Incidental Mutation 'R9546:Spi1'
ID 720102
Institutional Source Beutler Lab
Gene Symbol Spi1
Ensembl Gene ENSMUSG00000002111
Gene Name spleen focus forming virus (SFFV) proviral integration oncogene
Synonyms Dis-1, Sfpi-1, Tcfpu1, Sfpi1, Spi-1, PU.1, Tfpu.1
MMRRC Submission
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9546 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 90912750-90946104 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 90943617 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 54 (S54T)
Ref Sequence ENSEMBL: ENSMUSP00000002180 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000002180] [ENSMUST00000111430] [ENSMUST00000132741] [ENSMUST00000137942] [ENSMUST00000169776] [ENSMUST00000169852]
AlphaFold P17433
PDB Structure PU.1 ETS DOMAIN-DNA COMPLEX [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000002180
AA Change: S54T

PolyPhen 2 Score 0.078 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000002180
Gene: ENSMUSG00000002111
AA Change: S54T

DomainStartEndE-ValueType
low complexity region 56 73 N/A INTRINSIC
low complexity region 78 85 N/A INTRINSIC
low complexity region 154 167 N/A INTRINSIC
ETS 171 259 9.71e-43 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000111430
SMART Domains Protein: ENSMUSP00000107058
Gene: ENSMUSG00000002100

DomainStartEndE-ValueType
IG 24 103 4.86e-2 SMART
low complexity region 131 143 N/A INTRINSIC
IG 167 263 2.81e-7 SMART
IG 373 453 1.25e-4 SMART
IG 463 544 2.48e-8 SMART
IG 554 640 3.16e-1 SMART
IG 659 772 3.91e-6 SMART
FN3 775 858 2.5e-11 SMART
FN3 873 956 7.06e-11 SMART
IG 983 1066 3.3e-4 SMART
FN3 1069 1151 4.38e-7 SMART
IGc2 1196 1263 6.21e-9 SMART
Predicted Effect
Predicted Effect probably benign
Transcript: ENSMUST00000137942
SMART Domains Protein: ENSMUSP00000119994
Gene: ENSMUSG00000002100

DomainStartEndE-ValueType
IG 3 99 2.81e-7 SMART
low complexity region 135 152 N/A INTRINSIC
IG 209 289 1.25e-4 SMART
IG 299 380 2.48e-8 SMART
IG 390 476 3.16e-1 SMART
IG 495 608 3.91e-6 SMART
FN3 611 694 2.5e-11 SMART
FN3 709 792 7.06e-11 SMART
IG 819 902 3.3e-4 SMART
FN3 905 987 4.38e-7 SMART
IGc2 1032 1099 6.21e-9 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000169776
SMART Domains Protein: ENSMUSP00000127070
Gene: ENSMUSG00000002100

DomainStartEndE-ValueType
IG 24 103 4.86e-2 SMART
low complexity region 131 143 N/A INTRINSIC
IG 167 263 2.81e-7 SMART
IG 374 454 1.25e-4 SMART
IG 464 545 2.48e-8 SMART
IG 555 641 3.16e-1 SMART
IG 660 773 3.91e-6 SMART
FN3 776 859 2.5e-11 SMART
FN3 874 957 7.06e-11 SMART
IG 984 1067 3.3e-4 SMART
FN3 1070 1152 4.38e-7 SMART
IGc2 1197 1264 6.21e-9 SMART
Predicted Effect silent
Transcript: ENSMUST00000169852
SMART Domains Protein: ENSMUSP00000130368
Gene: ENSMUSG00000002111

DomainStartEndE-ValueType
low complexity region 50 63 N/A INTRINSIC
low complexity region 123 133 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.5%
  • 20x: 98.1%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an ETS-domain transcription factor that activates gene expression during myeloid and B-lymphoid cell development. The nuclear protein binds to a purine-rich sequence known as the PU-box found near the promoters of target genes, and regulates their expression in coordination with other transcription factors and cofactors. The protein can also regulate alternative splicing of target genes. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Nullizygous mice may exhibit fetal or perinatal lethality, absence of myeloid and B cells, and altered T cell and NK cell development. Mice carrying hypomorphic alleles display impaired B-cell and myeloid development, develop T cell derived lymphomas andacute myeloid leukemia, and die prematurely. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca6 G A 11: 110,135,042 (GRCm39) Q248* probably null Het
Adgrf4 A T 17: 42,978,283 (GRCm39) C353* probably null Het
Aifm3 T C 16: 17,317,604 (GRCm39) V75A probably benign Het
Apc A G 18: 34,445,311 (GRCm39) K736E possibly damaging Het
Atad2 A G 15: 57,989,973 (GRCm39) S168P probably damaging Het
Ccdc122 T A 14: 77,306,313 (GRCm39) V28E probably damaging Het
Cd5l T C 3: 87,268,201 (GRCm39) V16A probably benign Het
Cdk11b T C 4: 155,733,589 (GRCm39) S682P unknown Het
Chd8 T C 14: 52,453,408 (GRCm39) I1218V probably damaging Het
Clec1b A C 6: 129,382,167 (GRCm39) I215L probably benign Het
Dnah14 A C 1: 181,420,992 (GRCm39) probably null Het
Ednrb T C 14: 104,080,459 (GRCm39) I152V probably benign Het
Epha8 G T 4: 136,665,897 (GRCm39) L420M probably damaging Het
Epn2 T C 11: 61,437,407 (GRCm39) E55G probably damaging Het
Ern1 A G 11: 106,300,853 (GRCm39) S514P probably benign Het
Fbxo4 G A 15: 3,998,493 (GRCm39) P322S probably damaging Het
Gli3 T A 13: 15,788,443 (GRCm39) D149E probably benign Het
Gm12258 A G 11: 58,749,922 (GRCm39) K366E unknown Het
Gm9195 G T 14: 72,718,347 (GRCm39) H110N possibly damaging Het
Grb10 A G 11: 11,893,919 (GRCm39) I389T probably benign Het
Grip1 G A 10: 119,874,569 (GRCm39) E778K possibly damaging Het
Hexb T C 13: 97,322,176 (GRCm39) D203G probably damaging Het
Hhatl A G 9: 121,618,649 (GRCm39) Y118H probably damaging Het
Ighv1-69 A G 12: 115,586,885 (GRCm39) F83L possibly damaging Het
Iglon5 A T 7: 43,123,891 (GRCm39) M336K probably benign Het
Iyd A T 10: 3,501,884 (GRCm39) I177F possibly damaging Het
Kdm4c A C 4: 74,323,104 (GRCm39) D1012A possibly damaging Het
Klhl12 T A 1: 134,413,562 (GRCm39) L349Q probably damaging Het
Lrp2 A G 2: 69,287,165 (GRCm39) probably null Het
Mrm2 T A 5: 140,314,334 (GRCm39) H167L probably damaging Het
Mrpl50 T A 4: 49,514,338 (GRCm39) H111L probably damaging Het
Mtcl3 C A 10: 29,022,805 (GRCm39) R51S probably damaging Het
Nags A T 11: 102,039,081 (GRCm39) T471S probably damaging Het
Nod2 A T 8: 89,379,621 (GRCm39) R41W probably benign Het
Notch1 T A 2: 26,371,127 (GRCm39) N320Y probably damaging Het
Nr2c1 A G 10: 94,026,528 (GRCm39) K468E possibly damaging Het
Nsf G A 11: 103,801,275 (GRCm39) Q247* probably null Het
Obsl1 T C 1: 75,482,030 (GRCm39) H280R probably damaging Het
Or4p20 T C 2: 88,254,049 (GRCm39) M107V probably benign Het
Pcdha3 C T 18: 37,079,389 (GRCm39) R44C probably damaging Het
Pcsk4 A G 10: 80,157,741 (GRCm39) S623P possibly damaging Het
Pdcd6ip A T 9: 113,484,174 (GRCm39) Y818N unknown Het
Plk2 T A 13: 110,535,301 (GRCm39) I445K possibly damaging Het
Pramel51 C A 12: 88,148,651 (GRCm39) probably benign Het
Prdm2 A T 4: 142,861,561 (GRCm39) S576R probably damaging Het
Prl3d1 A T 13: 27,278,982 (GRCm39) Y59F probably benign Het
Ptprj C T 2: 90,274,805 (GRCm39) V1186I probably benign Het
Raly AGCAGCAGTGGTGGAGGAGGAGGCAGCAGTGGTGGAGG AGCAGCAGTGGTGGAGG 2: 154,705,754 (GRCm39) probably benign Het
Ros1 C T 10: 51,994,215 (GRCm39) probably null Het
Ryr2 C T 13: 11,602,101 (GRCm39) probably null Het
Scn7a A T 2: 66,582,603 (GRCm39) I98N possibly damaging Het
Ssna1 C T 2: 25,162,316 (GRCm39) V16I probably benign Het
Sult3a2 G A 10: 33,655,670 (GRCm39) P103L possibly damaging Het
Syne1 C T 10: 5,193,123 (GRCm39) G3975D probably damaging Het
Tbc1d1 T C 5: 64,330,950 (GRCm39) V43A possibly damaging Het
Tut4 A G 4: 108,370,429 (GRCm39) D776G probably benign Het
Uba5 A G 9: 103,931,567 (GRCm39) S222P probably damaging Het
Vmn2r24 A C 6: 123,764,266 (GRCm39) E381A probably damaging Het
Vmn2r95 G A 17: 18,661,721 (GRCm39) G489D probably benign Het
Wdr17 A T 8: 55,112,735 (GRCm39) F789I probably damaging Het
Xpnpep1 A T 19: 52,990,959 (GRCm39) L422Q probably damaging Het
Zfand3 T A 17: 30,372,302 (GRCm39) H107Q probably benign Het
Other mutations in Spi1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02591:Spi1 APN 2 90,927,295 (GRCm39) start codon destroyed probably null 0.93
R1778:Spi1 UTSW 2 90,929,867 (GRCm39) missense probably damaging 1.00
R1893:Spi1 UTSW 2 90,944,702 (GRCm39) missense probably benign 0.04
R4230:Spi1 UTSW 2 90,945,680 (GRCm39) missense probably damaging 1.00
R5169:Spi1 UTSW 2 90,945,428 (GRCm39) nonsense probably null
R6025:Spi1 UTSW 2 90,944,685 (GRCm39) missense probably benign
R6877:Spi1 UTSW 2 90,944,741 (GRCm39) missense probably damaging 0.98
R7052:Spi1 UTSW 2 90,943,685 (GRCm39) missense probably damaging 1.00
R8401:Spi1 UTSW 2 90,943,650 (GRCm39) missense probably benign 0.00
R8725:Spi1 UTSW 2 90,945,516 (GRCm39) missense probably damaging 1.00
R9026:Spi1 UTSW 2 90,912,862 (GRCm39) missense unknown
R9752:Spi1 UTSW 2 90,943,666 (GRCm39) missense probably benign 0.00
X0019:Spi1 UTSW 2 90,927,330 (GRCm39) missense possibly damaging 0.78
Predicted Primers PCR Primer
(F):5'- GTGACTGTCATTAGGGACTTTAAC -3'
(R):5'- GTGAAGGTTCCATGCCTCAC -3'

Sequencing Primer
(F):5'- GGCATGTTAGGAAACCTCTCTGC -3'
(R):5'- GGTTCCATGCCTCACCACAG -3'
Posted On 2022-07-18