Incidental Mutation 'R6307:Sdcbp'
ID 509453
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 044412-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.143) question?
Stock # R6307 (G1)
Quality Score 225.009
Status Not validated
Chromosome 4
Chromosomal Location 6365654-6396122 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 6385059 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Valine at position 93 (M93V)
Ref Sequence ENSEMBL: ENSMUSP00000104011 (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: M93V

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000029912
Gene: ENSMUSG00000028249
AA Change: M93V

DomainStartEndE-ValueType
PDZ 124 195 7.09e-15 SMART
PDZ 208 274 6.04e-9 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000103008
AA Change: M92V

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000100073
Gene: ENSMUSG00000028249
AA Change: M92V

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: M93V

PolyPhen 2 Score 0.063 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000104011
Gene: ENSMUSG00000028249
AA Change: M93V

DomainStartEndE-ValueType
PDZ 124 195 2.84e-14 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000140830
SMART Domains Protein: ENSMUSP00000122411
Gene: ENSMUSG00000028249

DomainStartEndE-ValueType
Blast:PDZ 56 91 1e-10 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000153861
AA Change: M92V

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000119838
Gene: ENSMUSG00000028249
AA Change: M92V

DomainStartEndE-ValueType
PDZ 123 194 7.09e-15 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000175769
AA Change: M93V

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000135777
Gene: ENSMUSG00000028249
AA Change: M93V

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: 99.3%
  • 20x: 97.6%
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca7 T C 10: 79,843,221 (GRCm39) L1232P probably damaging Het
Akap6 A T 12: 53,188,351 (GRCm39) I1922F possibly damaging Het
Ankdd1a C T 9: 65,415,343 (GRCm39) A227T possibly damaging Het
Arpc5 T C 1: 152,647,206 (GRCm39) V103A possibly damaging Het
Atp9a C A 2: 168,510,090 (GRCm39) V430F probably benign Het
Bod1 A G 11: 31,616,932 (GRCm39) S110P probably damaging Het
Cacna1c C A 6: 118,590,914 (GRCm39) V1453F probably damaging Het
Capn8 T A 1: 182,435,264 (GRCm39) M414K probably damaging Het
Cbl A T 9: 44,069,809 (GRCm39) probably null Het
Ccdc42 A T 11: 68,479,106 (GRCm39) Q98L probably damaging Het
Ccn3 T C 15: 54,611,421 (GRCm39) probably null Het
Cd200 C A 16: 45,217,545 (GRCm39) V49L probably benign Het
Celsr1 A G 15: 85,812,531 (GRCm39) S2060P probably benign Het
Ces1g A T 8: 94,057,820 (GRCm39) H160Q possibly damaging Het
Chrnb2 G T 3: 89,668,831 (GRCm39) H161Q probably damaging Het
Ctns G A 11: 73,082,559 (GRCm39) T57I probably benign Het
Cyp3a25 A T 5: 145,931,766 (GRCm39) M114K possibly damaging Het
D630003M21Rik A G 2: 158,057,871 (GRCm39) F536L probably benign Het
Dcc C T 18: 71,943,826 (GRCm39) R275Q probably benign Het
Dmxl2 A T 9: 54,289,990 (GRCm39) H2508Q possibly damaging Het
Elf5 C A 2: 103,269,757 (GRCm39) Q113K probably damaging Het
Fam83a T G 15: 57,849,507 (GRCm39) V17G possibly damaging Het
Farsa T C 8: 85,587,674 (GRCm39) probably null Het
Fat2 G C 11: 55,172,106 (GRCm39) T2869S possibly damaging Het
Fgg A T 3: 82,920,283 (GRCm39) Q354L probably damaging Het
Folh1 T C 7: 86,372,517 (GRCm39) D679G probably damaging Het
Gbp4 T A 5: 105,270,975 (GRCm39) R83* probably null Het
Gm17482 T A 6: 115,204,311 (GRCm39) probably benign Het
Hmgxb4 T A 8: 75,749,927 (GRCm39) V481D possibly damaging Het
Ifi207 A C 1: 173,552,619 (GRCm39) Y926D probably damaging Het
Ikzf5 T A 7: 130,993,377 (GRCm39) N264Y probably damaging Het
Kat6a T A 8: 23,430,384 (GRCm39) M1913K unknown Het
Krt33b A T 11: 99,915,694 (GRCm39) C351S probably benign Het
Lrp1 T C 10: 127,427,944 (GRCm39) D543G probably damaging Het
Lrrfip2 C T 9: 111,053,021 (GRCm39) R339W probably damaging Het
Mapk3 T G 7: 126,363,454 (GRCm39) M276R probably benign Het
Mgst1 T C 6: 138,127,827 (GRCm39) V137A probably benign Het
Muc16 T C 9: 18,558,884 (GRCm39) T2470A unknown Het
Muc4 C T 16: 32,575,237 (GRCm39) S1274F possibly damaging Het
Myo5c A C 9: 75,180,198 (GRCm39) K713T possibly damaging Het
Myzap T C 9: 71,466,146 (GRCm39) D170G possibly damaging Het
Naa50 T C 16: 43,979,831 (GRCm39) V113A probably damaging Het
Neu3 T C 7: 99,462,929 (GRCm39) T265A probably benign Het
Nin T C 12: 70,061,631 (GRCm39) T2078A possibly damaging Het
Nomo1 G A 7: 45,683,260 (GRCm39) probably benign Het
Nprl3 A G 11: 32,189,828 (GRCm39) L273P probably damaging Het
Oaf T A 9: 43,136,216 (GRCm39) H120L possibly damaging Het
Or10s1 T C 9: 39,985,824 (GRCm39) S78P probably damaging Het
Or13p4 C T 4: 118,547,145 (GRCm39) R168H probably benign Het
Or8b36 ATTGCTGTTT ATTGCTGTTTGCTGTTT 9: 37,937,836 (GRCm39) probably null Het
Or8k21 T C 2: 86,145,468 (GRCm39) H54R probably benign Het
Pcdhga3 T A 18: 37,809,674 (GRCm39) probably benign Het
Polq G A 16: 36,837,718 (GRCm39) probably null Het
Prdm8 C T 5: 98,333,162 (GRCm39) P243L possibly damaging Het
Prim2 T C 1: 33,701,373 (GRCm39) D138G probably benign Het
Prl2c5 A G 13: 13,365,175 (GRCm39) E107G probably benign Het
Prr14l T A 5: 32,984,869 (GRCm39) H1542L probably damaging Het
Rab26 T C 17: 24,749,072 (GRCm39) E203G probably damaging Het
Rtkn2 A T 10: 67,871,662 (GRCm39) H350L possibly damaging Het
Scara3 T C 14: 66,175,710 (GRCm39) D19G probably benign Het
Scn3a A G 2: 65,302,685 (GRCm39) S1254P probably damaging Het
Sema6a C A 18: 47,382,231 (GRCm39) R772L probably damaging Het
Slc5a7 T C 17: 54,584,006 (GRCm39) K428R probably benign Het
Sptbn2 G A 19: 4,774,674 (GRCm39) G109D probably damaging Het
Tmppe T C 9: 114,233,812 (GRCm39) L37P probably benign Het
Tuba1a T C 15: 98,849,410 (GRCm39) T56A probably benign Het
Tut4 T A 4: 108,412,817 (GRCm39) I1506N probably damaging Het
Vmn2r111 A G 17: 22,792,070 (GRCm39) I62T probably benign Het
Vmn2r73 A G 7: 85,506,828 (GRCm39) I828T probably damaging Het
Vmn2r79 T A 7: 86,686,976 (GRCm39) W786R probably damaging Het
Zp1 G A 19: 10,894,084 (GRCm39) T405M probably null 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
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'- CCACTGGCATTATTGTGGGAATC -3'
(R):5'- CCACTGTAGATGGGTTATTACAGC -3'

Sequencing Primer
(F):5'- TGTGGGAATCAGACTTCACTAG -3'
(R):5'- AGATGGGTTATTACAGCTAGCC -3'
Posted On 2018-04-02