SDCBP
syndecan binding protein, the group of PDZ domain containing
Basic information
Region (hg38): 8:58552924-58582859
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDCBP gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 1 | 0 |
Variants in SDCBP
This is a list of pathogenic ClinVar variants found in the SDCBP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-58570962-G-A | not specified | Likely benign (Mar 27, 2023) | ||
| 8-58572283-T-G | not specified | Uncertain significance (Jul 05, 2022) | ||
| 8-58572288-G-A | not specified | Likely benign (Apr 04, 2024) | ||
| 8-58575945-G-T | not specified | Uncertain significance (Aug 13, 2021) | ||
| 8-58576021-A-G | not specified | Uncertain significance (Dec 13, 2023) | ||
| 8-58578055-A-G | not specified | Uncertain significance (Mar 20, 2023) | ||
| 8-58579634-G-A | not specified | Uncertain significance (Dec 16, 2023) | ||
| 8-58581704-G-C | not specified | Uncertain significance (Dec 15, 2023) | ||
| 8-58581709-G-A | not specified | Uncertain significance (Nov 14, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SDCBP | protein_coding | protein_coding | ENST00000260130 | 8 | 29937 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000581 | 0.907 | 125714 | 0 | 31 | 125745 | 0.000123 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.04 | 128 | 166 | 0.772 | 0.00000855 | 1962 |
| Missense in Polyphen | 20 | 38.962 | 0.51332 | 514 | ||
| Synonymous | 0.0259 | 53 | 53.2 | 0.995 | 0.00000268 | 580 |
| Loss of Function | 1.49 | 7 | 12.8 | 0.549 | 5.35e-7 | 172 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000468 | 0.000464 |
| Ashkenazi Jewish | 0.000247 | 0.000198 |
| East Asian | 0.0000593 | 0.0000544 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000120 | 0.000114 |
| Middle Eastern | 0.0000593 | 0.0000544 |
| South Asian | 0.000106 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Multifunctional adapter protein involved in diverse array of functions including trafficking of transmembrane proteins, neuro and immunomodulation, exosome biogenesis, and tumorigenesis (PubMed:26291527). Positively regulates TGFB1- mediated SMAD2/3 activation and TGFB1-induced epithelial-to- mesenchymal transition (EMT) and cell migration in various cell types. May increase TGFB1 signaling by enhancing cell-surface expression of TGFR1 by preventing the interaction between TGFR1 and CAV1 and subsequent CAV1-dependent internalization and degradation of TGFR1 (PubMed:25893292). In concert with SDC1/4 and PDCD6IP, regulates exosome biogenesis (PubMed:22660413). Regulates migration, growth, proliferation, and cell cycle progression in a variety of cancer types (PubMed:26539120). In adherens junctions may function to couple syndecans to cytoskeletal proteins or signaling components. Seems to couple transcription factor SOX4 to the IL-5 receptor (IL5RA) (PubMed:11498591). May also play a role in vesicular trafficking (PubMed:11179419). Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway (PubMed:10230395). {ECO:0000269|PubMed:10230395, ECO:0000269|PubMed:11179419, ECO:0000269|PubMed:11498591, ECO:0000269|PubMed:22660413, ECO:0000269|PubMed:25893292, ECO:0000269|PubMed:26539120, ECO:0000303|PubMed:26291527}.;
- Pathway
- miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Ectoderm Differentiation;Developmental Biology;Neutrophil degranulation;EPH-Ephrin signaling;TCR;Innate Immune System;Immune System;Ephrin signaling;IL5-mediated signaling events;Neurofascin interactions;EGFR1;L1CAM interactions;Axon guidance;IL5;Syndecan-1-mediated signaling events;Syndecan-4-mediated signaling events;Syndecan-2-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.364
Intolerance Scores
- loftool
- 0.936
- rvis_EVS
- -0.52
- rvis_percentile_EVS
- 21.2
Haploinsufficiency Scores
- pHI
- 0.133
- hipred
- Y
- hipred_score
- 0.626
- ghis
- 0.610
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sdcbp
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- negative regulation of receptor internalization;protein targeting to membrane;substrate-dependent cell migration, cell extension;chemical synaptic transmission;regulation of mitotic cell cycle;positive regulation of cell population proliferation;positive regulation of epithelial to mesenchymal transition;positive regulation of pathway-restricted SMAD protein phosphorylation;actin cytoskeleton organization;positive regulation of cell growth;positive regulation of cell migration;positive regulation of transforming growth factor beta receptor signaling pathway;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;intracellular signal transduction;positive regulation of phosphorylation;neutrophil degranulation;positive regulation of JNK cascade;ephrin receptor signaling pathway;positive regulation of exosomal secretion;positive regulation of extracellular exosome assembly
- Cellular component
- extracellular region;extracellular space;nucleus;nucleoplasm;cytoplasm;endoplasmic reticulum membrane;cytosol;cytoskeleton;plasma membrane;interleukin-5 receptor complex;adherens junction;focal adhesion;membrane;nuclear membrane;azurophil granule lumen;melanosome;intracellular membrane-bounded organelle;membrane raft;extracellular exosome;blood microparticle;extracellular vesicle
- Molecular function
- frizzled binding;interleukin-5 receptor binding;protein binding;phosphatidylinositol-4,5-bisphosphate binding;cytoskeletal adaptor activity;identical protein binding;syndecan binding;protein heterodimerization activity;protein N-terminus binding