Incidental Mutation 'R3855:Nfia'
ID 276097
Institutional Source Beutler Lab
Gene Symbol Nfia
Ensembl Gene ENSMUSG00000028565
Gene Name nuclear factor I/A
Synonyms 1110047K16Rik, NF1-A, NF1A, 9430022M17Rik
MMRRC Submission 040901-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3855 (G1)
Quality Score 225
Status Validated
Chromosome 4
Chromosomal Location 97660971-98007111 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 97951259 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Arginine at position 362 (H362R)
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: H340R

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000099856
Gene: ENSMUSG00000028565
AA Change: H340R

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: H362R

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000074899
Gene: ENSMUSG00000028565
AA Change: H362R

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: H319R

PolyPhen 2 Score 0.663 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000130032
Gene: ENSMUSG00000028565
AA Change: H319R

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 probably benign
Transcript: ENSMUST00000107057
AA Change: H233R

PolyPhen 2 Score 0.032 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000102672
Gene: ENSMUSG00000028565
AA Change: H233R

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: H362R

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000102677
Gene: ENSMUSG00000028565
AA Change: H362R

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: H192R
SMART Domains Protein: ENSMUSP00000122641
Gene: ENSMUSG00000028565
AA Change: H192R

DomainStartEndE-ValueType
low complexity region 19 30 N/A INTRINSIC
Pfam:CTF_NFI 45 274 1.5e-102 PFAM
Meta Mutation Damage Score 0.0714 question?
Coding Region Coverage
  • 1x: 99.6%
  • 3x: 98.7%
  • 10x: 96.9%
  • 20x: 93.3%
Validation Efficiency 98% (45/46)
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: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Akna A T 4: 63,291,705 (GRCm39) S1144R probably damaging Het
Apbb1ip T C 2: 22,765,187 (GRCm39) S623P unknown Het
Apex1 A G 14: 51,163,714 (GRCm39) T109A probably benign Het
Arhgef1 G A 7: 24,618,697 (GRCm39) G107S probably damaging Het
Ccnq T C 11: 78,642,013 (GRCm39) N159S probably benign Het
Cdc42bpa A G 1: 179,983,543 (GRCm39) probably benign Het
Cog2 T C 8: 125,256,742 (GRCm39) probably null Het
Dennd4c G A 4: 86,698,084 (GRCm39) V191M probably damaging Het
Dthd1 T A 5: 62,984,472 (GRCm39) H392Q probably benign Het
Dthd1 T C 5: 63,045,366 (GRCm39) V710A probably benign Het
Galnt7 T C 8: 57,985,658 (GRCm39) probably benign Het
Gm4868 A G 5: 125,925,609 (GRCm39) noncoding transcript Het
Gpr179 T C 11: 97,232,260 (GRCm39) E648G probably damaging Het
Hk2 T C 6: 82,713,657 (GRCm39) E447G possibly damaging Het
Idi1 G T 13: 8,935,968 (GRCm39) A25S probably benign Het
Itgb3bp T C 4: 99,686,957 (GRCm39) E76G possibly damaging Het
Khk A G 5: 31,084,401 (GRCm39) D82G probably benign Het
Kif17 A G 4: 138,018,821 (GRCm39) S533G probably benign Het
Kmt2a A G 9: 44,741,796 (GRCm39) probably benign Het
Kmt5c T C 7: 4,749,255 (GRCm39) F104S probably damaging Het
Lmf1 G A 17: 25,873,445 (GRCm39) V317M probably damaging Het
Mdh1 C T 11: 21,509,281 (GRCm39) V234I probably benign Het
Nbas T A 12: 13,329,415 (GRCm39) I120N possibly damaging Het
Nhlrc2 T C 19: 56,576,703 (GRCm39) probably null Het
Nme5 A G 18: 34,702,884 (GRCm39) S135P possibly damaging Het
Nt5c2 A G 19: 46,884,957 (GRCm39) V252A probably damaging Het
Nufip2 T C 11: 77,583,715 (GRCm39) V543A probably damaging Het
Or1l4b A T 2: 37,036,835 (GRCm39) I204F possibly damaging Het
Or2y10 A G 11: 49,454,918 (GRCm39) T57A probably damaging Het
Otog T C 7: 45,923,184 (GRCm39) S1020P possibly damaging Het
Pear1 T C 3: 87,659,228 (GRCm39) H814R possibly damaging Het
Pkd1l1 A G 11: 8,915,047 (GRCm39) probably null Het
Pla2g4a T A 1: 149,705,928 (GRCm39) I711F possibly damaging Het
Ppig G A 2: 69,579,719 (GRCm39) V418I unknown Het
Prg4 T C 1: 150,327,751 (GRCm39) Y234C probably damaging Het
Prmt9 G A 8: 78,294,894 (GRCm39) V413I probably benign Het
Rnf145 G A 11: 44,422,120 (GRCm39) V68M possibly damaging Het
Sepsecs G A 5: 52,821,616 (GRCm39) R74C probably damaging Het
Sgsm1 A G 5: 113,411,125 (GRCm39) V580A probably benign Het
Sh3bp1 C T 15: 78,785,361 (GRCm39) probably benign Het
Sox11 C A 12: 27,391,501 (GRCm39) G303C probably damaging Het
Usp54 C A 14: 20,638,488 (GRCm39) M197I probably damaging Het
Vps26c A G 16: 94,311,665 (GRCm39) F95L probably benign Het
Xylt1 T G 7: 117,192,777 (GRCm39) L361R probably damaging Het
Zfp512 A G 5: 31,637,593 (GRCm39) R505G possibly 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
R1716:Nfia UTSW 4 97,951,365 (GRCm39) missense probably damaging 0.98
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'- GGCAACTTGAAATTCTATCCTCCTC -3'
(R):5'- TTACATTGAGGAACCCCACCTG -3'

Sequencing Primer
(F):5'- TGTCTTAGCGCCTTAAAGGAAC -3'
(R):5'- TGTCCAGCTTGCTGACCAG -3'
Posted On 2015-04-06