Incidental Mutation 'R6291:Spp1'
ID 508413
Institutional Source Beutler Lab
Gene Symbol Spp1
Ensembl Gene ENSMUSG00000029304
Gene Name secreted phosphoprotein 1
Synonyms Opn, Opnl, Apl-1, OP, BNSP, ETA-1, 44kDa bone phosphoprotein, osteopontin-like protein, minopontin, Ric, osteopontin, Spp-1, bone sialoprotein 1, 2ar
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6291 (G1)
Quality Score 225.009
Status Validated
Chromosome 5
Chromosomal Location 104582984-104588916 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 104587242 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 109 (S109T)
Ref Sequence ENSEMBL: ENSMUSP00000108368 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031243] [ENSMUST00000086833] [ENSMUST00000112746] [ENSMUST00000112747] [ENSMUST00000112748] [ENSMUST00000132457] [ENSMUST00000145084]
AlphaFold P10923
Predicted Effect possibly damaging
Transcript: ENSMUST00000031243
AA Change: S109T

PolyPhen 2 Score 0.888 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000031243
Gene: ENSMUSG00000029304
AA Change: S109T

DomainStartEndE-ValueType
signal peptide 1 16 N/A INTRINSIC
OSTEO 17 294 2.5e-157 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000086833
AA Change: S110T

PolyPhen 2 Score 0.317 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000084043
Gene: ENSMUSG00000029304
AA Change: S110T

DomainStartEndE-ValueType
signal peptide 1 16 N/A INTRINSIC
OSTEO 17 295 2.21e-158 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112746
AA Change: S110T

PolyPhen 2 Score 0.317 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000108366
Gene: ENSMUSG00000029304
AA Change: S110T

DomainStartEndE-ValueType
signal peptide 1 16 N/A INTRINSIC
Pfam:Osteopontin 20 164 2.2e-67 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000112747
AA Change: S109T

PolyPhen 2 Score 0.888 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000108367
Gene: ENSMUSG00000029304
AA Change: S109T

DomainStartEndE-ValueType
signal peptide 1 16 N/A INTRINSIC
OSTEO 17 294 2.5e-157 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000112748
AA Change: S109T

PolyPhen 2 Score 0.888 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000108368
Gene: ENSMUSG00000029304
AA Change: S109T

DomainStartEndE-ValueType
signal peptide 1 16 N/A INTRINSIC
OSTEO 17 294 2.5e-157 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000132457
Predicted Effect probably benign
Transcript: ENSMUST00000145084
AA Change: S110T

PolyPhen 2 Score 0.317 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000117338
Gene: ENSMUSG00000029304
AA Change: S110T

DomainStartEndE-ValueType
signal peptide 1 16 N/A INTRINSIC
Pfam:Osteopontin 20 152 1.2e-60 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000199139
Meta Mutation Damage Score 0.1002 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.6%
  • 20x: 96.3%
Validation Efficiency 98% (86/88)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is involved in the attachment of osteoclasts to the mineralized bone matrix. The encoded protein is secreted and binds hydroxyapatite with high affinity. The osteoclast vitronectin receptor is found in the cell membrane and may be involved in the binding to this protein. This protein is also a cytokine that upregulates expression of interferon-gamma and interleukin-12. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
PHENOTYPE: Two alleles determine natural resistance/susceptibility to the lethal effects of the Gilliam strain of Rickettsia tsutsugamushi. Mice homozygous for a knock-out allele exhibit abnormal osteoclast physiology, macrophage recruitment, wound healing, response to injury, and inflammatory response. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 91 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc12 C T 8: 87,293,173 (GRCm39) G5D possibly damaging Het
Adamts9 T C 6: 92,867,101 (GRCm39) K95R probably damaging Het
Adap1 G T 5: 139,259,246 (GRCm39) L314M probably benign Het
Alkbh1 T A 12: 87,475,864 (GRCm39) E306V possibly damaging Het
Alpk2 T A 18: 65,438,972 (GRCm39) D1274V possibly damaging Het
Ankrd31 A C 13: 97,014,746 (GRCm39) K1188N possibly damaging Het
Aox1 T A 1: 58,369,965 (GRCm39) M759K probably damaging Het
Atp13a3 T A 16: 30,155,061 (GRCm39) D961V probably damaging Het
Bcl11a G A 11: 24,108,321 (GRCm39) G100R probably damaging Het
Bpifc G A 10: 85,812,122 (GRCm39) A362V probably damaging Het
Btaf1 C T 19: 36,950,408 (GRCm39) T546I probably benign Het
Casd1 C A 6: 4,619,834 (GRCm39) P193Q probably damaging Het
Cdhr1 T C 14: 36,811,422 (GRCm39) T230A probably benign Het
Celsr3 T G 9: 108,706,041 (GRCm39) D841E probably damaging Het
Cenpj T C 14: 56,789,433 (GRCm39) D872G probably benign Het
Cep95 G T 11: 106,706,422 (GRCm39) A559S probably damaging Het
Chpt1 A T 10: 88,311,306 (GRCm39) C62* probably null Het
Cspg4b T A 13: 113,456,981 (GRCm39) I1009N possibly damaging Het
Cspp1 A G 1: 10,134,559 (GRCm39) K103R probably damaging Het
Ctla4 T C 1: 60,951,837 (GRCm39) V122A probably benign Het
Cyp3a11 A G 5: 145,799,237 (GRCm39) F317L possibly damaging Het
Daam1 T C 12: 71,993,025 (GRCm39) L338P unknown Het
Dcc T A 18: 71,815,238 (GRCm39) I379L probably benign Het
Dennd2c C A 3: 103,038,925 (GRCm39) C24* probably null Het
Dnai3 G A 3: 145,772,648 (GRCm39) S466L probably benign Het
Dnajc12 A G 10: 63,233,053 (GRCm39) I65V probably benign Het
Dock3 T A 9: 106,785,631 (GRCm39) M208L probably benign Het
Dsg1b T C 18: 20,537,848 (GRCm39) I588T possibly damaging Het
Eif1b T C 9: 120,323,206 (GRCm39) L22S probably benign Het
Ep300 T A 15: 81,532,708 (GRCm39) S1649T unknown Het
Eps15 CAAA CAA 4: 109,162,900 (GRCm39) probably null Het
Ercc6 A T 14: 32,291,943 (GRCm39) E1102D probably benign Het
Gsdmc3 T C 15: 63,732,090 (GRCm39) N312S probably benign Het
Guca2b A T 4: 119,514,890 (GRCm39) L57Q probably damaging Het
Heatr5b G T 17: 79,069,526 (GRCm39) H1740Q probably benign Het
Hecw1 G A 13: 14,697,592 (GRCm39) probably benign Het
Icam5 A G 9: 20,948,217 (GRCm39) H675R probably benign Het
Il18rap T C 1: 40,564,049 (GRCm39) F56L probably benign Het
Iqgap3 T A 3: 87,997,037 (GRCm39) probably null Het
Itsn1 T C 16: 91,664,984 (GRCm39) probably benign Het
Jakmip3 A T 7: 138,622,585 (GRCm39) D315V probably damaging Het
Kif24 A G 4: 41,413,959 (GRCm39) Y328H probably damaging Het
Kmt2a A T 9: 44,744,171 (GRCm39) probably benign Het
Kng1 A G 16: 22,898,475 (GRCm39) E625G probably damaging Het
Man2b1 C T 8: 85,823,675 (GRCm39) T973I probably benign Het
Masp2 G A 4: 148,687,210 (GRCm39) V31M probably damaging Het
Myo18b C T 5: 113,013,601 (GRCm39) R785H possibly damaging Het
Naa15 G A 3: 51,350,212 (GRCm39) G103D probably damaging Het
Or4f15 A G 2: 111,813,969 (GRCm39) V150A probably benign Het
Or5m11b A G 2: 85,805,926 (GRCm39) Y113C probably damaging Het
Or7e177 T A 9: 20,211,899 (GRCm39) D134E probably damaging Het
Papln A G 12: 83,829,789 (GRCm39) N970S probably benign Het
Pick1 T A 15: 79,135,928 (GRCm39) probably null Het
Pigr A C 1: 130,769,498 (GRCm39) D103A probably benign Het
Plekhf1 A C 7: 37,921,029 (GRCm39) F180V possibly damaging Het
Plxnc1 A G 10: 94,669,504 (GRCm39) probably null Het
Polr3f A G 2: 144,376,308 (GRCm39) I136V probably damaging Het
Ppp2r2c T C 5: 37,097,468 (GRCm39) M218T possibly damaging Het
Prox2 C T 12: 85,136,420 (GRCm39) V466I probably damaging Het
Prrc2a G A 17: 35,373,909 (GRCm39) L1479F probably damaging Het
Rbm24 T A 13: 46,575,313 (GRCm39) probably null Het
Rcc1l A T 5: 134,195,560 (GRCm39) probably null Het
Ripk4 A C 16: 97,556,323 (GRCm39) L140R probably damaging Het
Rmnd1 A T 10: 4,372,135 (GRCm39) L188Q probably damaging Het
Rnf170 C T 8: 26,630,992 (GRCm39) P249S probably damaging Het
Rras A G 7: 44,667,595 (GRCm39) probably null Het
Rsf1 G A 7: 97,229,117 (GRCm39) probably benign Het
Scn7a T A 2: 66,530,458 (GRCm39) D629V probably damaging Het
Sipa1l3 A G 7: 29,087,558 (GRCm39) S556P probably damaging Het
Smarca2 C T 19: 26,608,292 (GRCm39) A117V probably damaging Het
Snca C T 6: 60,792,702 (GRCm39) A69T probably damaging Het
Snx2 T C 18: 53,342,737 (GRCm39) probably null Het
Stoml3 T C 3: 53,414,937 (GRCm39) L243P probably damaging Het
Susd2 A G 10: 75,473,408 (GRCm39) F789L possibly damaging Het
Sycp1 A G 3: 102,816,277 (GRCm39) M419T probably damaging Het
Thoc1 T C 18: 9,993,330 (GRCm39) V563A probably benign Het
Tmprss11g T C 5: 86,635,281 (GRCm39) I398V probably damaging Het
Tox3 A G 8: 90,975,566 (GRCm39) L355P probably damaging Het
Tpp1 A G 7: 105,396,223 (GRCm39) I492T probably benign Het
Trim21 A T 7: 102,213,289 (GRCm39) L3Q probably damaging Het
Ttn A C 2: 76,738,080 (GRCm39) V4153G probably benign Het
Ttn T C 2: 76,744,638 (GRCm39) probably benign Het
Unc80 A G 1: 66,560,756 (GRCm39) E828G possibly damaging Het
Vav3 A G 3: 109,416,170 (GRCm39) N263S possibly damaging Het
Vmn1r183 A C 7: 23,754,982 (GRCm39) T262P possibly damaging Het
Vmn2r67 G A 7: 84,799,142 (GRCm39) P522S possibly damaging Het
Vps35 T A 8: 86,026,086 (GRCm39) M1L probably benign Het
Xpo7 A T 14: 70,942,130 (GRCm39) L79* probably null Het
Zc3h14 G A 12: 98,726,087 (GRCm39) R324H probably damaging Het
Zfp330 T C 8: 83,499,613 (GRCm39) T6A probably damaging Het
Zfp948 T A 17: 21,807,286 (GRCm39) H159Q unknown Het
Other mutations in Spp1
AlleleSourceChrCoordTypePredicted EffectPPH Score
R4755:Spp1 UTSW 5 104,583,081 (GRCm39) intron probably benign
R4969:Spp1 UTSW 5 104,588,153 (GRCm39) missense possibly damaging 0.68
R5531:Spp1 UTSW 5 104,588,424 (GRCm39) missense probably benign 0.12
R6198:Spp1 UTSW 5 104,587,374 (GRCm39) splice site probably null
R6636:Spp1 UTSW 5 104,588,396 (GRCm39) missense possibly damaging 0.51
R7029:Spp1 UTSW 5 104,587,167 (GRCm39) missense probably benign 0.02
R7228:Spp1 UTSW 5 104,588,311 (GRCm39) missense probably damaging 0.99
R7695:Spp1 UTSW 5 104,583,009 (GRCm39) start gained probably benign
R7793:Spp1 UTSW 5 104,588,200 (GRCm39) missense probably damaging 1.00
R8050:Spp1 UTSW 5 104,588,280 (GRCm39) missense probably benign 0.00
R8372:Spp1 UTSW 5 104,588,122 (GRCm39) missense probably benign 0.02
R9074:Spp1 UTSW 5 104,588,167 (GRCm39) missense probably benign 0.07
R9099:Spp1 UTSW 5 104,588,387 (GRCm39) missense probably benign 0.02
X0011:Spp1 UTSW 5 104,588,288 (GRCm39) missense possibly damaging 0.85
Predicted Primers PCR Primer
(F):5'- AGCTATTGTAGTCTAAAACCCAAGC -3'
(R):5'- GCAGACTCTGGTTTCCTAGAAG -3'

Sequencing Primer
(F):5'- GCGCTAATTTACTGAGCCAACTTG -3'
(R):5'- CTGGTTTCCTAGAAGTGAGATCAAGC -3'
Posted On 2018-03-15