Incidental Mutation 'R7807:Sdcbp'
ID 600847
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 045862-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.166) question?
Stock # R7807 (G1)
Quality Score 225.009
Status Validated
Chromosome 4
Chromosomal Location 6365654-6396122 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 6393688 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 269 (T269A)
Ref Sequence ENSEMBL: ENSMUSP00000029912 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029910] [ENSMUST00000029912] [ENSMUST00000103008] [ENSMUST00000108374] [ENSMUST00000153861] [ENSMUST00000175769]
AlphaFold O08992
Predicted Effect probably benign
Transcript: ENSMUST00000029910
SMART Domains Protein: ENSMUSP00000029910
Gene: ENSMUSG00000028245

DomainStartEndE-ValueType
low complexity region 23 28 N/A INTRINSIC
GRAM 176 247 2.22e-11 SMART
Beach 302 575 6.28e-190 SMART
WD40 622 661 4.55e-3 SMART
WD40 664 703 2.97e0 SMART
WD40 706 743 1.47e-6 SMART
WD40 756 794 1.7e-2 SMART
WD40 797 836 1.02e-5 SMART
WD40 839 875 9.55e0 SMART
WD40 878 917 1.5e-3 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000029912
AA Change: T269A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000029912
Gene: ENSMUSG00000028249
AA Change: T269A

DomainStartEndE-ValueType
PDZ 124 195 7.09e-15 SMART
PDZ 208 274 6.04e-9 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000103008
AA Change: T268A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000100073
Gene: ENSMUSG00000028249
AA Change: T268A

DomainStartEndE-ValueType
PDZ 123 194 7.09e-15 SMART
PDZ 207 273 6.04e-9 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000108374
SMART Domains Protein: ENSMUSP00000104011
Gene: ENSMUSG00000028249

DomainStartEndE-ValueType
PDZ 124 195 2.84e-14 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000153861
SMART Domains Protein: ENSMUSP00000119838
Gene: ENSMUSG00000028249

DomainStartEndE-ValueType
PDZ 123 194 7.09e-15 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000175769
SMART Domains Protein: ENSMUSP00000135777
Gene: ENSMUSG00000028249

DomainStartEndE-ValueType
PDZ 124 195 7.09e-15 SMART
Blast:PDZ 208 249 1e-21 BLAST
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 100% (68/68)
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
AB124611 C A 9: 21,447,276 (GRCm39) T146K probably benign Het
Alms1 T A 6: 85,599,958 (GRCm39) S1595T possibly damaging Het
Ankrd44 A T 1: 54,831,635 (GRCm39) I56N probably damaging Het
Anln C A 9: 22,272,176 (GRCm39) V648F probably damaging Het
Arhgap29 A G 3: 121,807,981 (GRCm39) D1053G probably benign Het
Baalc T C 15: 38,797,412 (GRCm39) S68P probably benign Het
Begain T C 12: 109,004,856 (GRCm39) D52G probably damaging Het
Blmh A G 11: 76,837,040 (GRCm39) I41V probably benign Het
Bpifc T A 10: 85,812,114 (GRCm39) I365F possibly damaging Het
C2 G T 17: 35,095,347 (GRCm39) S199R possibly damaging Het
Ccbe1 T A 18: 66,199,828 (GRCm39) H298L probably damaging Het
Ccdc112 T A 18: 46,423,826 (GRCm39) K304I probably damaging Het
Ccdc15 T C 9: 37,226,678 (GRCm39) E432G probably benign Het
Cdh13 T A 8: 119,010,594 (GRCm39) M1K probably null Het
Cipc T C 12: 87,008,899 (GRCm39) S253P possibly damaging Het
Clcn1 A G 6: 42,287,282 (GRCm39) probably null Het
Clock A T 5: 76,390,982 (GRCm39) N273K probably benign Het
Cyp19a1 T C 9: 54,074,126 (GRCm39) D476G probably benign Het
Dnaaf9 T C 2: 130,552,785 (GRCm39) K1092E probably damaging Het
Dnah7b A G 1: 46,253,527 (GRCm39) I1811V probably benign Het
Fat1 C A 8: 45,495,010 (GRCm39) T4091K probably damaging Het
Gm10340 T A 14: 14,826,724 (GRCm39) N64K probably damaging Het
Hectd1 G A 12: 51,792,171 (GRCm39) R2523C probably damaging Het
Hgf A G 5: 16,782,009 (GRCm39) H244R probably damaging Het
Hgs G T 11: 120,370,760 (GRCm39) A567S probably damaging Het
Igdcc4 T C 9: 65,041,077 (GRCm39) V1036A probably benign Het
Keg1 G A 19: 12,691,998 (GRCm39) probably null Het
Klhl8 A T 5: 104,023,932 (GRCm39) L156Q probably damaging Het
Lmln T C 16: 32,927,501 (GRCm39) Y521H probably benign Het
Lrrc7 A G 3: 157,866,124 (GRCm39) S1206P probably damaging Het
Mad1l1 T A 5: 140,074,541 (GRCm39) I550F probably benign Het
Marf1 C T 16: 13,971,753 (GRCm39) W28* probably null Het
Mfsd11 T G 11: 116,754,733 (GRCm39) S215A probably benign Het
Mpped2 C A 2: 106,575,085 (GRCm39) H57N possibly damaging Het
Mslnl A G 17: 25,965,751 (GRCm39) M542V probably benign Het
Myh6 G T 14: 55,179,897 (GRCm39) H1903Q probably damaging Het
Neo1 T C 9: 58,897,777 (GRCm39) T60A probably benign Het
Npm2 T A 14: 70,889,947 (GRCm39) probably null Het
Or5b123 C A 19: 13,597,285 (GRCm39) T210K probably damaging Het
Or5d20-ps1 T C 2: 87,931,909 (GRCm39) S141G probably benign Het
Or7a39 T A 10: 78,715,043 (GRCm39) S12R probably benign Het
Pax9 A T 12: 56,743,850 (GRCm39) I166F possibly damaging Het
Pcsk9 A G 4: 106,321,092 (GRCm39) S6P possibly damaging Het
Pikfyve A G 1: 65,309,101 (GRCm39) Y1893C probably damaging Het
Pirb T C 7: 3,722,864 (GRCm39) T43A possibly damaging Het
Pou3f1 A G 4: 124,552,074 (GRCm39) D192G possibly damaging Het
Pus3 C G 9: 35,478,021 (GRCm39) R418G probably damaging Het
Rexo1 C T 10: 80,385,970 (GRCm39) V363I probably benign Het
Sele T C 1: 163,881,462 (GRCm39) V523A probably benign Het
Serpinb8 T A 1: 107,532,457 (GRCm39) M183K probably damaging Het
Sh2d4a T G 8: 68,735,033 (GRCm39) S51A probably benign Het
Siglec15 A G 18: 78,090,696 (GRCm39) S201P probably damaging Het
Slc10a5 C T 3: 10,400,529 (GRCm39) V44I probably benign Het
Slc16a13 A G 11: 70,111,388 (GRCm39) V39A probably damaging Het
Slc25a13 G A 6: 6,117,164 (GRCm39) R184W probably damaging Het
Slc35f5 T A 1: 125,512,278 (GRCm39) D359E probably damaging Het
Slc3a1 A G 17: 85,371,371 (GRCm39) E641G probably benign Het
Slf1 T C 13: 77,194,823 (GRCm39) D834G probably damaging Het
Spata31f1e A C 4: 42,793,885 (GRCm39) H82Q probably benign Het
Stim1 T C 7: 102,076,348 (GRCm39) I433T probably damaging Het
Stra6 T A 9: 58,057,444 (GRCm39) I418K probably damaging Het
Tanc2 A G 11: 105,758,480 (GRCm39) N747S probably benign Het
Tet2 T C 3: 133,192,302 (GRCm39) T711A possibly damaging Het
Trpm6 T C 19: 18,807,220 (GRCm39) I988T probably benign Het
Ttc41 T A 10: 86,612,495 (GRCm39) I1256N probably benign Het
Uba2 T C 7: 33,862,638 (GRCm39) D100G possibly damaging Het
Vmn1r43 A G 6: 89,847,219 (GRCm39) I89T probably benign Het
Vmn2r58 T A 7: 41,521,910 (GRCm39) Y62F probably benign Het
Ylpm1 C T 12: 85,060,855 (GRCm39) Q428* probably null Het
Zcrb1 T C 15: 93,289,002 (GRCm39) D88G probably damaging Het
Zmym1 A C 4: 126,941,667 (GRCm39) I907S 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
R1353:Sdcbp UTSW 4 6,381,057 (GRCm39) missense probably damaging 0.99
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
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'- AGGACTTTTGGTCAGTACCTTC -3'
(R):5'- ACAGGCAAGCAATCCGTCAG -3'

Sequencing Primer
(F):5'- GTCAGTACCTTCAACTTTGTTACTAG -3'
(R):5'- GTCAGGAACCACCATGACTAGATTTC -3'
Posted On 2019-11-26