Incidental Mutation 'R1353:Sdcbp'
ID 157082
Institutional Source Beutler Lab
Gene Symbol Sdcbp
Ensembl Gene ENSMUSG00000028249
Gene Name syndecan binding protein
Synonyms syntenin-1, Sycl, MDA-9, syndecan interacting protein, syntenin
MMRRC Submission 039418-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.143) question?
Stock # R1353 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 6365654-6396122 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 6381057 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Methionine at position 67 (I67M)
Ref Sequence ENSEMBL: ENSMUSP00000122411 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029912] [ENSMUST00000103008] [ENSMUST00000108374] [ENSMUST00000140830] [ENSMUST00000153861] [ENSMUST00000175769]
AlphaFold O08992
Predicted Effect probably benign
Transcript: ENSMUST00000029912
AA Change: I67M

PolyPhen 2 Score 0.018 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000029912
Gene: ENSMUSG00000028249
AA Change: I67M

DomainStartEndE-ValueType
PDZ 124 195 7.09e-15 SMART
PDZ 208 274 6.04e-9 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000103008
AA Change: I67M

PolyPhen 2 Score 0.018 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000100073
Gene: ENSMUSG00000028249
AA Change: I67M

DomainStartEndE-ValueType
PDZ 123 194 7.09e-15 SMART
PDZ 207 273 6.04e-9 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000108371
Predicted Effect probably benign
Transcript: ENSMUST00000108374
AA Change: I67M

PolyPhen 2 Score 0.046 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000104011
Gene: ENSMUSG00000028249
AA Change: I67M

DomainStartEndE-ValueType
PDZ 124 195 2.84e-14 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000140830
AA Change: I67M

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000122411
Gene: ENSMUSG00000028249
AA Change: I67M

DomainStartEndE-ValueType
Blast:PDZ 56 91 1e-10 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000153861
AA Change: I67M

PolyPhen 2 Score 0.018 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000119838
Gene: ENSMUSG00000028249
AA Change: I67M

DomainStartEndE-ValueType
PDZ 123 194 7.09e-15 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000175769
AA Change: I67M

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000135777
Gene: ENSMUSG00000028249
AA Change: I67M

DomainStartEndE-ValueType
PDZ 124 195 7.09e-15 SMART
Blast:PDZ 208 249 1e-21 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000193139
Coding Region Coverage
  • 1x: 98.8%
  • 3x: 97.6%
  • 10x: 94.1%
  • 20x: 86.4%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene was initially identified as a molecule linking syndecan-mediated signaling to the cytoskeleton. The syntenin protein contains tandemly repeated PDZ domains that bind the cytoplasmic, C-terminal domains of a variety of transmembrane proteins. This protein may also affect cytoskeletal-membrane organization, cell adhesion, protein trafficking, and the activation of transcription factors. The protein is primarily localized to membrane-associated adherens junctions and focal adhesions but is also found at the endoplasmic reticulum and nucleus. Alternative splicing results in multiple transcript variants encoding different isoforms. Related pseudogenes have been identified on multiple chromosomes. [provided by RefSeq, Jan 2017]
PHENOTYPE: Mice heterozygous for a conditional allele activated in neurons exhibit abnormal dendrite morphology and reduced mEPSC frequency. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Astn2 T C 4: 66,184,572 (GRCm39) Q175R unknown Het
Capn9 A C 8: 125,332,305 (GRCm39) probably null Het
Car9 G T 4: 43,512,439 (GRCm39) probably null Het
Chd7 A G 4: 8,839,556 (GRCm39) N1364S probably damaging Het
Cmya5 A T 13: 93,178,033 (GRCm39) V3607E probably damaging Het
Crb2 T C 2: 37,677,293 (GRCm39) C262R probably damaging Het
Cyp2t4 A G 7: 26,856,055 (GRCm39) N204S probably benign Het
Epha1 T C 6: 42,338,771 (GRCm39) T676A probably damaging Het
Fancm G A 12: 65,134,944 (GRCm39) V246M probably damaging Het
Fcrl5 T C 3: 87,355,669 (GRCm39) S461P probably damaging Het
Gen1 A T 12: 11,293,220 (GRCm39) L394Q probably benign Het
Hsdl2 G T 4: 59,596,971 (GRCm39) probably null Het
Klri2 C T 6: 129,716,049 (GRCm39) G97S probably damaging Het
Lypla2 T C 4: 135,697,778 (GRCm39) I55V probably null Het
Malrd1 A G 2: 16,132,779 (GRCm39) D1900G unknown Het
Map1b A G 13: 99,563,834 (GRCm39) S2378P unknown Het
Marchf3 A T 18: 56,909,177 (GRCm39) probably null Het
Myom2 G T 8: 15,156,424 (GRCm39) W757L probably damaging Het
Nat10 T A 2: 103,584,418 (GRCm39) M120L possibly damaging Het
Ncam2 T G 16: 80,997,803 (GRCm39) M1R probably null Het
Ncoa4 G T 14: 31,892,815 (GRCm39) G33* probably null Het
Or1j1 C A 2: 36,702,926 (GRCm39) M59I possibly damaging Het
Or1x2 G A 11: 50,917,833 (GRCm39) M1I probably null Het
Or2a20 T A 6: 43,194,624 (GRCm39) M259K probably benign Het
Or4p21 T C 2: 88,276,895 (GRCm39) H129R probably benign Het
Or6c38 C T 10: 128,929,733 (GRCm39) V37I probably benign Het
Or8b41 A C 9: 38,055,024 (GRCm39) I198L probably benign Het
Osbpl8 A G 10: 111,112,340 (GRCm39) N485S probably damaging Het
Pkdrej A T 15: 85,703,119 (GRCm39) V939E probably damaging Het
Plaa T C 4: 94,459,926 (GRCm39) E607G possibly damaging Het
Rtel1 T A 2: 180,991,024 (GRCm39) C285S probably benign Het
Rtl1 A C 12: 109,558,633 (GRCm39) C1069G probably benign Het
Rtn4 C A 11: 29,657,595 (GRCm39) A583E probably damaging Het
Runx1 T A 16: 92,485,939 (GRCm39) R32* probably null Het
Slc22a12 G C 19: 6,587,812 (GRCm39) L259V possibly damaging Het
Sptlc2 A G 12: 87,388,520 (GRCm39) S321P probably damaging Het
Tmem30c C T 16: 57,098,028 (GRCm39) G131D probably damaging Het
Tnfaip2 A T 12: 111,411,403 (GRCm39) Q9L probably damaging Het
Ttn T C 2: 76,576,910 (GRCm39) Y24661C probably damaging Het
Vmn2r77 T G 7: 86,451,394 (GRCm39) F427V probably benign Het
Zcchc4 A G 5: 52,964,419 (GRCm39) I292V probably benign Het
Zfp354b A T 11: 50,814,240 (GRCm39) H228Q probably damaging Het
Zfp84 T A 7: 29,475,600 (GRCm39) N97K probably benign Het
Zfp976 T C 7: 42,265,442 (GRCm39) D49G probably damaging Het
Zgrf1 C T 3: 127,405,452 (GRCm39) T1550I probably damaging Het
Other mutations in Sdcbp
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00983:Sdcbp APN 4 6,392,953 (GRCm39) nonsense probably null
R0158:Sdcbp UTSW 4 6,379,042 (GRCm39) missense possibly damaging 0.81
R1066:Sdcbp UTSW 4 6,385,120 (GRCm39) missense probably damaging 0.98
R1115:Sdcbp UTSW 4 6,377,143 (GRCm39) critical splice donor site probably null
R2006:Sdcbp UTSW 4 6,386,536 (GRCm39) missense probably benign 0.23
R4879:Sdcbp UTSW 4 6,381,056 (GRCm39) missense possibly damaging 0.93
R4979:Sdcbp UTSW 4 6,378,980 (GRCm39) nonsense probably null
R5034:Sdcbp UTSW 4 6,393,118 (GRCm39) critical splice donor site probably null
R5072:Sdcbp UTSW 4 6,393,019 (GRCm39) missense probably benign 0.07
R6307:Sdcbp UTSW 4 6,385,059 (GRCm39) missense probably benign 0.06
R6329:Sdcbp UTSW 4 6,381,064 (GRCm39) missense probably benign 0.04
R7483:Sdcbp UTSW 4 6,393,089 (GRCm39) missense possibly damaging 0.95
R7665:Sdcbp UTSW 4 6,385,144 (GRCm39) missense probably benign 0.11
R7722:Sdcbp UTSW 4 6,385,063 (GRCm39) missense possibly damaging 0.93
R7729:Sdcbp UTSW 4 6,378,985 (GRCm39) missense probably benign 0.06
R7807:Sdcbp UTSW 4 6,393,688 (GRCm39) missense probably damaging 1.00
R8025:Sdcbp UTSW 4 6,393,022 (GRCm39) missense probably benign 0.09
R8941:Sdcbp UTSW 4 6,393,661 (GRCm39) missense probably benign 0.22
R9093:Sdcbp UTSW 4 6,386,709 (GRCm39) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- AAGACGGCTTCGGATGGGTTTCAG -3'
(R):5'- TGTCAGAATTCCAAACCTCAGTGCAG -3'

Sequencing Primer
(F):5'- GGGAAGATATCCTTCCATTTTATGC -3'
(R):5'- CACCAGTGGATGACAATGTTC -3'
Posted On 2014-02-11