Incidental Mutation 'R1568:Nfia'
ID 175409
Institutional Source Beutler Lab
Gene Symbol Nfia
Ensembl Gene ENSMUSG00000028565
Gene Name nuclear factor I/A
Synonyms 9430022M17Rik, NF1-A, 1110047K16Rik, NF1A
MMRRC Submission 039607-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1568 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 97772734-98118874 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to G at 98111224 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Aspartic acid at position 378 (Y378D)
Ref Sequence ENSEMBL: ENSMUSP00000102672 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000052018] [ENSMUST00000075448] [ENSMUST00000092532] [ENSMUST00000107057] [ENSMUST00000107062]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000052018
AA Change: Y485D

PolyPhen 2 Score 0.817 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000099856
Gene: ENSMUSG00000028565
AA Change: Y485D

DomainStartEndE-ValueType
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: Y507D

PolyPhen 2 Score 0.018 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000074899
Gene: ENSMUSG00000028565
AA Change: Y507D

DomainStartEndE-ValueType
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: Y464D

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000130032
Gene: ENSMUSG00000028565
AA Change: Y464D

DomainStartEndE-ValueType
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 possibly damaging
Transcript: ENSMUST00000107057
AA Change: Y378D

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000102672
Gene: ENSMUSG00000028565
AA Change: Y378D

DomainStartEndE-ValueType
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 possibly damaging
Transcript: ENSMUST00000107062
AA Change: V476G

PolyPhen 2 Score 0.822 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000102677
Gene: ENSMUSG00000028565
AA Change: V476G

DomainStartEndE-ValueType
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
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 95.8%
  • 20x: 90.9%
Validation Efficiency
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam18 T G 8: 24,647,783 (GRCm38) probably null Het
Adgb A T 10: 10,442,665 (GRCm38) Y138* probably null Het
Adra1d T C 2: 131,546,172 (GRCm38) R488G possibly damaging Het
Ahnak G A 19: 9,002,375 (GRCm38) G341E probably damaging Het
Ankmy1 T C 1: 92,881,116 (GRCm38) D690G probably damaging Het
Arhgef38 C T 3: 133,132,464 (GRCm38) E21K probably damaging Het
Atp8b2 T C 3: 89,949,848 (GRCm38) M402V probably damaging Het
Atp8b4 G T 2: 126,325,394 (GRCm38) H1062N probably benign Het
Bdnf A G 2: 109,723,794 (GRCm38) H131R probably damaging Het
Cblb C T 16: 52,135,829 (GRCm38) T265M probably damaging Het
Cenpe T A 3: 135,239,758 (GRCm38) M1011K probably benign Het
Clca2 A T 3: 145,075,649 (GRCm38) Y711* probably null Het
Clca4a A G 3: 144,952,929 (GRCm38) Y842H probably benign Het
Clspn T A 4: 126,581,517 (GRCm38) M1021K probably benign Het
Cpne8 G T 15: 90,619,642 (GRCm38) R107S probably damaging Het
D6Ertd527e C G 6: 87,111,524 (GRCm38) T223S unknown Het
Dna2 C T 10: 62,949,187 (GRCm38) R28W probably benign Het
Dnah5 T A 15: 28,409,177 (GRCm38) N3580K probably damaging Het
Dsp T C 13: 38,175,147 (GRCm38) I298T probably damaging Het
Dync2h1 T C 9: 7,157,553 (GRCm38) K858R probably null Het
Fasn A T 11: 120,813,249 (GRCm38) V1448E possibly damaging Het
Ghdc A G 11: 100,768,505 (GRCm38) I322T probably benign Het
Gins2 T C 8: 120,582,200 (GRCm38) D105G probably damaging Het
Insr A T 8: 3,165,576 (GRCm38) D975E probably benign Het
Klrc3 T C 6: 129,639,547 (GRCm38) D169G probably benign Het
Krt76 T A 15: 101,885,008 (GRCm38) S532C unknown Het
Lamp3 A T 16: 19,673,525 (GRCm38) M323K probably damaging Het
Lgmn T C 12: 102,394,609 (GRCm38) I423M possibly damaging Het
Lpgat1 A T 1: 191,776,426 (GRCm38) T359S possibly damaging Het
Lrguk T A 6: 34,086,438 (GRCm38) I466N probably damaging Het
Magi3 A C 3: 104,089,527 (GRCm38) M234R probably benign Het
Myh14 G A 7: 44,611,698 (GRCm38) R1042* probably null Het
Npffr1 T A 10: 61,626,233 (GRCm38) S383T possibly damaging Het
Or4f57 C A 2: 111,960,240 (GRCm38) V278F probably benign Het
Or52n4 T A 7: 104,644,770 (GRCm38) I199F probably benign Het
Or5b112 C A 19: 13,342,175 (GRCm38) P139Q probably benign Het
Or9s14 T C 1: 92,607,954 (GRCm38) L39P probably damaging Het
Osr1 G A 12: 9,579,798 (GRCm38) probably null Het
Pde4b A C 4: 102,597,699 (GRCm38) R375S probably damaging Het
Pde8a A G 7: 81,292,263 (GRCm38) E150G probably damaging Het
Pkhd1l1 A T 15: 44,545,501 (GRCm38) probably null Het
Ppp3ca A G 3: 136,928,544 (GRCm38) T422A probably benign Het
Proser1 T C 3: 53,477,759 (GRCm38) V354A possibly damaging Het
Rgs20 G T 1: 5,020,827 (GRCm38) R127S probably benign Het
Sanbr T C 11: 23,589,971 (GRCm38) K48E probably damaging Het
Sec22a T C 16: 35,347,628 (GRCm38) D171G probably benign Het
Secisbp2 A G 13: 51,673,107 (GRCm38) E417G possibly damaging Het
Serpinb6b T C 13: 32,974,912 (GRCm38) L32S probably damaging Het
Sf3b1 C G 1: 55,019,395 (GRCm38) E12Q possibly damaging Het
Slc39a10 A T 1: 46,826,215 (GRCm38) S487T probably benign Het
Slc6a1 G T 6: 114,307,770 (GRCm38) G263V probably damaging Het
Spag6 A G 2: 18,733,114 (GRCm38) D265G probably benign Het
Spata31e2 T C 1: 26,685,869 (GRCm38) T77A probably benign Het
Sybu G T 15: 44,718,832 (GRCm38) S132* probably null Het
Virma T C 4: 11,528,776 (GRCm38) S1288P probably damaging Het
Vmn1r229 T A 17: 20,814,805 (GRCm38) V104D probably damaging Het
Vmn1r238 T C 18: 3,123,358 (GRCm38) T19A probably benign Het
Vmn2r86 C T 10: 130,453,141 (GRCm38) V164I probably benign Het
Wfdc13 G T 2: 164,686,934 (GRCm38) A64S probably damaging Het
Zfp873 C A 10: 82,060,279 (GRCm38) H318Q probably damaging Het
Zyg11a A G 4: 108,183,646 (GRCm38) probably null Het
Other mutations in Nfia
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00904:Nfia APN 4 98,065,386 (GRCm38) missense probably damaging 0.97
IGL02663:Nfia APN 4 98,041,619 (GRCm38) missense probably benign 0.14
IGL02691:Nfia APN 4 98,081,808 (GRCm38) nonsense probably null
IGL02705:Nfia APN 4 97,783,368 (GRCm38) missense probably damaging 1.00
IGL03226:Nfia APN 4 98,063,049 (GRCm38) missense probably damaging 0.97
R0400:Nfia UTSW 4 98,063,136 (GRCm38) missense probably damaging 0.96
R0611:Nfia UTSW 4 97,783,457 (GRCm38) missense possibly damaging 0.75
R1716:Nfia UTSW 4 98,063,128 (GRCm38) missense probably damaging 0.98
R3855:Nfia UTSW 4 98,063,022 (GRCm38) missense probably damaging 1.00
R4038:Nfia UTSW 4 98,020,837 (GRCm38) missense probably damaging 1.00
R4441:Nfia UTSW 4 97,772,913 (GRCm38) critical splice donor site probably null
R4849:Nfia UTSW 4 98,081,811 (GRCm38) missense probably damaging 1.00
R5184:Nfia UTSW 4 97,783,348 (GRCm38) missense probably damaging 0.99
R5201:Nfia UTSW 4 98,111,225 (GRCm38) missense probably damaging 0.98
R5254:Nfia UTSW 4 98,014,297 (GRCm38) missense probably damaging 0.99
R5391:Nfia UTSW 4 97,783,301 (GRCm38) missense probably damaging 0.96
R5551:Nfia UTSW 4 98,014,260 (GRCm38) missense probably damaging 0.98
R5794:Nfia UTSW 4 97,783,601 (GRCm38) missense possibly damaging 0.92
R5905:Nfia UTSW 4 98,111,251 (GRCm38) missense possibly damaging 0.82
R5965:Nfia UTSW 4 98,111,292 (GRCm38) makesense probably null
R6028:Nfia UTSW 4 98,111,251 (GRCm38) missense possibly damaging 0.82
R7246:Nfia UTSW 4 98,065,342 (GRCm38) missense probably damaging 1.00
R7669:Nfia UTSW 4 97,783,505 (GRCm38) missense probably damaging 0.96
R8247:Nfia UTSW 4 98,065,407 (GRCm38) missense probably benign 0.01
R8864:Nfia UTSW 4 98,063,145 (GRCm38) missense possibly damaging 0.69
R8916:Nfia UTSW 4 98,000,430 (GRCm38) missense probably benign 0.24
R9175:Nfia UTSW 4 97,783,125 (GRCm38) missense probably damaging 1.00
R9691:Nfia UTSW 4 97,783,228 (GRCm38) missense probably damaging 0.99
X0018:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0019:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0020:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0021:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0022:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0023:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0024:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0027:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0050:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0052:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0053:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0054:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0057:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0058:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0060:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0061:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0062:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0063:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0064:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0065:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0066:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
X0067:Nfia UTSW 4 98,041,655 (GRCm38) missense probably damaging 0.97
Predicted Primers PCR Primer
(F):5'- AAGATAGCCAGGTTCCTTGCCCTC -3'
(R):5'- GCCTTTGCTGTTTGACCACGATG -3'

Sequencing Primer
(F):5'- ATTGGCTCACTACAGGGTTAC -3'
(R):5'- GACCACGATGTTTGCTGTTTC -3'
Posted On 2014-04-24