,297,921	Y35F	probably damaging	Het
Olfr1058	A	T	2: 86,386,140	S93T	possibly damaging	Het
Olfr262	A	G	19: 12,241,248	S138P	probably damaging	Het
Olfr305	A	T	7: 86,364,190	V49E	possibly damaging	Het
Olfr619	T	G	7: 103,603,789	I45R	probably benign	Het
Olfr723	A	T	14: 49,928,779	I255N	probably damaging	Het
Olfr725	C	A	14: 50,034,678	A242S	possibly damaging	Het
Olfr972	A	T	9: 39,873,445	T57S	possibly damaging	Het
Pcdhb17	A	T	18: 37,486,825	D556V	probably damaging	Het
Pcdhga8	A	T	18: 37,726,620	D243V	probably benign	Het
Polq	A	T	16: 37,089,319	Q2355L	probably damaging	Het
Slc22a30	G	A	19: 8,344,393	Q436*	probably null	Het
Slc5a4a	C	A	10: 76,182,738	Y506*	probably null	Het
Sp110	G	C	1: 85,577,202		probably benign	Het
Tarbp1	G	A	8: 126,467,156	H336Y	probably damaging	Het
Tas2r134	T	G	2: 51,627,547	F13V	probably benign	Het
Tgfb2	A	G	1: 186,704,483	Y98H	probably damaging	Het
Tmprss11a	C	A	5: 86,411,806	V376L	probably damaging	Het
Tmprss11f	T	A	5: 86,538,033	K158N	probably benign	Het
Tnip2	G	T	5: 34,503,578	Q177K	probably damaging	Het
Trp53inp1	T	A	4: 11,165,075		probably null	Het
Ttc28	C	T	5: 111,271,238	P1398S	probably benign	Het
Umodl1	T	G	17: 30,980,359	I308S	possibly damaging	Het
Vcan	A	T	13: 89,691,600	S1942T	probably damaging	Het
Vmn2r124	T	A	17: 18,063,077	N344K	probably benign	Het
Vmn2r25	C	G	6: 123,825,318	C542S	probably damaging	Het
Wiz	T	A	17: 32,378,496		probably benign	Het
Wrap73	A	G	4: 154,155,346	Y343C	probably benign	Het

Other mutations in Nfia

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00904:Nfia	APN	4	98065386	missense	probably damaging	0.97
IGL02663:Nfia	APN	4	98041619	missense	probably benign	0.14
IGL02691:Nfia	APN	4	98081808	nonsense	probably null
IGL02705:Nfia	APN	4	97783368	missense	probably damaging	1.00
IGL03226:Nfia	APN	4	98063049	missense	probably damaging	0.97
R0400:Nfia	UTSW	4	98063136	missense	probably damaging	0.96
R0611:Nfia	UTSW	4	97783457	missense	possibly damaging	0.75
R1568:Nfia	UTSW	4	98111224	missense	possibly damaging	0.93
R1716:Nfia	UTSW	4	98063128	missense	probably damaging	0.98
R3855:Nfia	UTSW	4	98063022	missense	probably damaging	1.00
R4038:Nfia	UTSW	4	98020837	missense	probably damaging	1.00
R4441:Nfia	UTSW	4	97772913	critical splice donor site	probably null
R4849:Nfia	UTSW	4	98081811	missense	probably damaging	1.00
R5184:Nfia	UTSW	4	97783348	missense	probably damaging	0.99
R5201:Nfia	UTSW	4	98111225	missense	probably damaging	0.98
R5391:Nfia	UTSW	4	97783301	missense	probably damaging	0.96
R5551:Nfia	UTSW	4	98014260	missense	probably damaging	0.98
R5794:Nfia	UTSW	4	97783601	missense	possibly damaging	0.92
R5905:Nfia	UTSW	4	98111251	missense	possibly damaging	0.82
R5965:Nfia	UTSW	4	98111292	makesense	probably null
R6028:Nfia	UTSW	4	98111251	missense	possibly damaging	0.82
R7246:Nfia	UTSW	4	98065342	missense	probably damaging	1.00
R7669:Nfia	UTSW	4	97783505	missense	probably damaging	0.96
R8247:Nfia	UTSW	4	98065407	missense	probably benign	0.01
R8864:Nfia	UTSW	4	98063145	missense	possibly damaging	0.69
R8916:Nfia	UTSW	4	98000430	missense	probably benign	0.24
R9175:Nfia	UTSW	4	97783125	missense	probably damaging	1.00
R9691:Nfia	UTSW	4	97783228	missense	probably damaging	0.99
X0018:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0019:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0020:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0021:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0022:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0023:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0024:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0027:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0050:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0052:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0053:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0054:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0057:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0058:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0060:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0061:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0062:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0063:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0064:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0065:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0066:Nfia	UTSW	4	98041655	missense	probably damaging	0.97
X0067:Nfia	UTSW	4	98041655	missense	probably damaging	0.97

Predicted Primers

PCR Primer
(F):5'- ACTGCACTAACATTGGTTCTTG -3'
(R):5'- GCACCTTACCATTTTGGACAAAG -3'

Sequencing Primer
(F):5'- GCACTAACATTGGTTCTTGATCAC -3'
(R):5'- TGTCTGGTTCCCTAATAAGAAAGC -3'

Posted On

2016-07-06