Incidental Mutation 'R1716:Nfia'
ID 190992
Institutional Source Beutler Lab
Gene Symbol Nfia
Ensembl Gene ENSMUSG00000028565
Gene Name nuclear factor I/A
Synonyms 1110047K16Rik, NF1-A, NF1A, 9430022M17Rik
MMRRC Submission 039749-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1716 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 97660971-98007111 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 97951365 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Asparagine at position 397 (K397N)
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: K375N

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000099856
Gene: ENSMUSG00000028565
AA Change: K375N

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 damaging
Transcript: ENSMUST00000075448
AA Change: K397N

PolyPhen 2 Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000074899
Gene: ENSMUSG00000028565
AA Change: K397N

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 possibly damaging
Transcript: ENSMUST00000092532
AA Change: K354N

PolyPhen 2 Score 0.816 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000130032
Gene: ENSMUSG00000028565
AA Change: K354N

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 unknown
Transcript: ENSMUST00000107057
AA Change: K268N
SMART Domains Protein: ENSMUSP00000102672
Gene: ENSMUSG00000028565
AA Change: K268N

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 probably damaging
Transcript: ENSMUST00000107062
AA Change: K397N

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000102677
Gene: ENSMUSG00000028565
AA Change: K397N

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
Predicted Effect unknown
Transcript: ENSMUST00000148930
AA Change: K227N
SMART Domains Protein: ENSMUSP00000122641
Gene: ENSMUSG00000028565
AA Change: K227N

DomainStartEndE-ValueType
low complexity region 19 30 N/A INTRINSIC
Pfam:CTF_NFI 45 274 1.5e-102 PFAM
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.5%
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: 90 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acan A G 7: 78,731,946 (GRCm39) T2A unknown Het
Adgrf3 T A 5: 30,402,549 (GRCm39) Q493L probably benign Het
Ak6 T C 13: 100,792,177 (GRCm39) S207P probably benign Het
Ang A G 14: 51,338,937 (GRCm39) D26G probably benign Het
Ang T C 14: 51,338,957 (GRCm39) F33L probably damaging Het
Arhgef38 T A 3: 132,846,598 (GRCm39) Y389F probably benign Het
Arhgef7 C A 8: 11,858,713 (GRCm39) probably null Het
Bicd2 C A 13: 49,531,786 (GRCm39) H343N probably benign Het
Casp4 G A 9: 5,308,919 (GRCm39) probably null Het
Cd22 A G 7: 30,577,103 (GRCm39) F68S probably damaging Het
Cd46 T A 1: 194,760,117 (GRCm39) Q245L probably benign Het
Cntnap2 A T 6: 47,084,826 (GRCm39) R1096* probably null Het
Cntnap3 A G 13: 64,909,816 (GRCm39) V763A probably damaging Het
Cyp3a11 T C 5: 145,805,776 (GRCm39) T171A probably benign Het
Defa30 A G 8: 21,625,431 (GRCm39) Y65C probably damaging Het
Defb18 A T 1: 18,306,875 (GRCm39) M27K probably benign Het
Dnah17 A G 11: 117,923,424 (GRCm39) S4071P probably benign Het
Dnah7b T A 1: 46,230,943 (GRCm39) D1400E probably damaging Het
Dpysl5 C T 5: 30,935,338 (GRCm39) T147I probably benign Het
Dsg4 C T 18: 20,595,518 (GRCm39) R574* probably null Het
Entrep2 A T 7: 64,426,633 (GRCm39) probably null Het
Epm2a A G 10: 11,324,580 (GRCm39) E223G probably benign Het
Etl4 T C 2: 20,748,492 (GRCm39) S75P probably damaging Het
Fbxw15 T A 9: 109,386,204 (GRCm39) M312L probably benign Het
Fcgr4 C T 1: 170,847,672 (GRCm39) T90I probably damaging Het
Fras1 T A 5: 96,700,584 (GRCm39) D201E probably benign Het
Gadl1 A T 9: 115,835,576 (GRCm39) K335* probably null Het
Gcsam T G 16: 45,440,356 (GRCm39) V133G probably damaging Het
Gml G T 15: 74,685,665 (GRCm39) L107I possibly damaging Het
Golga2 T A 2: 32,192,909 (GRCm39) L409Q probably damaging Het
Gtf2a1l A T 17: 89,002,008 (GRCm39) Q241L probably benign Het
Gtf3c3 A G 1: 54,438,419 (GRCm39) Y799H probably damaging Het
Guca1b T G 17: 47,702,126 (GRCm39) probably benign Het
Igdcc4 C A 9: 65,034,179 (GRCm39) H617Q probably damaging Het
Ip6k1 G A 9: 107,918,195 (GRCm39) E77K possibly damaging Het
Itga2b A C 11: 102,351,603 (GRCm39) I574S probably benign Het
Kcnk7 A T 19: 5,756,859 (GRCm39) I283F probably damaging Het
Kirrel3 T A 9: 34,934,843 (GRCm39) L450M probably damaging Het
Lmntd1 A T 6: 145,365,600 (GRCm39) S176R probably damaging Het
Lrrc39 C T 3: 116,373,216 (GRCm39) T292I probably benign Het
Ltbp1 A T 17: 75,622,019 (GRCm39) H801L probably benign Het
Macf1 T A 4: 123,295,196 (GRCm39) Q3318L probably damaging Het
Man1b1 T A 2: 25,235,032 (GRCm39) N282K probably benign Het
Map2k6 A T 11: 110,388,727 (GRCm39) E223V probably damaging Het
Marf1 C A 16: 13,960,450 (GRCm39) R531S possibly damaging Het
Mfge8 G A 7: 78,792,191 (GRCm39) R245C probably damaging Het
Mogat1 T G 1: 78,514,681 (GRCm39) N318K probably benign Het
Myh4 T A 11: 67,141,135 (GRCm39) S732R possibly damaging Het
Myt1l T A 12: 29,861,537 (GRCm39) D106E unknown Het
Ndc1 T C 4: 107,241,992 (GRCm39) F302L probably damaging Het
Ndrg4 C T 8: 96,438,956 (GRCm39) A290V probably benign Het
Nlrp4e A T 7: 23,020,458 (GRCm39) Q315L possibly damaging Het
Oga C A 19: 45,740,613 (GRCm39) K907N probably benign Het
Or10p22 A C 10: 128,826,721 (GRCm39) *313C probably null Het
Or1ad8 T A 11: 50,898,679 (GRCm39) N293K probably damaging Het
Peg3 T C 7: 6,710,780 (GRCm39) I1481V possibly damaging Het
Phldb2 C T 16: 45,595,413 (GRCm39) G883D probably benign Het
Pik3c2b T A 1: 133,022,564 (GRCm39) Y1169N probably damaging Het
Plcl1 A T 1: 55,734,997 (GRCm39) I113F probably damaging Het
Pomt2 T C 12: 87,171,610 (GRCm39) I457V probably benign Het
Ppil1 T C 17: 29,480,809 (GRCm39) N38S possibly damaging Het
Prf1 A G 10: 61,136,231 (GRCm39) N169S probably benign Het
Prmt8 A C 6: 127,703,486 (GRCm39) probably null Het
Ptprg T A 14: 12,154,360 (GRCm38) S694T probably benign Het
Rab12 A T 17: 66,807,315 (GRCm39) M138K possibly damaging Het
Reln T C 5: 22,160,093 (GRCm39) T2159A probably damaging Het
Retsat A T 6: 72,583,063 (GRCm39) Y36F probably damaging Het
Rgs14 A T 13: 55,526,696 (GRCm39) Q116L probably damaging Het
Rlbp1 A T 7: 79,025,684 (GRCm39) N252K probably damaging Het
Rtraf A G 14: 19,862,242 (GRCm39) L215P probably damaging Het
Sec1 A T 7: 45,328,789 (GRCm39) M86K probably benign Het
Sec24b A T 3: 129,834,665 (GRCm39) S42T possibly damaging Het
Serpinb9d T C 13: 33,380,500 (GRCm39) S129P probably damaging Het
Slc35f5 T G 1: 125,512,269 (GRCm39) D356E possibly damaging Het
Smpd4 T C 16: 17,460,365 (GRCm39) S694P probably damaging Het
Spag6 G T 2: 18,750,420 (GRCm39) probably null Het
Spata31d1c T C 13: 65,181,030 (GRCm39) I43T possibly damaging Het
Ssh1 T C 5: 114,090,081 (GRCm39) D314G possibly damaging Het
Tnfrsf17 G A 16: 11,137,595 (GRCm39) D111N probably benign Het
Ttn A G 2: 76,553,635 (GRCm39) I30994T probably damaging Het
Ttn A T 2: 76,614,320 (GRCm39) F8737L probably damaging Het
Ush1c G T 7: 45,845,152 (GRCm39) F890L probably benign Het
Usp36 C T 11: 118,162,957 (GRCm39) probably null Het
Vmn2r115 T C 17: 23,566,795 (GRCm39) Y436H probably benign Het
Vmn2r94 T A 17: 18,477,635 (GRCm39) M259L probably benign Het
Wwp1 T C 4: 19,659,698 (GRCm39) T197A probably benign Het
Zbtb37 T A 1: 160,847,814 (GRCm39) M398L probably benign Het
Zfp804b C T 5: 6,819,673 (GRCm39) C1130Y probably benign Het
Zfp9 A G 6: 118,441,712 (GRCm39) C317R probably damaging Het
Zscan20 T C 4: 128,480,334 (GRCm39) H719R probably damaging Het
Other mutations in Nfia
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00904:Nfia APN 4 97,953,623 (GRCm39) missense probably damaging 0.97
IGL02663:Nfia APN 4 97,929,856 (GRCm39) missense probably benign 0.14
IGL02691:Nfia APN 4 97,970,045 (GRCm39) nonsense probably null
IGL02705:Nfia APN 4 97,671,605 (GRCm39) missense probably damaging 1.00
IGL03226:Nfia APN 4 97,951,286 (GRCm39) missense probably damaging 0.97
R0400:Nfia UTSW 4 97,951,373 (GRCm39) missense probably damaging 0.96
R0611:Nfia UTSW 4 97,671,694 (GRCm39) missense possibly damaging 0.75
R1568:Nfia UTSW 4 97,999,461 (GRCm39) missense possibly damaging 0.93
R3855:Nfia UTSW 4 97,951,259 (GRCm39) missense probably damaging 1.00
R4038:Nfia UTSW 4 97,909,074 (GRCm39) missense probably damaging 1.00
R4441:Nfia UTSW 4 97,661,150 (GRCm39) critical splice donor site probably null
R4849:Nfia UTSW 4 97,970,048 (GRCm39) missense probably damaging 1.00
R5184:Nfia UTSW 4 97,671,585 (GRCm39) missense probably damaging 0.99
R5201:Nfia UTSW 4 97,999,462 (GRCm39) missense probably damaging 0.98
R5254:Nfia UTSW 4 97,902,534 (GRCm39) missense probably damaging 0.99
R5391:Nfia UTSW 4 97,671,538 (GRCm39) missense probably damaging 0.96
R5551:Nfia UTSW 4 97,902,497 (GRCm39) missense probably damaging 0.98
R5794:Nfia UTSW 4 97,671,838 (GRCm39) missense possibly damaging 0.92
R5905:Nfia UTSW 4 97,999,488 (GRCm39) missense possibly damaging 0.82
R5965:Nfia UTSW 4 97,999,529 (GRCm39) makesense probably null
R6028:Nfia UTSW 4 97,999,488 (GRCm39) missense possibly damaging 0.82
R7246:Nfia UTSW 4 97,953,579 (GRCm39) missense probably damaging 1.00
R7669:Nfia UTSW 4 97,671,742 (GRCm39) missense probably damaging 0.96
R8247:Nfia UTSW 4 97,953,644 (GRCm39) missense probably benign 0.01
R8864:Nfia UTSW 4 97,951,382 (GRCm39) missense possibly damaging 0.69
R8916:Nfia UTSW 4 97,888,667 (GRCm39) missense probably benign 0.24
R9175:Nfia UTSW 4 97,671,362 (GRCm39) missense probably damaging 1.00
R9691:Nfia UTSW 4 97,671,465 (GRCm39) missense probably damaging 0.99
X0018:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0019:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0020:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0021:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0022:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0023:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0024:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0027:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0050:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0052:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0053:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0054:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0057:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0058:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0060:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0061:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0062:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0063:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0064:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0065:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0066:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
X0067:Nfia UTSW 4 97,929,892 (GRCm39) missense probably damaging 0.97
Predicted Primers PCR Primer
(F):5'- GTCCACTGAACATGGAGAGGCAAC -3'
(R):5'- TCAGTCAGCATGGACATTACAACCC -3'

Sequencing Primer
(F):5'- GTCTTAGCGCCTTAAAGGAAC -3'
(R):5'- GCATGGACATTACAACCCAAAGTC -3'
Posted On 2014-05-14