O00560
EV
Gene name |
SDCBP (MDA9, SYCL) |
Protein name |
Syntenin-1 |
Names |
Melanoma differentiation-associated protein 9, MDA-9, Pro-TGF-alpha cytoplasmic domain-interacting protein 18, TACIP18, Scaffold protein Pbp1, Syndecan-binding protein 1 |
Species |
Homo sapiens (Human) |
KEGG Pathway |
hsa:6386 |
EC number |
|
Protein Class |
SYNTENIN RELATED (PTHR12345) |
Descriptions
SDCBP (Syntenin-1) is a multifunctional adapter protein that regulates TGFB1-mediated SMAD2/3 activation, TGFB1-induced epithelial-to-mesenchymal transition (EMT) and cell migration in various cell types. The 100 amino acid long N-terminal domain (NTD) works as an autoinhibitory region, which restricts the membrane targeting by flanking to PDZ tandem. The deletion of the first 102 amino acids confers a strong plasma membrane enrichment. The region between amino acids 56 and 59 is highly conserved among systenin-1 proteins. In particular, phosphorylation of Tyr56 may regulate the plasma membrane binding of syntenin-1 by modulating the interaction strength between the internal peptide stretch and PDZ1-PDZ2.
Autoinhibitory domains (AIDs)
Target domain |
103-275 (PDZ tandem) |
Relief mechanism |
PTM |
Assay |
Deletion assay, Mutagenesis experiment |
Accessory elements
No accessory elements
Autoinhibited structure
Activated structure
56 structures for O00560
| Entry ID | Method | Resolution | Chain | Position | Source |
|---|---|---|---|---|---|
| 1N99 | X-ray | 194 A | A/B | 113-273 | PDB |
| 1NTE | X-ray | 124 A | A | 197-273 | PDB |
| 1OBX | X-ray | 135 A | A | 197-270 | PDB |
| 1OBY | X-ray | 185 A | A/B | 197-270 | PDB |
| 1OBZ | X-ray | 169 A | A/B | 113-273 | PDB |
| 1R6J | X-ray | 073 A | A | 197-273 | PDB |
| 1V1T | X-ray | 180 A | A/B | 113-273 | PDB |
| 1W9E | X-ray | 156 A | A/B | 113-273 | PDB |
| 1W9O | X-ray | 225 A | A/B | 113-273 | PDB |
| 1W9Q | X-ray | 170 A | A/B | 113-273 | PDB |
| 1YBO | X-ray | 230 A | A/B | 113-273 | PDB |
| 4Z33 | X-ray | 245 A | A/B | 111-275 | PDB |
| 6R9H | X-ray | 200 A | A/B/C/D | 113-273 | PDB |
| 6RLC | X-ray | 220 A | A/B/C/D | 113-273 | PDB |
| 7FSG | X-ray | 202 A | A/B/C/D | 106-298 | PDB |
| 7FSH | X-ray | 211 A | A/B/C/D | 106-298 | PDB |
| 7FSI | X-ray | 231 A | A/B/C/D | 106-298 | PDB |
| 7FSJ | X-ray | 197 A | A/B/C/D | 106-298 | PDB |
| 7FSK | X-ray | 240 A | A/B/C/D | 106-298 | PDB |
| 7FSL | X-ray | 238 A | A/B/C/D | 106-298 | PDB |
| 7FSM | X-ray | 210 A | A/B/C/D | 106-298 | PDB |
| 7FSN | X-ray | 240 A | A/B/C/D | 106-298 | PDB |
| 7FSO | X-ray | 190 A | A/B/C/D | 106-298 | PDB |
| 7FSP | X-ray | 186 A | A/B/C/D | 106-298 | PDB |
| 7FSQ | X-ray | 207 A | A/B/C/D | 106-298 | PDB |
| 7FSR | X-ray | 229 A | A/B/C/D | 106-298 | PDB |
| 7FSS | X-ray | 211 A | A/B/C/D | 106-298 | PDB |
| 7FST | X-ray | 198 A | A/B/C/D | 106-298 | PDB |
| 7FSU | X-ray | 197 A | A/B/C/D | 106-298 | PDB |
| 7FSV | X-ray | 225 A | A/B/C/D | 106-298 | PDB |
| 7FSW | X-ray | 214 A | A/B/C/D | 106-298 | PDB |
| 7FSX | X-ray | 191 A | A/B/C/D | 106-298 | PDB |
| 7FSY | X-ray | 280 A | A/B/C/D | 106-298 | PDB |
| 7FSZ | X-ray | 205 A | A/B/C/D | 106-298 | PDB |
| 7FT0 | X-ray | 245 A | A/B/C/D | 106-298 | PDB |
| 7FT1 | X-ray | 211 A | A/B/C/D | 106-298 | PDB |
| 7FT2 | X-ray | 204 A | A/B/C/D | 106-298 | PDB |
| 7FT3 | X-ray | 205 A | A/B/C/D | 106-298 | PDB |
| 7FT4 | X-ray | 217 A | A/B/C/D | 106-298 | PDB |
| 7FT5 | X-ray | 177 A | A/B/C/D | 106-298 | PDB |
| 7FT6 | X-ray | 185 A | A/B/C/D | 106-298 | PDB |
| 7FT7 | X-ray | 178 A | A/B/C/D | 106-298 | PDB |
| 7FT8 | X-ray | 240 A | A/B/C/D | 106-298 | PDB |
| 7FT9 | X-ray | 177 A | A/B/C/D | 106-298 | PDB |
| 7FTA | X-ray | 203 A | A/B/C/D | 106-298 | PDB |
| 7FTB | X-ray | 222 A | A/B/C/D | 106-298 | PDB |
| 7FTC | X-ray | 187 A | A/B/C/D | 106-298 | PDB |
| 7FTD | X-ray | 180 A | A/B/C/D | 106-298 | PDB |
| 8AAI | X-ray | 276 A | A/B/C/D | 113-273 | PDB |
| 8AAK | X-ray | 255 A | A/B | 113-273 | PDB |
| 8AAO | X-ray | 247 A | A/B | 113-273 | PDB |
| 8AAP | X-ray | 217 A | A/B | 113-273 | PDB |
| 8BLU | X-ray | 150 A | A/B/C/D | 106-298 | PDB |
| 8BLV | X-ray | 150 A | A/B | 106-298 | PDB |
| 8HCK | X-ray | 200 A | A | 113-191 | PDB |
| AF-O00560-F1 | Predicted | AlphaFoldDB |
201 variants for O00560
| Variant ID(s) | Position | Change | Description | Diseaes Association | Provenance |
|---|---|---|---|---|---|
|
rs771184646 CA4756938 |
8 | E>K | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA4756939 rs200120124 |
9 | D>E | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA4756940 rs759644725 |
10 | L>S | No |
ClinGen ExAC gnomAD |
|
|
CA4756942 rs775515488 |
12 | V>I | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA177303227 rs199904016 |
14 | K>T | No |
ClinGen Ensembl |
|
|
rs764365452 CA371292674 |
15 | V>I | No |
ClinGen ExAC TOPMed gnomAD |
|
|
rs764365452 CA4756944 |
15 | V>L | No |
ClinGen ExAC TOPMed gnomAD |
|
|
rs750874251 CA4756969 |
19 | Q>E | No |
ClinGen ExAC gnomAD |
|
|
CA4756972 rs751271561 |
25 | N>T | No |
ClinGen ExAC gnomAD |
|
|
rs201721790 CA4756973 |
26 | P>A | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA371292778 rs1305591455 |
29 | P>S | No |
ClinGen TOPMed gnomAD |
|
|
rs1305591455 CA371292776 |
29 | P>T | No |
ClinGen TOPMed gnomAD |
|
|
rs375215978 CA371292782 |
30 | A>P | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
CA4756974 rs375215978 |
30 | A>S | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
rs919727229 CA177305830 |
32 | L>F | No |
ClinGen Ensembl |
|
|
CA177305831 rs868513290 |
33 | S>* | No |
ClinGen Ensembl |
|
|
rs1267251896 CA371292800 |
33 | S>T | No |
ClinGen TOPMed |
|
|
CA371292824 rs1226700533 |
36 | S>F | No |
ClinGen gnomAD |
|
|
CA371292833 rs1308338532 |
38 | P>S | No |
ClinGen gnomAD |
|
|
CA371292841 rs1294225272 |
39 | I>T | No |
ClinGen TOPMed gnomAD |
|
|
rs1242995193 CA371292838 |
39 | I>V | No |
ClinGen gnomAD |
|
|
CA4756976 rs755914055 |
40 | P>L | No |
ClinGen ExAC gnomAD |
|
|
CA4756977 rs777855850 |
41 | H>Y | No |
ClinGen ExAC gnomAD |
|
|
rs530791906 CA4756980 |
42 | D>G | No |
ClinGen 1000Genomes ExAC gnomAD |
|
|
CA4756979 rs772253346 |
42 | D>N | No |
ClinGen ExAC gnomAD |
|
|
rs768796354 CA4756982 |
43 | G>R | No |
ClinGen ExAC gnomAD |
|
|
rs1468744917 CA371292887 |
44 | N>K | No |
ClinGen TOPMed gnomAD |
|
|
rs186938508 CA177306318 |
46 | Y>C | No |
ClinGen 1000Genomes |
|
|
CA371293102 rs1407384132 |
53 | L>I | No |
ClinGen TOPMed gnomAD |
|
|
CA371293103 rs1407384132 |
53 | L>V | No |
ClinGen TOPMed gnomAD |
|
|
rs770189965 CA371293126 |
54 | S>F | No |
ClinGen ExAC gnomAD |
|
|
rs770189965 CA4757004 |
54 | S>Y | No |
ClinGen ExAC gnomAD |
|
|
rs1457275304 CA371293147 |
56 | Y>H | No |
ClinGen gnomAD |
|
|
rs771363713 CA4757007 |
57 | M>L | No |
ClinGen ExAC gnomAD |
|
|
rs745960220 CA177306334 |
58 | G>R | No |
ClinGen TOPMed |
|
|
rs1585699807 CA371293258 |
64 | E>K | No |
ClinGen Ensembl |
|
|
CA4757011 rs144425100 |
67 | R>C | No |
ClinGen 1000Genomes ESP ExAC TOPMed gnomAD |
|
|
CA4757012 rs148588308 |
67 | R>H | No |
ClinGen 1000Genomes ESP ExAC TOPMed gnomAD |
|
|
rs369499089 CA4757014 |
68 | A>E | No |
ClinGen ESP ExAC gnomAD |
|
|
CA4757013 rs142951384 |
68 | A>P | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
CA4757015 rs757032692 |
70 | V>G | No |
ClinGen ExAC gnomAD |
|
|
CA177306402 rs202037754 |
70 | V>M | No |
ClinGen 1000Genomes |
|
|
CA371293363 rs1430532079 |
72 | V>A | No |
ClinGen TOPMed gnomAD |
|
|
rs372417488 CA4757017 |
72 | V>M | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA371293388 rs1387865016 |
75 | G>R | No |
ClinGen TOPMed |
|
|
rs1457045260 CA371293418 |
77 | P>Q | No |
ClinGen TOPMed gnomAD |
|
|
CA371293412 rs1305500924 |
77 | P>S | No |
ClinGen TOPMed |
|
|
CA4757018 rs755083095 |
79 | Q>P | No |
ClinGen ExAC gnomAD |
|
|
rs1365971778 CA371293797 |
85 | R>K | No |
ClinGen TOPMed |
|
|
rs746404793 CA4757044 |
85 | R>S | No |
ClinGen ExAC gnomAD |
|
|
CA371293832 rs1181599207 |
88 | S>G | No |
ClinGen gnomAD |
|
|
rs1395359217 CA371293836 |
88 | S>T | No |
ClinGen TOPMed |
|
|
rs772737023 CA4757045 |
92 | M>T | No |
ClinGen ExAC gnomAD |
|
|
CA371293912 rs1164419392 |
93 | V>G | No |
ClinGen gnomAD |
|
|
CA177307755 rs893675309 |
94 | A>T | No |
ClinGen Ensembl |
|
|
CA4757046 rs201473558 |
94 | A>V | No |
ClinGen 1000Genomes ExAC TOPMed gnomAD |
|
|
rs767373376 CA4757047 |
96 | V>L | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA4757048 rs372504616 |
98 | G>A | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
CA371293964 rs372504616 |
98 | G>D | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
rs11550277 CA371293983 |
100 | D>H | No |
ClinGen TOPMed gnomAD |
|
|
CA177307786 rs11550277 |
100 | D>N | No |
ClinGen TOPMed gnomAD |
|
|
rs761516720 CA4757050 |
104 | R>C | No |
ClinGen ExAC TOPMed gnomAD |
|
|
rs761516720 CA4757051 |
104 | R>G | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA177307798 rs371193260 COSM486554 |
104 | R>H | kidney [Cosmic] | No |
ClinGen cosmic curated TOPMed gnomAD |
|
CA371294036 rs371193260 |
104 | R>P | No |
ClinGen TOPMed gnomAD |
|
|
CA4757052 rs773087947 |
107 | E>G | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA4757053 rs762682896 |
109 | K>E | No |
ClinGen ExAC TOPMed gnomAD |
|
|
rs371437317 CA177307810 |
110 | Q>R | No |
ClinGen ESP TOPMed |
|
|
CA371294121 rs1296401235 |
111 | G>V | No |
ClinGen gnomAD |
|
|
CA4757054 rs753892979 |
113 | R>C | No |
ClinGen ExAC TOPMed gnomAD |
|
|
rs751430708 CA4757055 |
113 | R>H | No |
ClinGen ExAC TOPMed gnomAD |
|
|
rs202039014 CA4757056 |
114 | E>G | No |
ClinGen 1000Genomes ESP ExAC TOPMed gnomAD |
|
|
rs764218169 CA4757057 |
116 | I>T | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA371294198 rs377675926 |
117 | L>F | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
CA177307822 rs570270016 |
118 | C>Y | No |
ClinGen gnomAD |
|
|
rs28714565 CA177307829 |
119 | K>E | No |
ClinGen Ensembl |
|
|
rs28719137 CA177307842 |
119 | K>R | No |
ClinGen Ensembl |
|
|
CA4757059 rs757472608 |
120 | D>E | No |
ClinGen ExAC TOPMed gnomAD |
|
|
rs1462930732 CA371294228 |
120 | D>N | No |
ClinGen gnomAD |
|
|
rs778963752 CA4757060 |
121 | Q>H | No |
ClinGen ExAC gnomAD |
|
|
rs989618777 CA177307851 |
121 | Q>R | No |
ClinGen TOPMed gnomAD |
|
|
CA4757062 rs758781851 |
124 | K>N | No |
ClinGen ExAC |
|
|
CA4757061 rs146809015 |
124 | K>R | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
rs542469774 CA4757064 |
125 | I>L | No |
ClinGen 1000Genomes ExAC gnomAD |
|
|
rs542469774 CA371294299 |
125 | I>V | No |
ClinGen 1000Genomes ExAC gnomAD |
|
|
rs1413885808 CA371294320 |
126 | G>A | No |
ClinGen gnomAD |
|
|
CA371294379 rs1369677544 |
130 | K>N | No |
ClinGen TOPMed |
|
|
rs1305843011 CA371294395 |
132 | I>T | No |
ClinGen TOPMed |
|
|
rs747517255 CA4757065 |
132 | I>V | No |
ClinGen ExAC gnomAD |
|
|
CA371294451 rs1563514098 |
134 | N>K | No |
ClinGen Ensembl |
|
|
rs754442194 CA4757066 |
135 | G>* | No |
ClinGen ExAC |
|
|
CA4757088 rs777548665 |
135 | G>C | No |
ClinGen ExAC gnomAD |
|
|
rs1180926525 CA371295243 |
135 | G>V | No |
ClinGen gnomAD |
|
|
rs1490208880 CA371295298 |
138 | V>F | No |
ClinGen gnomAD |
|
|
CA371295463 rs1197315426 |
143 | A>V | No |
ClinGen gnomAD |
|
|
CA371295509 rs1270991037 |
145 | S>C | No |
ClinGen gnomAD |
|
|
CA4757089 rs140482504 |
147 | A>S | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
CA4757090 rs770760245 |
149 | L>W | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA177309006 rs886202166 |
150 | V>L | No |
ClinGen TOPMed |
|
|
rs1455142429 CA371295617 |
151 | G>S | No |
ClinGen gnomAD |
|
|
CA371295690 rs1422243641 |
155 | G>E | No |
ClinGen gnomAD |
|
|
rs1481651709 CA371295723 |
156 | D>E | No |
ClinGen TOPMed |
|
|
CA177309017 rs201651070 |
156 | D>N | No |
ClinGen TOPMed |
|
|
rs1003728151 CA177309021 |
157 | Q>H | No |
ClinGen TOPMed |
|
|
CA4757093 rs772069450 |
159 | L>V | No |
ClinGen ExAC |
|
|
rs943829698 CA371295829 |
160 | Q>H | No |
ClinGen gnomAD |
|
|
rs943829698 CA177309036 |
160 | Q>H | No |
ClinGen gnomAD |
|
|
CA4757095 rs775234871 |
161 | I>T | No |
ClinGen ExAC gnomAD |
|
|
rs761960405 CA4757096 |
162 | N>S | No |
ClinGen ExAC gnomAD |
|
|
rs761960405 CA4757097 |
162 | N>T | No |
ClinGen ExAC gnomAD |
|
|
rs200538918 CA177309060 |
163 | G>D | No |
ClinGen 1000Genomes |
|
|
rs763247744 CA4757100 |
166 | C>R | No |
ClinGen ExAC gnomAD |
|
|
rs1295445780 CA371295969 |
166 | C>S | No |
ClinGen TOPMed |
|
|
rs766665963 CA4757101 |
167 | A>V | No |
ClinGen ExAC |
|
|
CA4757102 rs751992243 |
172 | D>G | No |
ClinGen ExAC gnomAD |
|
|
CA4757103 rs755236342 |
174 | A>V | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA177309075 rs945527521 |
175 | H>Y | No |
ClinGen Ensembl |
|
|
CA177309078 rs145153031 |
177 | V>L | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
rs145153031 CA4757105 |
177 | V>L | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
CA371296366 rs1420655777 |
179 | K>R | No |
ClinGen gnomAD |
|
|
rs1182205215 CA371296403 |
180 | Q>* | No |
ClinGen TOPMed gnomAD |
|
|
CA371296465 rs1459505976 |
182 | F>L | No |
ClinGen TOPMed |
|
|
CA371296484 rs1384243781 |
184 | E>* | No |
ClinGen gnomAD |
|
|
rs370441759 COSM3728291 CA4757106 |
187 | T>A | haematopoietic_and_lymphoid_tissue [Cosmic] | No |
ClinGen cosmic curated ESP ExAC TOPMed gnomAD |
|
rs777239980 CA4757107 |
188 | M>V | No |
ClinGen ExAC gnomAD |
|
|
rs188278289 CA4757108 |
190 | I>V | No |
ClinGen 1000Genomes ExAC TOPMed gnomAD |
|
|
CA371296689 rs1298110777 |
191 | R>C | No |
ClinGen TOPMed gnomAD |
|
|
rs756936045 CA4757109 |
191 | R>H | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA371296737 rs1440282247 |
193 | R>K | No |
ClinGen TOPMed |
|
|
CA371297424 rs1585713059 |
194 | P>H | No |
ClinGen Ensembl |
|
|
rs1293579380 CA371297422 |
194 | P>S | No |
ClinGen gnomAD |
|
|
rs764543908 CA4757127 |
195 | F>S | No |
ClinGen ExAC TOPMed gnomAD |
|
|
rs544424949 CA177309769 |
196 | E>G | No |
ClinGen TOPMed gnomAD |
|
|
CA371297457 rs544424949 |
196 | E>V | No |
ClinGen TOPMed gnomAD |
|
|
CA4757129 rs756701491 |
197 | R>Q | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA4757128 rs753370023 |
197 | R>W | No |
ClinGen ExAC TOPMed gnomAD |
|
|
rs567927664 CA4757131 |
198 | T>M | No |
ClinGen 1000Genomes ExAC TOPMed gnomAD |
|
|
rs976845640 CA177309804 |
201 | M>I | No |
ClinGen Ensembl |
|
|
rs747009733 CA4757135 |
201 | M>R | No |
ClinGen ExAC gnomAD |
|
|
CA177309817 rs922468323 |
203 | K>R | No |
ClinGen TOPMed gnomAD |
|
|
rs945894998 CA177309828 |
205 | S>G | No |
ClinGen gnomAD |
|
|
rs1012833111 CA177309852 |
208 | H>R | No |
ClinGen TOPMed |
|
|
rs749378649 CA4757138 |
208 | H>Y | No |
ClinGen ExAC gnomAD |
|
|
rs771127412 CA4757139 |
213 | F>C | No |
ClinGen ExAC gnomAD |
|
|
CA371297707 rs1453365815 |
214 | K>N | No |
ClinGen gnomAD |
|
|
CA371297726 rs1287327534 |
215 | N>K | No |
ClinGen gnomAD |
|
|
CA4757140 rs148497982 |
218 | I>V | No |
ClinGen 1000Genomes ESP ExAC TOPMed gnomAD |
|
|
rs759655543 CA4757141 |
219 | T>P | No |
ClinGen ExAC gnomAD |
|
|
rs772524805 CA4757142 |
221 | I>R | No |
ClinGen ExAC gnomAD |
|
|
CA371297814 rs1443621734 |
221 | I>V | No |
ClinGen TOPMed |
|
|
rs376181221 CA4757143 |
224 | D>N | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
rs113820935 CA4757145 |
225 | S>I | No |
ClinGen ExAC gnomAD |
|
|
CA177309891 rs935673158 |
230 | N>S | No |
ClinGen gnomAD |
|
|
rs145919468 CA4757146 |
231 | G>D | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
rs1262066631 CA371298002 |
232 | L>V | No |
ClinGen gnomAD |
|
|
CA4757147 rs766403080 |
234 | T>M | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA4757149 rs369166523 |
235 | E>K | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
CA371298046 rs369166523 |
235 | E>Q | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
CA371298074 rs1202181041 |
236 | H>R | No |
ClinGen TOPMed gnomAD |
|
|
CA4757150 rs757961090 |
238 | I>V | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA371298118 rs1398386986 |
239 | C>Y | No |
ClinGen TOPMed |
|
|
CA177309899 rs965045151 |
241 | I>V | No |
ClinGen TOPMed |
|
|
rs766019004 CA4757151 |
242 | N>I | No |
ClinGen ExAC gnomAD |
|
|
CA371298187 rs1478345859 |
242 | N>K | No |
ClinGen TOPMed |
|
|
CA177309903 rs753909359 |
244 | Q>* | No |
ClinGen Ensembl |
|
|
CA4757152 rs777371212 |
244 | Q>H | No |
ClinGen ExAC TOPMed gnomAD |
|
|
rs754749476 CA4757153 |
247 | I>T | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA371298333 rs781342209 |
249 | L>M | No |
ClinGen ExAC TOPMed gnomAD |
|
|
rs201221126 CA177309912 |
250 | K>T | No |
ClinGen Ensembl |
|
|
CA371299245 rs1402506285 |
253 | Q>* | No |
ClinGen TOPMed |
|
|
rs765948570 CA4757174 |
257 | I>M | No |
ClinGen ExAC gnomAD |
|
|
CA371299333 rs1353818263 |
258 | L>V | No |
ClinGen gnomAD |
|
|
CA177310370 rs900061205 |
260 | T>I | No |
ClinGen TOPMed |
|
|
CA4757177 rs767396889 |
262 | G>W | No |
ClinGen ExAC gnomAD |
|
|
CA4757178 rs3739325 |
263 | T>A | No |
ClinGen 1000Genomes ExAC TOPMed gnomAD |
|
|
rs1312443855 CA371299413 |
263 | T>S | No |
ClinGen TOPMed gnomAD |
|
|
CA4757179 rs373039131 |
264 | V>A | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
|
CA371299468 rs1447048243 |
267 | I>V | No |
ClinGen TOPMed |
|
|
CA4757181 rs745949652 |
269 | I>V | No |
ClinGen ExAC TOPMed gnomAD |
|
|
CA371299538 rs1203001296 |
271 | P>S | No |
ClinGen gnomAD |
|
|
CA4757183 rs780210085 |
273 | F>Y | No |
ClinGen ExAC gnomAD |
|
|
rs1349308881 CA371299596 |
275 | F>L | No |
ClinGen gnomAD |
|
|
CA371299629 rs1198326399 |
277 | H>Y | No |
ClinGen TOPMed |
|
|
COSM461418 rs769061064 CA4757185 |
278 | I>T | cervix [Cosmic] | No |
ClinGen cosmic curated ExAC gnomAD |
|
rs1163866157 CA371299672 |
280 | K>E | No |
ClinGen gnomAD |
|
|
CA4757187 rs568136446 |
281 | R>Q | No |
ClinGen 1000Genomes ExAC TOPMed gnomAD |
|
|
COSM284840 rs377175958 CA4757186 |
281 | R>W | large_intestine [Cosmic] | No |
ClinGen cosmic curated ESP ExAC TOPMed gnomAD |
|
CA371299851 rs1443650308 |
282 | M>T | No |
ClinGen Ensembl |
|
|
CA4757201 rs758466824 |
283 | A>T | No |
ClinGen ExAC gnomAD |
|
|
rs1407989444 CA371299880 |
283 | A>V | No |
ClinGen gnomAD |
|
|
rs780161605 CA4757202 |
285 | S>G | No |
ClinGen ExAC TOPMed gnomAD |
|
|
rs751821751 CA4757203 |
286 | I>V | No |
ClinGen ExAC gnomAD |
|
|
rs776079667 CA177310978 |
287 | M>I | No |
ClinGen TOPMed gnomAD |
|
|
CA371299988 rs1490005543 |
289 | S>C | No |
ClinGen TOPMed |
|
|
CA177310984 rs949826513 |
289 | S>N | No |
ClinGen TOPMed |
|
|
rs755228065 CA4757205 |
292 | D>E | No |
ClinGen ExAC gnomAD |
|
|
CA371300043 rs1222574515 |
293 | H>D | No |
ClinGen TOPMed |
|
|
CA177311001 rs759989358 |
294 | T>N | No |
ClinGen Ensembl |
|
|
rs1280686991 CA371300082 |
295 | I>L | No |
ClinGen gnomAD |
|
|
rs1280686991 CA371300081 |
295 | I>V | No |
ClinGen gnomAD |
|
|
CA4757207 rs770186719 |
298 | V>I | No |
ClinGen ExAC TOPMed gnomAD |
No associated diseases with O00560
3 regional properties for O00560
| Type | Name | Position | InterPro Accession |
|---|---|---|---|
| domain | PDZ domain | 114 - 194 | IPR001478-1 |
| domain | PDZ domain | 198 - 273 | IPR001478-2 |
| domain | Peptidase M50 | 88 - 206 | IPR008915 |
Functions
| Description | ||
|---|---|---|
| EC Number | ||
| Subcellular Localization |
|
|
| PANTHER Family | PTHR12345 | SYNTENIN RELATED |
| PANTHER Subfamily | PTHR12345:SF10 | SYNTENIN-1 |
| PANTHER Protein Class | membrane trafficking regulatory protein | |
| PANTHER Pathway Category | No pathway information available | |
21 GO annotations of cellular component
| Name | Definition |
|---|---|
| adherens junction | A cell-cell junction composed of the epithelial cadherin-catenin complex. The epithelial cadherins, or E-cadherins, of each interacting cell extend through the plasma membrane into the extracellular space and bind to each other. The E-cadherins bind to catenins on the cytoplasmic side of the membrane, where the E-cadherin-catenin complex binds to cytoskeletal components and regulatory and signaling molecules. |
| azurophil granule lumen | The volume enclosed by the membrane of an azurophil granule, a primary lysosomal granule found in neutrophil granulocytes that contains a wide range of hydrolytic enzymes and is released into the extracellular fluid. |
| blood microparticle | A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids. |
| cytoplasm | The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. |
| cytoskeleton | A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. |
| cytosol | The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. |
| endoplasmic reticulum membrane | The lipid bilayer surrounding the endoplasmic reticulum. |
| extracellular exosome | A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. |
| extracellular region | The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. |
| extracellular space | That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. |
| extracellular vesicle | Any vesicle that is part of the extracellular region. |
| focal adhesion | A cell-substrate junction that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. In insects focal adhesion has also been referred to as hemi-adherens junction (HAJ). |
| interleukin-5 receptor complex | A protein complex that binds interleukin-3; comprises an alpha and a beta subunit. The alpha chain is specific to the interleukin-5 receptor, whereas the beta chain is shared with the receptors for granulocyte-macrophage colony-stimulating factor and interleukin-3. |
| melanosome | A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. |
| membrane | A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. |
| membrane raft | Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions. |
| nuclear membrane | Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. |
| nucleoplasm | That part of the nuclear content other than the chromosomes or the nucleolus. |
| nucleus | A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. |
| plasma membrane | The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. |
| synapse | The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. |
14 GO annotations of molecular function
| Name | Definition |
|---|---|
| cell adhesion molecule binding | Binding to a cell adhesion molecule. |
| cytoskeletal anchor activity | The binding activity of a protein that brings together a cytoskeletal protein (either a microtubule or actin filament, spindle pole body, or protein directly bound to them) and one or more other molecules, permitting them to function in a coordinated way. |
| ephrin receptor binding | Binding to an ephrin receptor. |
| frizzled binding | Binding to a frizzled (fz) receptor. |
| growth factor binding | Binding to a growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate. |
| identical protein binding | Binding to an identical protein or proteins. |
| interleukin-5 receptor binding | Binding to an interleukin-5 receptor. |
| neurexin family protein binding | Binding to a neurexin, a synaptic cell surface protein related to latrotoxin receptor, laminin and agrin. Neurexins act as cell recognition molecules at nerve terminals. |
| phosphatidylinositol-4,5-bisphosphate binding | Binding to phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions. |
| protein C-terminus binding | Binding to a protein C-terminus, the end of a peptide chain at which the 1-carboxyl function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue. |
| protein heterodimerization activity | Binding to a nonidentical protein to form a heterodimer. |
| protein N-terminus binding | Binding to a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue. |
| protein-containing complex binding | Binding to a macromolecular complex. |
| syndecan binding | Binding to syndecan, an integral membrane proteoglycan (250-300 kDa) associated largely with epithelial cells. |
21 GO annotations of biological process
| Name | Definition |
|---|---|
| actin cytoskeleton organization | A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. |
| chemical synaptic transmission | The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. |
| intracellular signal transduction | The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. |
| negative regulation of proteasomal ubiquitin-dependent protein catabolic process | Any process that stops, prevents, or reduces the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome. |
| negative regulation of receptor internalization | Any process that stops, prevents, or reduces the frequency, rate or extent of receptor internalization. |
| negative regulation of transcription by RNA polymerase II | Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II. |
| positive regulation of cell growth | Any process that activates or increases the frequency, rate, extent or direction of cell growth. |
| positive regulation of cell migration | Any process that activates or increases the frequency, rate or extent of cell migration. |
| positive regulation of cell population proliferation | Any process that activates or increases the rate or extent of cell proliferation. |
| positive regulation of epithelial to mesenchymal transition | Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell. |
| positive regulation of exosomal secretion | Any process that activates or increases the frequency, rate or extent of exosomal secretion. |
| positive regulation of extracellular exosome assembly | Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly. |
| positive regulation of JNK cascade | Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade. |
| positive regulation of pathway-restricted SMAD protein phosphorylation | Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways. |
| positive regulation of phosphorylation | Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. |
| positive regulation of transforming growth factor beta receptor signaling pathway | Any process that activates or increases the frequency, rate or extent of TGF-beta receptor signaling pathway activity. |
| presynapse assembly | The aggregation, arrangement and bonding together of a set of components to form a presynapse. |
| protein targeting to membrane | The process of directing proteins towards a membrane, usually using signals contained within the protein. |
| Ras protein signal transduction | The series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state. |
| regulation of mitotic cell cycle | Any process that modulates the rate or extent of progress through the mitotic cell cycle. |
| substrate-dependent cell migration, cell extension | The formation of a cell surface protrusion, such as a lamellipodium or filopodium, at the leading edge of a migrating cell. |
7 homologous proteins in AiPD
| UniProt AC | Gene Name | Protein Name | Species | Evidence Code |
|---|---|---|---|---|
| Q02410 | APBA1 | Amyloid-beta A4 precursor protein-binding family A member 1 | Homo sapiens (Human) | SS |
| Q99767 | APBA2 | Amyloid-beta A4 precursor protein-binding family A member 2 | Homo sapiens (Human) | SS |
| Q9H190 | SDCBP2 | Syntenin-2 | Homo sapiens (Human) | SS |
| O08992 | Sdcbp | Syntenin-1 | Mus musculus (Mouse) | SS |
| Q99JZ0 | Sdcbp2 | Syntenin-2 | Mus musculus (Mouse) | SS |
| Q9JI92 | Sdcbp | Syntenin-1 | Rattus norvegicus (Rat) | SS |
| Q4KLN0 | Sdcbp2 | Syntenin-2 | Rattus norvegicus (Rat) | SS |
| 10 | 20 | 30 | 40 | 50 | 60 |
| MSLYPSLEDL | KVDKVIQAQT | AFSANPANPA | ILSEASAPIP | HDGNLYPRLY | PELSQYMGLS |
| 70 | 80 | 90 | 100 | 110 | 120 |
| LNEEEIRANV | AVVSGAPLQG | QLVARPSSIN | YMVAPVTGND | VGIRRAEIKQ | GIREVILCKD |
| 130 | 140 | 150 | 160 | 170 | 180 |
| QDGKIGLRLK | SIDNGIFVQL | VQANSPASLV | GLRFGDQVLQ | INGENCAGWS | SDKAHKVLKQ |
| 190 | 200 | 210 | 220 | 230 | 240 |
| AFGEKITMTI | RDRPFERTIT | MHKDSTGHVG | FIFKNGKITS | IVKDSSAARN | GLLTEHNICE |
| 250 | 260 | 270 | 280 | 290 | |
| INGQNVIGLK | DSQIADILST | SGTVVTITIM | PAFIFEHIIK | RMAPSIMKSL | MDHTIPEV |