Mutagenetix > Incidental Mutation

Incidental Mutation 'R8247:Nfia'

640691

Institutional Source

Beutler Lab

Gene Symbol

Nfia

Ensembl Gene

ENSMUSG00000028565

Gene Name

nuclear factor I/A

Synonyms

9430022M17Rik, NF1-A, 1110047K16Rik, NF1A

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8247 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

97772734-98118874 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 98065407 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 461 (T461S)

Ref Sequence

ENSEMBL: ENSMUSP00000074899 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000052018
AA Change: T439S

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000099856
Gene: ENSMUSG00000028565
AA Change: T439S

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 benign
Transcript: ENSMUST00000075448
AA Change: T461S

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000074899
Gene: ENSMUSG00000028565
AA Change: T461S

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: T418S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000130032
Gene: ENSMUSG00000028565
AA Change: T418S

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
AA Change: T332S

PolyPhen 2 Score 0.091 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000102672
Gene: ENSMUSG00000028565
AA Change: T332S

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 benign
Transcript: ENSMUST00000107062
AA Change: T461S

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000102677
Gene: ENSMUSG00000028565
AA Change: T461S

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

probably benign
Transcript: ENSMUST00000148930

SMART Domains

Protein: ENSMUSP00000122641
Gene: ENSMUSG00000028565

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

Meta Mutation Damage Score

0.1288

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

99% (69/70)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5730596B20Rik	T	C	6: 52,178,962	S3P	unknown	Het
Abca15	A	T	7: 120,337,222	Y170F	possibly damaging	Het
Alpl	C	T	4: 137,746,453	V313M	probably damaging	Het
Ankrd44	T	C	1: 54,752,943	H311R	probably damaging	Het
Atm	A	T	9: 53,450,570	L2749Q		Het
Bicd2	C	T	13: 49,379,986	R683W	probably damaging	Het
Brat1	C	A	5: 140,713,138	P342T	possibly damaging	Het
Camta1	T	A	4: 151,075,264	T482S	probably damaging	Het
Carhsp1	A	G	16: 8,663,671	V67A	probably damaging	Het
Ccdc126	C	T	6: 49,339,841	T85M	probably damaging	Het
Cd274	C	T	19: 29,385,395	Q286*	probably null	Het
Cep192	T	A	18: 67,841,117	I1097N	probably benign	Het
Clvs1	A	T	4: 9,281,885	N110Y	possibly damaging	Het
Cntln	A	G	4: 85,100,780	T102A	probably benign	Het
Cp	A	C	3: 19,966,406	I188L	possibly damaging	Het
Crh	A	G	3: 19,694,127	L117P	probably benign	Het
Dennd2c	A	G	3: 103,152,321	D521G	probably damaging	Het
E2f2	C	T	4: 136,172,815	T12M	possibly damaging	Het
Eid2	G	A	7: 28,268,547	R198H	probably damaging	Het
Exosc4	G	T	15: 76,329,079	C74F	probably damaging	Het
Fanca	A	T	8: 123,283,955		probably benign	Het
Ganc	A	T	2: 120,436,700	Q499L	probably null	Het
Gfy	T	C	7: 45,178,286	T129A	possibly damaging	Het
Gli3	G	T	13: 15,726,775	M1582I	possibly damaging	Het
Gm4744	A	G	6: 40,949,468	S63P		Het
Htr2b	T	C	1: 86,100,095	T230A	probably benign	Het
Iqcb1	T	A	16: 36,858,474	N383K	probably benign	Het
Lpcat1	A	T	13: 73,513,952	I471F	probably damaging	Het
Lrch3	T	G	16: 33,009,343	L781*	probably null	Het
Lrif1	T	A	3: 106,734,376	S3T	probably damaging	Het
Lrp2	T	A	2: 69,431,087	R4503S	possibly damaging	Het
Lrrc16a	T	A	13: 24,099,015	N512I	probably damaging	Het
Lrrc8c	T	C	5: 105,608,444	I695T	probably damaging	Het
Mak	G	A	13: 41,039,670	T473M	possibly damaging	Het
Map2k5	A	T	9: 63,371,737	Y62N	probably damaging	Het
Mbd3l2	T	C	9: 18,445,003	L208P	probably damaging	Het
Myo18b	T	C	5: 112,692,196	E2577G	probably damaging	Het
Oaz3	A	G	3: 94,436,434	Y41H	probably damaging	Het
Olfr1368	A	G	13: 21,142,125	S311P	probably benign	Het
Olfr509	T	A	7: 108,646,163	I138F	probably damaging	Het
Olfr59	C	A	11: 74,289,489	T281K	noncoding transcript	Het
Olfr631	T	C	7: 103,929,576	V251A	possibly damaging	Het
Pin1rt1	T	C	2: 104,714,547	E80G	probably damaging	Het
Pmpcb	T	C	5: 21,756,854	Y457H	probably damaging	Het
Polr2b	T	C	5: 77,320,215	S121P	possibly damaging	Het
Ppm1e	C	T	11: 87,231,275	G619R	probably benign	Het
Pramel5	T	A	4: 144,272,825	M231L	probably damaging	Het
Prex2	G	T	1: 11,199,970	C1293F	probably benign	Het
Psg20	A	G	7: 18,682,637	F185L	probably benign	Het
Psg28	A	G	7: 18,422,939	V457A	probably benign	Het
Pxmp2	A	G	5: 110,274,579	L188P	probably damaging	Het
Scd3	A	T	19: 44,238,564	N279I	possibly damaging	Het
Scg2	T	G	1: 79,436,519	K162N	possibly damaging	Het
Sipa1l2	T	C	8: 125,422,633	E1629G	probably benign	Het
Slc27a2	T	A	2: 126,553,595	F147L	probably benign	Het
Smco1	T	C	16: 32,273,739	V76A	probably benign	Het
Spic	T	C	10: 88,676,061	K111R	probably damaging	Het
Spidr	A	G	16: 15,968,526		probably null	Het
Sptbn1	T	A	11: 30,113,906	I1971F	possibly damaging	Het
Stard8	C	T	X: 99,065,964	S155L	probably benign	Het
Tex33	A	C	15: 78,378,792	S221A	probably benign	Het
Tiam1	G	A	16: 89,898,149	T140M	probably benign	Het
Ttc28	G	A	5: 111,233,341	D1240N	probably benign	Het
Ufl1	T	C	4: 25,250,606	E749G	probably benign	Het
Vmn1r168	G	T	7: 23,541,062	V115F	possibly damaging	Het
Vprbp	A	T	9: 106,854,228	I635F	possibly damaging	Het
Wars2	G	A	3: 99,187,649	V87I	probably benign	Het
Zdhhc14	T	A	17: 5,685,756	C170S	probably damaging	Het
Zfp113	C	T	5: 138,145,034	C318Y	possibly damaging	Het
Zfp367	A	G	13: 64,152,668	S108P	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
R5254:Nfia	UTSW	4	98014297	missense	probably damaging	0.99
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
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'- CCTTTTGGAAACAGCTGGTG -3'
(R):5'- GATATGGGCTCCAGCTTATGC -3'

Sequencing Primer
(F):5'- CTGGTGGCTGACATCTGTTTC -3'
(R):5'- GCTTATGCTATAGACATAACAGGGC -3'

Posted On

2020-07-28