Incidental Mutation 'R4879:Sdcbp'
ID 375111
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 042488-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.143) question?
Stock # R4879 (G1)
Quality Score 225
Status Validated
Chromosome 4
Chromosomal Location 6365654-6396122 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 6381056 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 67 (I67T)
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: I67T

PolyPhen 2 Score 0.079 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000029912
Gene: ENSMUSG00000028249
AA Change: I67T

DomainStartEndE-ValueType
PDZ 124 195 7.09e-15 SMART
PDZ 208 274 6.04e-9 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000103008
AA Change: I67T

PolyPhen 2 Score 0.079 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000100073
Gene: ENSMUSG00000028249
AA Change: I67T

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: I67T

PolyPhen 2 Score 0.180 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000104011
Gene: ENSMUSG00000028249
AA Change: I67T

DomainStartEndE-ValueType
PDZ 124 195 2.84e-14 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000140830
AA Change: I67T

PolyPhen 2 Score 0.933 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000122411
Gene: ENSMUSG00000028249
AA Change: I67T

DomainStartEndE-ValueType
Blast:PDZ 56 91 1e-10 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000153861
AA Change: I67T

PolyPhen 2 Score 0.079 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000119838
Gene: ENSMUSG00000028249
AA Change: I67T

DomainStartEndE-ValueType
PDZ 123 194 7.09e-15 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000175769
AA Change: I67T

PolyPhen 2 Score 0.048 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000135777
Gene: ENSMUSG00000028249
AA Change: I67T

DomainStartEndE-ValueType
PDZ 124 195 7.09e-15 SMART
Blast:PDZ 208 249 1e-21 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000193139
Meta Mutation Damage Score 0.2094 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.4%
Validation Efficiency 97% (86/89)
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: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca6 T A 11: 110,110,526 (GRCm39) Y541F probably damaging Het
Acot12 T A 13: 91,911,083 (GRCm39) V136E probably benign Het
Aftph A G 11: 20,648,311 (GRCm39) probably null Het
Ambra1 C T 2: 91,603,039 (GRCm39) probably benign Het
Anks6 C T 4: 47,030,795 (GRCm39) G601S probably damaging Het
Ano9 T C 7: 140,690,415 (GRCm39) D73G probably benign Het
Asap3 G A 4: 135,969,975 (GRCm39) D778N probably benign Het
Atp8a2 G T 14: 60,245,918 (GRCm39) Y591* probably null Het
Blk T C 14: 63,613,414 (GRCm39) T365A probably benign Het
C4b G T 17: 34,962,621 (GRCm39) S27Y probably damaging Het
C6 G T 15: 4,833,129 (GRCm39) probably null Het
Ccdc33 T A 9: 57,974,839 (GRCm39) I345F possibly damaging Het
Cetn3 T A 13: 81,940,268 (GRCm39) probably benign Het
Cntn3 T A 6: 102,244,389 (GRCm39) I387L possibly damaging Het
Cog8 A G 8: 107,782,984 (GRCm39) C102R probably damaging Het
Cspg4b T C 13: 113,456,321 (GRCm39) I789T probably benign Het
Cyp2c55 CA C 19: 39,030,522 (GRCm39) probably null Het
Defa40 T A 8: 21,740,380 (GRCm39) L62Q probably damaging Het
Dmxl1 C T 18: 50,022,534 (GRCm39) A1624V probably damaging Het
Dnah1 T G 14: 31,022,705 (GRCm39) E1144A possibly damaging Het
Dnah12 T A 14: 26,439,201 (GRCm39) probably null Het
Dnah2 G A 11: 69,367,517 (GRCm39) T1794I probably damaging Het
Entrep1 T C 19: 23,953,019 (GRCm39) probably null Het
Erbin A T 13: 103,971,282 (GRCm39) M778K probably benign Het
Fbxw10 G T 11: 62,738,573 (GRCm39) A156S probably damaging Het
Flnc T A 6: 29,460,805 (GRCm39) F2632Y probably damaging Het
Frmd4a A G 2: 4,534,628 (GRCm39) K160E probably damaging Het
Glipr1l2 A G 10: 111,943,029 (GRCm39) K295E probably benign Het
Herc1 T A 9: 66,370,119 (GRCm39) C465* probably null Het
Hoxb4 A G 11: 96,211,014 (GRCm39) I205V probably damaging Het
Ikbke GCC G 1: 131,203,004 (GRCm39) probably null Het
Il36a A G 2: 24,106,032 (GRCm39) N29S probably benign Het
Ilk A G 7: 105,391,011 (GRCm39) S292G probably benign Het
Itgb5 G C 16: 33,696,348 (GRCm39) G180R probably damaging Het
Josd1-ps T C 7: 27,648,768 (GRCm39) noncoding transcript Het
Kcnip4 T C 5: 48,567,207 (GRCm39) D120G possibly damaging Het
Kin A G 2: 10,085,455 (GRCm39) D5G probably benign Het
Lrrtm2 C A 18: 35,346,372 (GRCm39) G310V probably damaging Het
Med1 T C 11: 98,046,186 (GRCm39) probably benign Het
Mepce C A 5: 137,783,544 (GRCm39) probably benign Het
Nckipsd T A 9: 108,691,114 (GRCm39) probably benign Het
Notch3 T A 17: 32,366,937 (GRCm39) Q866L probably benign Het
Or52b4 A T 7: 102,183,962 (GRCm39) T3S probably benign Het
Or5l14 A T 2: 87,793,040 (GRCm39) H65Q possibly damaging Het
Or8k20 A T 2: 86,106,107 (GRCm39) C241* probably null Het
Orai1 T C 5: 123,149,894 (GRCm39) probably benign Het
Pate12 G A 9: 36,344,089 (GRCm39) C24Y probably damaging Het
Pcdhb8 A T 18: 37,489,219 (GRCm39) E299V probably damaging Het
Pcnx4 G A 12: 72,613,959 (GRCm39) D635N probably damaging Het
Pex5 T C 6: 124,375,322 (GRCm39) I567V probably benign Het
Ppfibp2 T C 7: 107,328,390 (GRCm39) S485P probably benign Het
Sbno1 T C 5: 124,542,087 (GRCm39) Y356C probably damaging Het
Slc5a7 A G 17: 54,583,679 (GRCm39) I537T probably benign Het
Slc66a1 A T 4: 139,029,095 (GRCm39) probably null Het
Smad4 A G 18: 73,774,974 (GRCm39) C442R probably damaging Het
Smpd5 A G 15: 76,179,070 (GRCm39) H146R possibly damaging Het
Snai2 A G 16: 14,524,605 (GRCm39) Y37C probably benign Het
Snapc4 C T 2: 26,256,004 (GRCm39) S840N possibly damaging Het
Stpg2 T C 3: 138,921,134 (GRCm39) I113T probably benign Het
Tbc1d32 T C 10: 55,925,125 (GRCm39) probably null Het
Tfg A T 16: 56,521,520 (GRCm39) S39R probably damaging Het
Thsd7b T A 1: 130,116,236 (GRCm39) S1330T possibly damaging Het
Tnfaip3 T C 10: 18,881,321 (GRCm39) T322A probably benign Het
Tpra1 A G 6: 88,888,691 (GRCm39) Y291C probably damaging Het
Trcg1 A G 9: 57,154,003 (GRCm39) D658G probably damaging Het
Trip4 C T 9: 65,782,304 (GRCm39) V143I probably benign Het
Trp53bp1 T C 2: 121,033,084 (GRCm39) K1691E probably damaging Het
Ttc8 T A 12: 98,908,562 (GRCm39) M77K possibly damaging Het
Tubb2a A T 13: 34,258,572 (GRCm39) M406K probably benign Het
Txnrd1 T A 10: 82,717,751 (GRCm39) probably null Het
Ugt2a3 C A 5: 87,479,144 (GRCm39) R268L probably benign Het
Usp34 T G 11: 23,323,410 (GRCm39) M982R possibly damaging Het
Vmn2r43 T A 7: 8,258,102 (GRCm39) K370N probably benign Het
Vopp1 A T 6: 57,739,355 (GRCm39) probably benign Het
Vps11 A C 9: 44,264,597 (GRCm39) C660G probably benign Het
Wnk1 T C 6: 119,926,338 (GRCm39) H1137R probably damaging Het
Wtap A G 17: 13,188,322 (GRCm39) Y193H probably damaging Het
Zfp462 T A 4: 55,009,444 (GRCm39) V470D probably benign 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
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'- TCATTCTAATTGTGTCAGAGATGGG -3'
(R):5'- ACCAGTGGATGACAATGTTCAG -3'

Sequencing Primer
(F):5'- TTGTGTCAGAGATGGGAAGATATC -3'
(R):5'- CAGTGGATGACAATGTTCAGAAATAC -3'
Posted On 2016-03-17