Incidental Mutation 'R5531:Spp1'
ID 433690
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
MMRRC Submission 043089-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5531 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 104582984-104588916 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 104588424 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 276 (D276E)
Ref Sequence ENSEMBL: ENSMUSP00000084043 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031243] [ENSMUST00000086833] [ENSMUST00000112746] [ENSMUST00000112747] [ENSMUST00000112748] [ENSMUST00000132457] [ENSMUST00000145084]
AlphaFold P10923
Predicted Effect probably benign
Transcript: ENSMUST00000031243
AA Change: D275E

PolyPhen 2 Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000031243
Gene: ENSMUSG00000029304
AA Change: D275E

DomainStartEndE-ValueType
signal peptide 1 16 N/A INTRINSIC
OSTEO 17 294 2.5e-157 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000086833
AA Change: D276E

PolyPhen 2 Score 0.115 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000084043
Gene: ENSMUSG00000029304
AA Change: D276E

DomainStartEndE-ValueType
signal peptide 1 16 N/A INTRINSIC
OSTEO 17 295 2.21e-158 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112746
SMART Domains Protein: ENSMUSP00000108366
Gene: ENSMUSG00000029304

DomainStartEndE-ValueType
signal peptide 1 16 N/A INTRINSIC
Pfam:Osteopontin 20 164 2.2e-67 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000112747
AA Change: D275E

PolyPhen 2 Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000108367
Gene: ENSMUSG00000029304
AA Change: D275E

DomainStartEndE-ValueType
signal peptide 1 16 N/A INTRINSIC
OSTEO 17 294 2.5e-157 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112748
AA Change: D275E

PolyPhen 2 Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000108368
Gene: ENSMUSG00000029304
AA Change: D275E

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
SMART Domains Protein: ENSMUSP00000117338
Gene: ENSMUSG00000029304

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 0.1635 question?
Coding Region Coverage
  • 1x: 98.6%
  • 3x: 97.5%
  • 10x: 95.6%
  • 20x: 92.2%
Validation Efficiency 97% (64/66)
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acacb T C 5: 114,342,767 (GRCm39) F878L possibly damaging Het
Acr T A 15: 89,458,146 (GRCm39) Y276N probably damaging Het
AI987944 A T 7: 41,023,814 (GRCm39) Y388* probably null Het
Ankrd29 G A 18: 12,412,835 (GRCm39) T114I probably damaging Het
Ap5z1 T C 5: 142,453,536 (GRCm39) M168T probably benign Het
Bard1 A C 1: 71,085,880 (GRCm39) C608W probably damaging Het
Brd10 A G 19: 29,731,072 (GRCm39) S647P possibly damaging Het
Clspn A G 4: 126,471,566 (GRCm39) R907G probably benign Het
Cubn C T 2: 13,355,743 (GRCm39) V1830I probably benign Het
Cwc22 T C 2: 77,754,913 (GRCm39) N221S probably damaging Het
Dact3 A G 7: 16,609,540 (GRCm39) E64G possibly damaging Het
Dhx40 T C 11: 86,680,330 (GRCm39) E381G possibly damaging Het
Dnah7a A G 1: 53,458,907 (GRCm39) S3744P possibly damaging Het
Epha4 A G 1: 77,351,513 (GRCm39) V914A probably benign Het
Fbxw10 G A 11: 62,753,482 (GRCm39) C492Y probably damaging Het
G930045G22Rik C A 6: 50,824,756 (GRCm39) noncoding transcript Het
Gm21103 A T 14: 17,484,855 (GRCm39) I63K probably damaging Het
Gpr156 T C 16: 37,825,619 (GRCm39) V612A probably benign Het
Gucy2g A G 19: 55,229,572 (GRCm39) S33P probably benign Het
Hibch A G 1: 52,884,228 (GRCm39) probably benign Het
Hmcn1 A T 1: 150,619,539 (GRCm39) C1192S probably damaging Het
Hsd11b1 CGG CG 1: 192,922,557 (GRCm39) probably null Het
Ifi214 A G 1: 173,352,686 (GRCm39) Y248H probably damaging Het
Igf2bp2 T G 16: 21,907,835 (GRCm39) I89L probably damaging Het
Il2ra A T 2: 11,681,703 (GRCm39) T103S possibly damaging Het
Ino80 T A 2: 119,276,056 (GRCm39) M407L probably benign Het
Jade1 A C 3: 41,567,946 (GRCm39) K671N probably benign Het
Lca5 C T 9: 83,280,648 (GRCm39) S384N probably benign Het
Lce1l G T 3: 92,757,804 (GRCm39) P18H unknown Het
Lrrc8d T C 5: 105,945,536 (GRCm39) probably benign Het
Ly75 T C 2: 60,195,489 (GRCm39) N223S probably damaging Het
Mcm3 A T 1: 20,873,768 (GRCm39) F784Y possibly damaging Het
Ncf4 T G 15: 78,144,988 (GRCm39) probably benign Het
Ncoa1 T A 12: 4,303,746 (GRCm39) M1362L probably benign Het
Or1e16 T C 11: 73,286,003 (GRCm39) T282A probably benign Het
Or5p5 A G 7: 107,414,451 (GRCm39) Y220C probably benign Het
Or6c8b G C 10: 128,882,433 (GRCm39) F166L probably damaging Het
Prkg2 T C 5: 99,115,593 (GRCm39) R543G probably damaging Het
Ptprd A C 4: 75,977,904 (GRCm39) probably null Het
Scap A G 9: 110,210,497 (GRCm39) S969G possibly damaging Het
Sgk2 T C 2: 162,836,624 (GRCm39) F60S probably benign Het
Sgpp1 G T 12: 75,781,981 (GRCm39) Y119* probably null Het
Siglech A T 7: 55,418,413 (GRCm39) K31* probably null Het
Slc40a1 A G 1: 45,951,498 (GRCm39) Y220H probably damaging Het
Smurf2 G A 11: 106,743,389 (GRCm39) T219M possibly damaging Het
Speer4f2 A G 5: 17,581,526 (GRCm39) K156R possibly damaging Het
Stk32b T C 5: 37,617,078 (GRCm39) probably null Het
Stxbp5 G A 10: 9,638,668 (GRCm39) Q1044* probably null Het
Sv2c T A 13: 96,097,886 (GRCm39) T696S probably damaging Het
Tubgcp2 A C 7: 139,584,937 (GRCm39) probably null Het
Ubap1l C T 9: 65,278,973 (GRCm39) P91S probably damaging Het
Vmn2r76 A T 7: 85,874,657 (GRCm39) D773E probably damaging Het
Xirp2 C G 2: 67,345,646 (GRCm39) S2629C probably benign Het
Zbtb20 C A 16: 43,431,230 (GRCm39) C580* probably null Het
Zfp957 T A 14: 79,450,622 (GRCm39) Q392H unknown Het
Zfyve19 C T 2: 119,042,427 (GRCm39) T178M probably damaging Het
Zswim6 T C 13: 107,906,128 (GRCm39) noncoding transcript 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
R6198:Spp1 UTSW 5 104,587,374 (GRCm39) splice site probably null
R6291:Spp1 UTSW 5 104,587,242 (GRCm39) missense possibly damaging 0.89
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'- TCAAGTCAGCTGGATGAACC -3'
(R):5'- ACAACGGTGTTTGCATGAAAC -3'

Sequencing Primer
(F):5'- TGGATGAACCAAGTCTGGAAACAC -3'
(R):5'- GTTTGCATGAAACAACAGACTAAGC -3'
Posted On 2016-10-06